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GATK4 joint and pooled calling example -- bcbio commands
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| [2017-08-23T18:20Z] zcat /home/chapmanb/bio/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-Test1.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmppr3F3t/7_100326_FC6107FAAXX-Test1.vcf.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpYZCwp9/7_100326_FC6107FAAXX-Test1.vcf.gz | |
| [2017-08-23T18:20Z] bamtofastq filename=/home/chapmanb/bio/bcbio-nextgen/tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX.cram inputformat=cram T=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiMWXEy/7_100326_FC6107FAAXXfull-s1-sort gz=1 collate=1 colsbs=1048576 exclude=SECONDARY,SUPPLEMENTARY F=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiMWXEy/7_100326_FC6107FAAXXfull-p1.fq.gz F2=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiMWXEy/7_100326_FC6107FAAXXfull-p2.fq.gz S=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiMWXEy/7_100326_FC6107FAAXXfull-s1.fq.gz O=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiMWXEy/7_100326_FC6107FAAXXfull-o1.fq.gz O2=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiMWXEy/7_100326_FC6107FAAXXfull-o2.fq.gz reference=/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa | |
| [2017-08-23T18:20Z] /bin/bash /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-p1-merge.bash | |
| [2017-08-23T18:20Z] /bin/bash /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-p2-merge.bash | |
| [2017-08-23T18:20Z] /usr/local/bin/grabix index /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpD8tZjp/7_100326_FC6107FAAXX-p1.fq.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/grabix index /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpIVX7xK/7_100326_FC6107FAAXX-p2.fq.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/bgzip -c /home/chapmanb/bio/bcbio-nextgen/tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX_1_fastq.txt > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpynZrTn/7_100326_FC6107FAAXX_1_fastq.txt.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/bgzip -c /home/chapmanb/bio/bcbio-nextgen/tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX_2_fastq.txt > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpRFOT_h/7_100326_FC6107FAAXX_2_fastq.txt.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/grabix index /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpRDUQnO/7_100326_FC6107FAAXX_1_fastq.txt.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/grabix index /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpP0ask0/7_100326_FC6107FAAXX_2_fastq.txt.gz | |
| [2017-08-23T18:20Z] unset JAVA_HOME && /usr/local/bin/bwa mem -c 250 -M -t 1 -R '@RG\tID:Test1\tPL:illumina\tPU:Test1\tSM:Test1' -v 1 /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-p1.fq.gz /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-p2.fq.gz | bamsormadup inputformat=sam threads=1 tmpfile=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpecdb1y/Test1-sort-sorttmp-markdup SO=coordinate level=0 | variant - -b --mark-as-qc-fail --max-coverage 16711 > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpecdb1y/Test1-sort.bam | |
| [2017-08-23T18:20Z] /usr/local/bin/samtools index -@ 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp7rX58k/Test1-sort.bam.bai | |
| [2017-08-23T18:20Z] unset JAVA_HOME && /usr/local/bin/bwa mem -c 250 -M -t 1 -R '@RG\tID:Test2\tPL:illumina\tPU:Test2\tSM:Test2' -v 1 /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX_1_fastq.txt.gz /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX_2_fastq.txt.gz | bamsormadup inputformat=sam threads=1 tmpfile=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpQy9Xb9/Test2-sort-sorttmp-markdup SO=coordinate level=0 | variant - -b --mark-as-qc-fail --max-coverage 16716 > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpQy9Xb9/Test2-sort.bam | |
| [2017-08-23T18:20Z] /usr/local/bin/samtools index -@ 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort.bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpU0rsJY/Test2-sort.bam.bai | |
| [2017-08-23T18:20Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/automated/variant_regions-bam.bed | grep -v ^track | grep -v ^browser | grep -v ^# | /usr/local/bin/py -x 'bcbio.variation.bedutils.remove_bad(x)' | sort -V -k1,1 -k2,2n > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpPWi7g8/variant_regions-bam.bed | |
| [2017-08-23T18:20Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpDubu_g/variant_regions-bam.bed.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/tabix -f -p bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpbm5aQf/variant_regions-bam.bed.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/bedtools merge -i /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpuITXpa/variant_regions-bam-merged.bed | |
| [2017-08-23T18:20Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam-merged.bed | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpXCAdlB/variant_regions-bam-merged.bed.gz | |
| [2017-08-23T18:20Z] /usr/local/bin/tabix -f -p bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpjzROqA/variant_regions-bam-merged.bed.gz | |
| [2017-08-23T18:20Z] goleft depth --q 1 --mincov 4 --processes 1 --ordered --reference /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-bamref.fa --prefix /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpxycypK/Test1-coverage /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam | |
| [2017-08-23T18:20Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpgzbZLX' BaseRecalibratorSpark -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --sparkMaster local[1] --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpgzbZLX/Test1-sort-recal.grp --reference /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/ucsc/hg19.2bit --knownSites /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed --interval_set_rule INTERSECTION | |
| [2017-08-23T18:20Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpoRHbBM' ApplyBQSRSpark --sparkMaster local[1] --input /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpoRHbBM/Test1-sort-recal.bam --bqsr_recal_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.grp | |
| [2017-08-23T18:21Z] /usr/local/bin/samtools index -@ 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpXsmMGw/Test1-sort-recal.bam.bai | |
| [2017-08-23T18:21Z] goleft depth --q 1 --mincov 4 --processes 1 --ordered --reference /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-bamref.fa --prefix /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpWLUi13/Test2-coverage /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort.bam | |
| [2017-08-23T18:21Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpxSestZ' BaseRecalibratorSpark -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort.bam --sparkMaster local[1] --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpxSestZ/Test2-sort-recal.grp --reference /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/ucsc/hg19.2bit --knownSites /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed --interval_set_rule INTERSECTION | |
| [2017-08-23T18:21Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpf6zi41' ApplyBQSRSpark --sparkMaster local[1] --input /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort.bam --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpf6zi41/Test2-sort-recal.bam --bqsr_recal_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.grp | |
| [2017-08-23T18:21Z] /usr/local/bin/samtools index -@ 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpUdBgcZ/Test2-sort-recal.bam.bai | |
| [2017-08-23T18:21Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpWH7lXl' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chr22/Test2-chr22_0_14496-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpg47qxu/Test2-chr22_0_14496.vcf.gz --emitRefConfidence GVCF -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 60 -GQB 80 | |
| [2017-08-23T18:21Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpmiGgc9/Test2-chr22_0_14496.vcf.gz | |
| [2017-08-23T18:21Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp7UV1qD' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chrM/Test2-chrM_2000_5000-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmppaDlQE/Test2-chrM_2000_5000.vcf.gz --emitRefConfidence GVCF -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 60 -GQB 80 | |
| [2017-08-23T18:21Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpW2Zxuw/Test2-chrM_2000_5000.vcf.gz | |
| [2017-08-23T18:21Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpQS7lIu' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chrM/Test2-chrM_0_1000-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpvF8Ndd/Test2-chrM_0_1000.vcf.gz --emitRefConfidence GVCF -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 60 -GQB 80 | |
| [2017-08-23T18:22Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpNtv9Tl/Test2-chrM_0_1000.vcf.gz | |
| [2017-08-23T18:22Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpLcicVe' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chr22/Test2-chr22_15128_15500-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpeO6Iru/Test2-chr22_15128_15500.vcf.gz --emitRefConfidence GVCF -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 60 -GQB 80 | |
| [2017-08-23T18:22Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpPbhgb8/Test2-chr22_15128_15500.vcf.gz | |
| [2017-08-23T18:22Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpun0WH3' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chr22/Test1-chr22_0_14496-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp6aMWj7/Test1-chr22_0_14496.vcf.gz --emitRefConfidence GVCF -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 60 -GQB 80 | |
| [2017-08-23T18:22Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpAwYEVN/Test1-chr22_0_14496.vcf.gz | |
| [2017-08-23T18:22Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpvCe8Zi' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chrM/Test1-chrM_2000_5000-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpsa3tOM/Test1-chrM_2000_5000.vcf.gz --emitRefConfidence GVCF -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 60 -GQB 80 | |
| [2017-08-23T18:22Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpGkoLBn/Test1-chrM_2000_5000.vcf.gz | |
| [2017-08-23T18:22Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpeR_kBJ' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chrM/Test1-chrM_0_1000-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpT1jnww/Test1-chrM_0_1000.vcf.gz --emitRefConfidence GVCF -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 60 -GQB 80 | |
| [2017-08-23T18:22Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpLLSdm6/Test1-chrM_0_1000.vcf.gz | |
| [2017-08-23T18:22Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpuo6aRy' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chr22/Test1-chr22_15128_15500-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpHJBQBL/Test1-chr22_15128_15500.vcf.gz --emitRefConfidence GVCF -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 60 -GQB 80 | |
| [2017-08-23T18:22Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpZ8dqlk/Test1-chr22_15128_15500.vcf.gz | |
| [2017-08-23T18:22Z] zgrep ^# /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chr22/Test2-chr22_0_14496.vcf.gz | sed 's/ID=MMQ,Number=A/ID=MMQ,Number=R/' | sed 's/ID=MCL,Number=A/ID=MCL,Number=R/' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp1pH41m/Test2-chrM_0_1000-fixheader-header.vcf | |
| [2017-08-23T18:22Z] bcftools reheader -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp1pH41m/Test2-chrM_0_1000-fixheader-header.vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chrM/Test2-chrM_0_1000.vcf.gz -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test2-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T18:22Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpnv3dY1/Test2-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T18:22Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpQ5Let_' GatherVcfs -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test2-files.list -O /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpXjCkw1/Test2.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpUQP7vo/Test2.vcf.gz | |
| [2017-08-23T18:23Z] zgrep ^# /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chr22/Test1-chr22_0_14496.vcf.gz | sed 's/ID=MMQ,Number=A/ID=MMQ,Number=R/' | sed 's/ID=MCL,Number=A/ID=MCL,Number=R/' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmptJ2EJB/Test1-chrM_0_1000-fixheader-header.vcf | |
| [2017-08-23T18:23Z] bcftools reheader -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmptJ2EJB/Test1-chrM_0_1000-fixheader-header.vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chrM/Test1-chrM_0_1000.vcf.gz -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpxH3L3D/Test1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmppaB4T2' GatherVcfs -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test1-files.list -O /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpncqnEg/Test1.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpHv9UCQ/Test1.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpENdqMJ' GenomicsDBImport --readerThreads 1 --genomicsDBWorkspace /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chrM/TestBatch1-chrM_0_1000_genomicsdb -L chrM:1-1000 --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test2.vcf.gz --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test1.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmplNhLSX' GenotypeGVCFs --variant gendb:///home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chrM/TestBatch1-chrM_0_1000_genomicsdb -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpsTksIz/TestBatch1-chrM_0_1000.vcf.gz -L chrM:1-1000 | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp59idge' GenomicsDBImport --readerThreads 1 --genomicsDBWorkspace /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chrM/TestBatch1-chrM_2000_5000_genomicsdb -L chrM:2001-5000 --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test2.vcf.gz --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test1.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp7n447o' GenotypeGVCFs --variant gendb:///home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chrM/TestBatch1-chrM_2000_5000_genomicsdb -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp6WpvGj/TestBatch1-chrM_2000_5000.vcf.gz -L chrM:2001-5000 | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpQ4uKSv' GenomicsDBImport --readerThreads 1 --genomicsDBWorkspace /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chr22/TestBatch1-chr22_0_14496_genomicsdb -L chr22:1-14496 --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test2.vcf.gz --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test1.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpWu4RdX' GenotypeGVCFs --variant gendb:///home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chr22/TestBatch1-chr22_0_14496_genomicsdb -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpe4qxgg/TestBatch1-chr22_0_14496.vcf.gz -L chr22:1-14496 | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp8GtRlK' GenomicsDBImport --readerThreads 1 --genomicsDBWorkspace /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chr22/TestBatch1-chr22_15128_15500_genomicsdb -L chr22:15129-15500 --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test2.vcf.gz --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test1.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp8_yRra' GenotypeGVCFs --variant gendb:///home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chr22/TestBatch1-chr22_15128_15500_genomicsdb -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpcKYch4/TestBatch1-chr22_15128_15500.vcf.gz -L chr22:15129-15500 | |
| [2017-08-23T18:23Z] zgrep ^# /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chr22/TestBatch1-chr22_0_14496.vcf.gz | sed 's/ID=MMQ,Number=A/ID=MMQ,Number=R/' | sed 's/ID=MCL,Number=A/ID=MCL,Number=R/' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpUbcI1Q/TestBatch1-chrM_0_1000-fixheader-header.vcf | |
| [2017-08-23T18:23Z] bcftools reheader -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpUbcI1Q/TestBatch1-chrM_0_1000-fixheader-header.vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/chrM/TestBatch1-chrM_0_1000.vcf.gz -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp1Ofkgh/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpPwexbT' GatherVcfs -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-files.list -O /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpcdDoRS/TestBatch1-joint.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpVOt0Cq/TestBatch1-joint.vcf.gz | |
| [2017-08-23T18:23Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/snpEff -Xms750m -Xmx11g -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpL3zNoU/tmp eff -dataDir /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/snpeff -hgvs -noLog -i vcf -o vcf -csvStats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-stats.csv -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpL3zNoU/TestBatch1-joint-effects.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpIeigb0/TestBatch1-joint-effects.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/bcftools view -O z /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects.vcf.gz --types snps > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp2vzzwb/TestBatch1-joint-effects-snp.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpiuuFgR/TestBatch1-joint-effects-snp.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/bcftools view -O z /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects.vcf.gz --exclude-types snps > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpwHXJYc/TestBatch1-joint-effects-indel.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpmgZpkM/TestBatch1-joint-effects-indel.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpUuFAOD' VariantRecalibrator -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --mode SNP --tranches_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpimNwTX/TestBatch1-joint-effects-snp.tranches --rscript_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpimNwTX/TestBatch1-joint-effects-snp-plots.R --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-snp.vcf.gz --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpimNwTX/TestBatch1-joint-effects-snp-vqsrrecal.vcf.gz --resource hapmap,known=false,training=true,truth=true,prior=15.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/hapmap_3.3.vcf.gz --resource omni,known=false,training=true,truth=true,prior=12.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/1000G_omni2.5.vcf.gz --resource 1000g,known=false,training=true,truth=false,prior=10.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/1000G_phase1.snps.high_confidence.vcf.gz --resource dbsnp,known=true,training=false,truth=false,prior=2.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -tranche 100.0 -tranche 99.99 -tranche 99.98 -tranche 99.97 -tranche 99.96 -tranche 99.95 -tranche 99.94 -tranche 99.93 -tranche 99.92 -tranche 99.91 -tranche 99.9 -tranche 99.8 -tranche 99.7 -tranche 99.6 -tranche 99.5 -tranche 99.0 -tranche 98.0 -tranche 90.0 -an DP -an QD -an FS -an ReadPosRankSum | |
| [2017-08-23T18:23Z] /usr/local/bin/bcftools filter -O v -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed.gz --soft-filter 'GATKCutoffSNP' -e 'TYPE="snp" && (MQ < 30.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || QD < 2.0 || FS > 60.0 || (QD < 10.0 && AD[1] / (AD[1] + AD[0]) < 0.25 && ReadPosRankSum < 0.0))' -m '+' /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-snp.vcf.gz | sed 's/\\"//g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpF_jO6_/TestBatch1-joint-effects-snp-filterSNP.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpGh_VeY/TestBatch1-joint-effects-snp-filterSNP.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpug1MaL' VariantRecalibrator -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --mode INDEL --tranches_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpnSUW7r/TestBatch1-joint-effects-indel.tranches --rscript_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpnSUW7r/TestBatch1-joint-effects-indel-plots.R --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-indel.vcf.gz --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpnSUW7r/TestBatch1-joint-effects-indel-vqsrrecal.vcf.gz --resource mills,known=true,training=true,truth=true,prior=12.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz --maxGaussians 4 -tranche 100.0 -tranche 99.99 -tranche 99.98 -tranche 99.97 -tranche 99.96 -tranche 99.95 -tranche 99.94 -tranche 99.93 -tranche 99.92 -tranche 99.91 -tranche 99.9 -tranche 99.8 -tranche 99.7 -tranche 99.6 -tranche 99.5 -tranche 99.0 -tranche 98.0 -tranche 90.0 -an DP -an QD -an FS -an ReadPosRankSum | |
| [2017-08-23T18:23Z] /usr/local/bin/bcftools filter -O v -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed.gz --soft-filter 'GATKCutoffIndel' -e 'TYPE="indel" && (ReadPosRankSum < -20.0 || QD < 2.0 || FS > 200.0 || SOR > 10.0 || (QD < 10.0 && AD[1] / (AD[1] + AD[0]) < 0.25 && ReadPosRankSum < 0.0))' -m '+' /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-indel.vcf.gz | sed 's/\\"//g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpQZQPad/TestBatch1-joint-effects-indel-filterINDEL.vcf.gz | |
| [2017-08-23T18:23Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp7rhX35/TestBatch1-joint-effects-indel-filterINDEL.vcf.gz | |
| [2017-08-23T18:23Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/share/bcbio_nextgen/anaconda/bin/gatk-framework -Xms750m -Xmx2500m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp07AmIc -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp07AmIc/TestBatch1-joint-effects-combined.vcf.gz --variant:v0 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-snp-filterSNP.vcf.gz --variant:v1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-indel-filterINDEL.vcf.gz --rod_priority_list v0,v1 --genotypemergeoption PRIORITIZE --suppressCommandLineHeader --setKey null | |
| [2017-08-23T18:24Z] bcftools annotate -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpOigcTJ/TestBatch1-joint-effects-combined-gatkclean-updateheaders.txt -o - /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-combined.vcf.gz | grep -v NON_REF | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpOigcTJ/TestBatch1-joint-effects-combined-gatkclean.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpqu2RRl/TestBatch1-joint-effects-combined-gatkclean.vcf.gz | |
| [2017-08-23T18:24Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-grade.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmprOhtzI/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpBcHHqn/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/bcftools view -O z /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/joint/gatk-haplotype-joint/TestBatch1/TestBatch1-joint-effects-combined-gatkclean.vcf.gz -s Test1 > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpsC5P_J/TestBatch1-joint-effects-combined-gatkclean-Test1.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp0iwKc2/TestBatch1-joint-effects-combined-gatkclean-Test1.vcf.gz | |
| [2017-08-23T18:24Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && export RTG_JAVA_OPTS='-Xms750m' && export RTG_MEM=2500m && rtg vcfeval --threads 1 -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype-joint/7_100326_FC6107FAAXX-grade.vcf.gz --bed-regions /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample.bed -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype-joint/TestBatch1-joint-effects-combined-gatkclean-Test1.vcf.gz -t /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/rtg/hg19.sdf -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype-joint/rtg --vcf-score-field='GQ' | |
| [2017-08-23T18:24Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpmmxxqg/tp-baseline-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype-joint/rtg/tp-baseline.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpmmxxqg/tp-baseline-context.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpfWYvDN/tp-baseline-context.vcf.gz | |
| [2017-08-23T18:24Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpu2VDzr/tp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype-joint/rtg/tp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpu2VDzr/tp-context.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpn53DFP/tp-context.vcf.gz | |
| [2017-08-23T18:24Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp33oOWW/fp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype-joint/rtg/fp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp33oOWW/fp-context.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmploxcZR/fp-context.vcf.gz | |
| [2017-08-23T18:24Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpLA9M6V/fn-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype-joint/rtg/fn.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpLA9M6V/fn-context.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpQfRTRV/fn-context.vcf.gz | |
| [2017-08-23T18:24Z] gunzip -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-gatk-haplotype-joint.vcf.gz | sed 's/ID=AD,Number=./ID=AD,Number=R/' | vt decompose -s - | vt normalize -n -r /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa - | awk '{ gsub("./-65", "./."); print $0 }'| bcftools view -f 'PASS,.' | sed -e 's/Number=A/Number=1/g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp55h2Bq/TestBatch1-gatk-haplotype-joint-decompose.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpswpLIH/TestBatch1-gatk-haplotype-joint-decompose.vcf.gz | |
| [2017-08-23T18:24Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/snpEff -Xms750m -Xmx11g -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpDueWVo/tmp eff -dataDir /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/snpeff -hgvs -noLog -i vcf -o vcf -csvStats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-gatk-haplotype-joint-decompose-effects-stats.csv -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-gatk-haplotype-joint-decompose-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-gatk-haplotype-joint-decompose.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpDueWVo/TestBatch1-gatk-haplotype-joint-decompose-effects.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp0nBwe4/TestBatch1-gatk-haplotype-joint-decompose-effects.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/vcfanno -p 1 -lua /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.lua -base-path /usr/local/share/bcbio_nextgen/gemini_data /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-gatk-haplotype-joint-decompose-effects.vcf.gz | sed -e 's/Number=A/Number=1/g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpVfxIL2/TestBatch1-gatk-haplotype-joint-decompose-effects-annotated-gemini.vcf.gz | |
| [2017-08-23T18:24Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmprke35o/TestBatch1-gatk-haplotype-joint-decompose-effects-annotated-gemini.vcf.gz | |
| [2017-08-23T18:24Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/gemini load --passonly --skip-gene-tables --test-mode --skip-cadd --skip-gerp-bp -v /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-gatk-haplotype-joint-decompose-effects-annotated-gemini.vcf.gz -t snpEff --cores 1 --tempdir /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmphfZS54 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmphfZS54/TestBatch1-gatk-haplotype-joint.db | |
| [2017-08-23T18:24Z] /usr/local/bin/gemini amend --sample /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-gatk-haplotype-joint-decompose-effects-annotated-gemini.ped /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmphfZS54/TestBatch1-gatk-haplotype-joint.db | |
| [2017-08-23T18:24Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/fastqc -d /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/Test2/bcbiotx/tmpSAZWI8 -t 1 --extract -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/Test2/bcbiotx/tmpSAZWI8 -f bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.bam | |
| [2017-08-23T18:24Z] /usr/local/bin/samtools stats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.bam > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp3f_mo3/Test2.txt | |
| [2017-08-23T18:24Z] /usr/local/bin/samtools stats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.bam > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpCoSS6D/Test2.txt | |
| [2017-08-23T18:24Z] goleft indexcov --directory /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpIUf3M7/Test2 -- /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test2/Test2-sort-recal.bam | |
| [2017-08-23T18:24Z] gunzip -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/Test2/coverage/indexcov/Test2-indexcov.bed.gz > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpPS3v2_/Test2-indexcov.tsv | |
| [2017-08-23T18:24Z] /usr/local/bin/bcftools stats -s Test2 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test2.vcf.gz > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp_3PeyT/orig_Test2_bcftools_stats.txt | |
| [2017-08-23T18:24Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/fastqc -d /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/Test1/bcbiotx/tmpeiBLdS -t 1 --extract -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/Test1/bcbiotx/tmpeiBLdS -f bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T18:24Z] /usr/local/bin/samtools stats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpCWVyMp/Test1.txt | |
| [2017-08-23T18:24Z] /usr/local/bin/samtools stats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpTOTLHQ/Test1.txt | |
| [2017-08-23T18:24Z] goleft indexcov --directory /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpfWW1mI/Test1 -- /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T18:24Z] gunzip -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/Test1/coverage/indexcov/Test1-indexcov.bed.gz > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpniW9Pc/Test1-indexcov.tsv | |
| [2017-08-23T18:24Z] /usr/local/bin/bcftools stats -s Test1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/Test1.vcf.gz > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpFY7pUq/orig_Test1_bcftools_stats.txt | |
| [2017-08-23T18:24Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/multiqc -f -l /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/multiqc/list_files.txt -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpnE2hEr |
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| [2017-08-23T19:14Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-grade.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp4zbwgX/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:14Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpdHWtS1/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:14Z] /usr/local/bin/bamtofastq filename=/home/chapmanb/bio/bcbio-nextgen/tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam T=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpyAU4Vh/7_100326_FC6107FAAXX-1.fq-sort F=>(/usr/local/bin/bgzip -c /dev/stdin > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpyAU4Vh/7_100326_FC6107FAAXX-1.fq.gz) F2=>(/usr/local/bin/bgzip -c /dev/stdin > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-2.fq.gz) S=/dev/null O=/dev/null O2=/dev/null collate=1 colsbs=1048576 | |
| [2017-08-23T19:14Z] atropos trim --quality-base 33 --format fastq -pe1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-1.fq.gz -pe2 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-2.fq.gz -o >(bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpmF8cO1/7_100326_FC6107FAAXX-1-trimmed.fq.gz) -p >(bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpmF8cO1/7_100326_FC6107FAAXX-2-trimmed.fq.gz) --report-file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpmF8cO1/7_100326_FC6107FAAXX-1-report.json --report-formats json --sample-id Test1 --quality-cutoff=5 --minimum-length=25 | |
| [2017-08-23T19:14Z] /usr/local/bin/grabix index /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpL2Y_5g/7_100326_FC6107FAAXX-1-trimmed.fq.gz | |
| [2017-08-23T19:14Z] /usr/local/bin/grabix index /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpMNJ4e1/7_100326_FC6107FAAXX-2-trimmed.fq.gz | |
| [2017-08-23T19:14Z] unset JAVA_HOME && /usr/local/bin/bwa mem -c 250 -M -t 1 -R '@RG\tID:Test1\tPL:illumina\tPU:7_20150229_develtest\tSM:Test1' -v 1 /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa <(grabix grab /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/trimmed/7_100326_FC6107FAAXX-1-trimmed.fq.gz 1 60000) <(grabix grab /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/trimmed/7_100326_FC6107FAAXX-2-trimmed.fq.gz 1 60000) | /usr/local/bin/samtools sort -n -@ 1 -m 384M -O bam -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpAixRY5/Test1-sort-1_60000-sorttmp-namesort -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpAixRY5/Test1-sort-1_60000.bam - | |
| [2017-08-23T19:14Z] unset JAVA_HOME && /usr/local/bin/bwa mem -c 250 -M -t 1 -R '@RG\tID:Test1\tPL:illumina\tPU:7_20150229_develtest\tSM:Test1' -v 1 /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa <(grabix grab /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/trimmed/7_100326_FC6107FAAXX-1-trimmed.fq.gz 60001 120000) <(grabix grab /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/trimmed/7_100326_FC6107FAAXX-2-trimmed.fq.gz 60001 120000) | /usr/local/bin/samtools sort -n -@ 1 -m 384M -O bam -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp8MDNNa/Test1-sort-60001_120000-sorttmp-namesort -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp8MDNNa/Test1-sort-60001_120000.bam - | |
| [2017-08-23T19:14Z] unset JAVA_HOME && /usr/local/bin/bwa mem -c 250 -M -t 1 -R '@RG\tID:Test1\tPL:illumina\tPU:7_20150229_develtest\tSM:Test1' -v 1 /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/bwa/hg19.fa <(grabix grab /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/trimmed/7_100326_FC6107FAAXX-1-trimmed.fq.gz 120001 159332) <(grabix grab /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/trimmed/7_100326_FC6107FAAXX-2-trimmed.fq.gz 120001 159332) | /usr/local/bin/samtools sort -n -@ 1 -m 384M -O bam -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpkRdWJi/Test1-sort-120001_159332-sorttmp-namesort -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpkRdWJi/Test1-sort-120001_159332.bam - | |
| [2017-08-23T19:14Z] /usr/local/bin/samtools quickcheck -v /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/split/Test1-sort-120001_159332.bam | |
| [2017-08-23T19:14Z] /usr/local/bin/samtools quickcheck -v /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/split/Test1-sort-1_60000.bam | |
| [2017-08-23T19:14Z] /usr/local/bin/samtools quickcheck -v /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/split/Test1-sort-60001_120000.bam | |
| [2017-08-23T19:14Z] bamcat level=0 tmpfile=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpBkibV7/Test1-sort.bam-bammerge `cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpBkibV7/Test1-sort.list` | bamsormadup threads=1 tmpfile=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpBkibV7/Test1-sort.bam-bamsormaduptmp level=0 | variant - -b --mark-as-qc-fail --max-coverage 16007 > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpBkibV7/Test1-sort.bam | |
| [2017-08-23T19:14Z] /usr/local/bin/samtools quickcheck -v /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpBkibV7/Test1-sort.bam | |
| [2017-08-23T19:14Z] /usr/local/bin/samtools quickcheck -v /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam | |
| [2017-08-23T19:14Z] /usr/local/bin/samtools index -@ 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpPFuG36/Test1-sort.bam.bai | |
| [2017-08-23T19:14Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/automated/variant_regions-bam.bed | grep -v ^track | grep -v ^browser | grep -v ^# | /usr/local/bin/py -x 'bcbio.variation.bedutils.remove_bad(x)' | sort -V -k1,1 -k2,2n > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmplv5KHX/variant_regions-bam.bed | |
| [2017-08-23T19:14Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpN3rzmX/variant_regions-bam.bed.gz | |
| [2017-08-23T19:14Z] /usr/local/bin/tabix -f -p bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp0ATlit/variant_regions-bam.bed.gz | |
| [2017-08-23T19:14Z] /usr/local/bin/bedtools merge -i /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpVRfykW/variant_regions-bam-merged.bed | |
| [2017-08-23T19:14Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam-merged.bed | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpM1AJoe/variant_regions-bam-merged.bed.gz | |
| [2017-08-23T19:14Z] /usr/local/bin/tabix -f -p bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp3adAck/variant_regions-bam-merged.bed.gz | |
| [2017-08-23T19:14Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/automated/coverage_transcripts-bam.bed | grep -v ^track | grep -v ^browser | grep -v ^# | iconv -c -f utf-8 -t ascii | sed 's/ //g' | /usr/local/bin/py -x 'bcbio.variation.bedutils.remove_bad(x)' | sort -V -k1,1 -k2,2n > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpkZNT88/cov-coverage_transcripts-bam.bed | |
| [2017-08-23T19:14Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/cov-coverage_transcripts-bam.bed | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpx0jld3/cov-coverage_transcripts-bam.bed.gz | |
| [2017-08-23T19:14Z] /usr/local/bin/tabix -f -p bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmplgjx_7/cov-coverage_transcripts-bam.bed.gz | |
| [2017-08-23T19:14Z] /usr/local/bin/bedtools merge -i /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/cov-coverage_transcripts-bam.bed > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp_LJ8KL/cov-coverage_transcripts-bam-merged.bed | |
| [2017-08-23T19:14Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/cov-coverage_transcripts-bam-merged.bed | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpp_uo6J/cov-coverage_transcripts-bam-merged.bed.gz | |
| [2017-08-23T19:14Z] /usr/local/bin/tabix -f -p bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpulnJv4/cov-coverage_transcripts-bam-merged.bed.gz | |
| [2017-08-23T19:14Z] goleft depth --q 1 --mincov 4 --processes 1 --ordered --reference /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-bamref.fa --prefix /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpsjFUS2/Test1-coverage /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam | |
| [2017-08-23T19:14Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp2f0Tju' BaseRecalibratorSpark -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --sparkMaster local[1] --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp2f0Tju/Test1-sort-recal.grp --reference /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/ucsc/hg19.2bit --knownSites /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed --interval_set_rule INTERSECTION | |
| [2017-08-23T19:14Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpkT3UEF' ApplyBQSRSpark --sparkMaster local[1] --input /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort.bam --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpkT3UEF/Test1-sort-recal.bam --bqsr_recal_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.grp | |
| [2017-08-23T19:14Z] /usr/local/bin/samtools index -@ 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpak0pDA/Test1-sort-recal.bam.bai | |
| [2017-08-23T19:14Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpj6k3yP' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chr22/TestBatch1-chr22_0_14496-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpSPZNT0/TestBatch1-chr22_0_14496.vcf.gz -ploidy 2 | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpRMmQM6/TestBatch1-chr22_0_14496.vcf.gz | |
| [2017-08-23T19:15Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpklb6WL' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chrM/TestBatch1-chrM_2000_5000-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpR92JrI/TestBatch1-chrM_2000_5000.vcf.gz -ploidy 1 | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpQ7NuMs/TestBatch1-chrM_2000_5000.vcf.gz | |
| [2017-08-23T19:15Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmptCOSPu' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chrM/TestBatch1-chrM_0_1000-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpsq2WHH/TestBatch1-chrM_0_1000.vcf.gz -ploidy 1 | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp0JJjie/TestBatch1-chrM_0_1000.vcf.gz | |
| [2017-08-23T19:15Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpEqFWyk' HaplotypeCaller -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --annotation FisherStrand --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation BaseQualityRankSumTest --annotation MappingQuality --annotation ClippedBases --annotation DepthPerAlleleBySample --annotation Coverage -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --dbsnp /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chr22/TestBatch1-chr22_15128_15500-regions.bed --interval_set_rule INTERSECTION --annotation ClippingRankSumTest --annotation DepthPerSampleHC --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpo88RwA/TestBatch1-chr22_15128_15500.vcf.gz -ploidy 2 | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpi6ECg1/TestBatch1-chr22_15128_15500.vcf.gz | |
| [2017-08-23T19:15Z] platypus callVariants --regions=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/chr22/TestBatch1-chr22_0_14496-regions.bed --bamFiles=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --refFile=/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --output=- --logFileName /dev/null --verbosity=1 | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | /usr/local/share/bcbio_nextgen/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa")' | vcfallelicprimitives -t DECOMPOSED --keep-geno | vcffixup - | vcfstreamsort | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpG71Nds/TestBatch1-chr22_0_14496.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpbzuBpF/TestBatch1-chr22_0_14496.vcf.gz | |
| [2017-08-23T19:15Z] platypus callVariants --regions=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/chrM/TestBatch1-chrM_2000_5000-regions.bed --bamFiles=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --refFile=/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --output=- --logFileName /dev/null --verbosity=1 | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | /usr/local/share/bcbio_nextgen/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa")' | vcfallelicprimitives -t DECOMPOSED --keep-geno | vcffixup - | vcfstreamsort | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpiVJx5M/TestBatch1-chrM_2000_5000.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp9ABKci/TestBatch1-chrM_2000_5000.vcf.gz | |
| [2017-08-23T19:15Z] platypus callVariants --regions=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/chrM/TestBatch1-chrM_0_1000-regions.bed --bamFiles=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --refFile=/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --output=- --logFileName /dev/null --verbosity=1 | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | /usr/local/share/bcbio_nextgen/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa")' | vcfallelicprimitives -t DECOMPOSED --keep-geno | vcffixup - | vcfstreamsort | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpthJZQS/TestBatch1-chrM_0_1000.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp5HSvuM/TestBatch1-chrM_0_1000.vcf.gz | |
| [2017-08-23T19:15Z] platypus callVariants --regions=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/chr22/TestBatch1-chr22_15128_15500-regions.bed --bamFiles=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam --refFile=/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --output=- --logFileName /dev/null --verbosity=1 | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | /usr/local/share/bcbio_nextgen/anaconda/bin/py -x 'bcbio.variation.vcfutils.add_contig_to_header(x, "/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa")' | vcfallelicprimitives -t DECOMPOSED --keep-geno | vcffixup - | vcfstreamsort | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp_Qxa1W/TestBatch1-chr22_15128_15500.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpay2r6s/TestBatch1-chr22_15128_15500.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/freebayes -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --genotype-qualities --strict-vcf --ploidy 2 --targets /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_0_14496-regions.bed --min-repeat-entropy 1 --no-partial-observations -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | bcftools filter -i 'ALT="<*>" || QUAL > 5' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | bcftools view -a - | /usr/local/bin/py -x 'bcbio.variation.freebayes.remove_missingalt(x)' | vcfallelicprimitives -t DECOMPOSED --keep-geno | vcffixup - | vcfstreamsort | vt normalize -n -r /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -q - | vcfuniqalleles | vt uniq - 2> /dev/null | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpaTK_t6/TestBatch1-chr22_0_14496-raw.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp5e8C93/TestBatch1-chr22_0_14496-raw.vcf.gz | |
| [2017-08-23T19:15Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp_VIGLM/dbsnp.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_0_14496-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp_VIGLM/TestBatch1-chr22_0_14496.vcf.gz -O z | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpByFCLG/TestBatch1-chr22_0_14496.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/freebayes -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --genotype-qualities --strict-vcf --ploidy 1 --targets /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_2000_5000-regions.bed --min-repeat-entropy 1 --no-partial-observations -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | bcftools filter -i 'ALT="<*>" || QUAL > 5' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | bcftools view -a - | /usr/local/bin/py -x 'bcbio.variation.freebayes.remove_missingalt(x)' | vcfallelicprimitives -t DECOMPOSED --keep-geno | vcffixup - | vcfstreamsort | vt normalize -n -r /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -q - | vcfuniqalleles | vt uniq - 2> /dev/null | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpiIcW_p/TestBatch1-chrM_2000_5000-raw.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp8GDTm6/TestBatch1-chrM_2000_5000-raw.vcf.gz | |
| [2017-08-23T19:15Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp217FcX/dbsnp.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_2000_5000-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp217FcX/TestBatch1-chrM_2000_5000.vcf.gz -O z | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpj2nWlp/TestBatch1-chrM_2000_5000.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/freebayes -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --genotype-qualities --strict-vcf --ploidy 1 --targets /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000-regions.bed --min-repeat-entropy 1 --no-partial-observations -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | bcftools filter -i 'ALT="<*>" || QUAL > 5' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | bcftools view -a - | /usr/local/bin/py -x 'bcbio.variation.freebayes.remove_missingalt(x)' | vcfallelicprimitives -t DECOMPOSED --keep-geno | vcffixup - | vcfstreamsort | vt normalize -n -r /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -q - | vcfuniqalleles | vt uniq - 2> /dev/null | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpwdUokh/TestBatch1-chrM_0_1000-raw.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp4uTW0c/TestBatch1-chrM_0_1000-raw.vcf.gz | |
| [2017-08-23T19:15Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpLMJMZ2/dbsnp.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpLMJMZ2/TestBatch1-chrM_0_1000.vcf.gz -O z | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpYll5LM/TestBatch1-chrM_0_1000.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/freebayes -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --genotype-qualities --strict-vcf --ploidy 2 --targets /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_15128_15500-regions.bed --min-repeat-entropy 1 --no-partial-observations -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | bcftools filter -i 'ALT="<*>" || QUAL > 5' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | bcftools view -a - | /usr/local/bin/py -x 'bcbio.variation.freebayes.remove_missingalt(x)' | vcfallelicprimitives -t DECOMPOSED --keep-geno | vcffixup - | vcfstreamsort | vt normalize -n -r /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -q - | vcfuniqalleles | vt uniq - 2> /dev/null | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpGBbNvB/TestBatch1-chr22_15128_15500-raw.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpzBveGS/TestBatch1-chr22_15128_15500-raw.vcf.gz | |
| [2017-08-23T19:15Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp6OZUm_/dbsnp.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_15128_15500-raw.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp6OZUm_/TestBatch1-chr22_15128_15500.vcf.gz -O z | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpUgewbi/TestBatch1-chr22_15128_15500.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/samtools mpileup -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -t DP -u -g -l /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chr22/TestBatch1-chr22_0_14496-regions.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | /usr/local/bin/bcftools call -v -m - | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | vt normalize -n -q -r /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa - | sed 's/VCFv4.2/VCFv4.1/' | sed 's/,Version=3>/>/' | sed 's/,Version="3">/>/' | sed 's/Number=R/Number=./' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpQ7RI3E/TestBatch1-chr22_0_14496.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp6wTM5I/TestBatch1-chr22_0_14496.vcf.gz | |
| [2017-08-23T19:15Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpayi2kn/dbsnp.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chr22/TestBatch1-chr22_0_14496.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpayi2kn/TestBatch1-chr22_0_14496-wdbsnp.vcf.gz -O z | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpZy8i6S/TestBatch1-chr22_0_14496-wdbsnp.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/samtools mpileup -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -t DP -u -g -l /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chrM/TestBatch1-chrM_2000_5000-regions.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | /usr/local/bin/bcftools call -v -m - | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | vt normalize -n -q -r /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa - | sed 's/VCFv4.2/VCFv4.1/' | sed 's/,Version=3>/>/' | sed 's/,Version="3">/>/' | sed 's/Number=R/Number=./' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpdd6j7J/TestBatch1-chrM_2000_5000.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpv8r58q/TestBatch1-chrM_2000_5000.vcf.gz | |
| [2017-08-23T19:15Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpnhpxzB/dbsnp.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chrM/TestBatch1-chrM_2000_5000.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpnhpxzB/TestBatch1-chrM_2000_5000-wdbsnp.vcf.gz -O z | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpXPcIXs/TestBatch1-chrM_2000_5000-wdbsnp.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/samtools mpileup -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -t DP -u -g -l /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chrM/TestBatch1-chrM_0_1000-regions.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | /usr/local/bin/bcftools call -v -m - | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | vt normalize -n -q -r /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa - | sed 's/VCFv4.2/VCFv4.1/' | sed 's/,Version=3>/>/' | sed 's/,Version="3">/>/' | sed 's/Number=R/Number=./' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmppX90kC/TestBatch1-chrM_0_1000.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpVQ7a7Y/TestBatch1-chrM_0_1000.vcf.gz | |
| [2017-08-23T19:15Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp3Bzyfl/dbsnp.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chrM/TestBatch1-chrM_0_1000.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp3Bzyfl/TestBatch1-chrM_0_1000-wdbsnp.vcf.gz -O z | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpg88KHg/TestBatch1-chrM_0_1000-wdbsnp.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/samtools mpileup -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -t DP -u -g -l /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chr22/TestBatch1-chr22_15128_15500-regions.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | /usr/local/bin/bcftools call -v -m - | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $4) } {print}' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDXkmryswbvhdx]/, "N", $5) } {print}' | vt normalize -n -q -r /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa - | sed 's/VCFv4.2/VCFv4.1/' | sed 's/,Version=3>/>/' | sed 's/,Version="3">/>/' | sed 's/Number=R/Number=./' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpMkK4AI/TestBatch1-chr22_15128_15500.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpAlaKZM/TestBatch1-chr22_15128_15500.vcf.gz | |
| [2017-08-23T19:15Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp8U_2p5/dbsnp.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chr22/TestBatch1-chr22_15128_15500.vcf.gz | bcftools annotate --set-id +'%INFO/rs_ids' -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp8U_2p5/TestBatch1-chr22_15128_15500-wdbsnp.vcf.gz -O z | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpDW3_Gr/TestBatch1-chr22_15128_15500-wdbsnp.vcf.gz | |
| [2017-08-23T19:15Z] zgrep ^# /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chr22/TestBatch1-chr22_0_14496.vcf.gz | sed 's/ID=MMQ,Number=A/ID=MMQ,Number=R/' | sed 's/ID=MCL,Number=A/ID=MCL,Number=R/' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpbBU7xd/TestBatch1-chrM_0_1000-fixheader-header.vcf | |
| [2017-08-23T19:15Z] bcftools reheader -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpbBU7xd/TestBatch1-chrM_0_1000-fixheader-header.vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/chrM/TestBatch1-chrM_0_1000.vcf.gz -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjypz8B/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T19:15Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpD0sLIf' GatherVcfs -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/TestBatch1-files.list -O /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpWWNmg3/TestBatch1.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp1w0Jq9/TestBatch1.vcf.gz | |
| [2017-08-23T19:15Z] zgrep ^# /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/chr22/TestBatch1-chr22_0_14496.vcf.gz | sed 's/ID=MMQ,Number=A/ID=MMQ,Number=R/' | sed 's/ID=MCL,Number=A/ID=MCL,Number=R/' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpXRBjcj/TestBatch1-chrM_0_1000-fixheader-header.vcf | |
| [2017-08-23T19:15Z] bcftools reheader -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpXRBjcj/TestBatch1-chrM_0_1000-fixheader-header.vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/chrM/TestBatch1-chrM_0_1000.vcf.gz -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T19:15Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpz38GUl/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T19:15Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp2Lxwa2' GatherVcfs -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/TestBatch1-files.list -O /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpmualeW/TestBatch1.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp3lvYGf/TestBatch1.vcf.gz | |
| [2017-08-23T19:16Z] zgrep ^# /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chr22/TestBatch1-chr22_0_14496.vcf.gz | sed 's/ID=MMQ,Number=A/ID=MMQ,Number=R/' | sed 's/ID=MCL,Number=A/ID=MCL,Number=R/' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp1mS193/TestBatch1-chrM_0_1000-fixheader-header.vcf | |
| [2017-08-23T19:16Z] bcftools reheader -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp1mS193/TestBatch1-chrM_0_1000-fixheader-header.vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/chrM/TestBatch1-chrM_0_1000.vcf.gz -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp1N6fc7/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T19:16Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpbpvVRA' GatherVcfs -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-files.list -O /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpXxy7wY/TestBatch1.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpEbODlw/TestBatch1.vcf.gz | |
| [2017-08-23T19:16Z] zgrep ^# /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/TestBatch1-chr22_0_14496.vcf.gz | sed 's/ID=MMQ,Number=A/ID=MMQ,Number=R/' | sed 's/ID=MCL,Number=A/ID=MCL,Number=R/' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmprWTDiy/TestBatch1-chrM_0_1000-fixheader-header.vcf | |
| [2017-08-23T19:16Z] bcftools reheader -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmprWTDiy/TestBatch1-chrM_0_1000-fixheader-header.vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chrM/TestBatch1-chrM_0_1000.vcf.gz -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpGthz3Z/TestBatch1-chrM_0_1000-fixheader.vcf.gz | |
| [2017-08-23T19:16Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms930M -Xmx2g -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmptuPlSX' GatherVcfs -I /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-files.list -O /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmptEnyi8/TestBatch1.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp82AeTd/TestBatch1.vcf.gz | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/snpEff -Xms750m -Xmx11g -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp4Wt35l/tmp eff -dataDir /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/snpeff -hgvs -noLog -i vcf -o vcf -csvStats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/precalled/VarOnly-precalled-effects-stats.csv -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/precalled/VarOnly-precalled-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/precalled/VarOnly-precalled.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp4Wt35l/VarOnly-precalled-effects.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp3lPDNf/VarOnly-precalled-effects.vcf.gz | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/snpEff -Xms750m -Xmx11g -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp0aQK23/tmp eff -dataDir /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/snpeff -hgvs -noLog -i vcf -o vcf -csvStats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-stats.csv -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp0aQK23/TestBatch1-effects.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp5xpbjZ/TestBatch1-effects.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/bcftools view -O z /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects.vcf.gz --types snps > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpUdFJrn/TestBatch1-effects-snp.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpw4LPM8/TestBatch1-effects-snp.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/bcftools view -O z /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects.vcf.gz --exclude-types snps > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp6maN6i/TestBatch1-effects-indel.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpsBdoEp/TestBatch1-effects-indel.vcf.gz | |
| [2017-08-23T19:16Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpL9mrGN' VariantRecalibrator -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --mode SNP --tranches_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp71HHB8/TestBatch1-effects-snp.tranches --rscript_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp71HHB8/TestBatch1-effects-snp-plots.R --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-snp.vcf.gz --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp71HHB8/TestBatch1-effects-snp-vqsrrecal.vcf.gz --resource hapmap,known=false,training=true,truth=true,prior=15.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/hapmap_3.3.vcf.gz --resource omni,known=false,training=true,truth=true,prior=12.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/1000G_omni2.5.vcf.gz --resource 1000g,known=false,training=true,truth=false,prior=10.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/1000G_phase1.snps.high_confidence.vcf.gz --resource dbsnp,known=true,training=false,truth=false,prior=2.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/dbsnp_132.vcf.gz -tranche 100.0 -tranche 99.99 -tranche 99.98 -tranche 99.97 -tranche 99.96 -tranche 99.95 -tranche 99.94 -tranche 99.93 -tranche 99.92 -tranche 99.91 -tranche 99.9 -tranche 99.8 -tranche 99.7 -tranche 99.6 -tranche 99.5 -tranche 99.0 -tranche 98.0 -tranche 90.0 -an DP -an QD -an FS -an ReadPosRankSum | |
| [2017-08-23T19:16Z] /usr/local/bin/bcftools filter -O v -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed.gz --soft-filter 'GATKCutoffSNP' -e 'TYPE="snp" && (MQ < 30.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || QD < 2.0 || FS > 60.0 || (QD < 10.0 && AD[1] / (AD[1] + AD[0]) < 0.25 && ReadPosRankSum < 0.0))' -m '+' /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-snp.vcf.gz | sed 's/\\"//g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpS_DYMq/TestBatch1-effects-snp-filterSNP.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpvfOyYL/TestBatch1-effects-snp-filterSNP.vcf.gz | |
| [2017-08-23T19:16Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gatk-launch --javaOptions '-Xms681m -Xmx2272m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp8BPnDf' VariantRecalibrator -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --mode INDEL --tranches_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpustoY2/TestBatch1-effects-indel.tranches --rscript_file /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpustoY2/TestBatch1-effects-indel-plots.R --variant /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-indel.vcf.gz --output /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpustoY2/TestBatch1-effects-indel-vqsrrecal.vcf.gz --resource mills,known=true,training=true,truth=true,prior=12.0:/home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz --maxGaussians 4 -tranche 100.0 -tranche 99.99 -tranche 99.98 -tranche 99.97 -tranche 99.96 -tranche 99.95 -tranche 99.94 -tranche 99.93 -tranche 99.92 -tranche 99.91 -tranche 99.9 -tranche 99.8 -tranche 99.7 -tranche 99.6 -tranche 99.5 -tranche 99.0 -tranche 98.0 -tranche 90.0 -an DP -an QD -an FS -an ReadPosRankSum | |
| [2017-08-23T19:16Z] /usr/local/bin/bcftools filter -O v -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed.gz --soft-filter 'GATKCutoffIndel' -e 'TYPE="indel" && (ReadPosRankSum < -20.0 || QD < 2.0 || FS > 200.0 || SOR > 10.0 || (QD < 10.0 && AD[1] / (AD[1] + AD[0]) < 0.25 && ReadPosRankSum < 0.0))' -m '+' /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-indel.vcf.gz | sed 's/\\"//g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpCRDBBh/TestBatch1-effects-indel-filterINDEL.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp_uNAZc/TestBatch1-effects-indel-filterINDEL.vcf.gz | |
| [2017-08-23T19:16Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/share/bcbio_nextgen/anaconda/bin/gatk-framework -Xms750m -Xmx2500m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp24T2m0 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp24T2m0/TestBatch1-effects-combined.vcf.gz --variant:v0 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-snp-filterSNP.vcf.gz --variant:v1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-indel-filterINDEL.vcf.gz --rod_priority_list v0,v1 --genotypemergeoption PRIORITIZE --suppressCommandLineHeader --setKey null | |
| [2017-08-23T19:16Z] bcftools annotate -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpvjwmkt/TestBatch1-effects-combined-gatkclean-updateheaders.txt -o - /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-combined.vcf.gz | grep -v NON_REF | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpvjwmkt/TestBatch1-effects-combined-gatkclean.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmptmq_tz/TestBatch1-effects-combined-gatkclean.vcf.gz | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/snpEff -Xms750m -Xmx11g -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpsB8WZ8/tmp eff -dataDir /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/snpeff -hgvs -noLog -i vcf -o vcf -csvStats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/TestBatch1-effects-stats.csv -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/TestBatch1-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/TestBatch1.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpsB8WZ8/TestBatch1-effects.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpL4XRAQ/TestBatch1-effects.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/bcftools filter -O v -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed.gz --soft-filter 'PlatQualDepth' -e '(FR[0] <= 0.5 && TC < 4 && %QUAL < 20) || (TC < 13 && %QUAL < 10) || (FR[0] > 0.5 && TC < 4 && %QUAL < 50)' -m '+' /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/TestBatch1-effects.vcf.gz | sed 's/\tQ20\t/\tPASS\t/' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpxxp8JA/TestBatch1-effects-filter.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmprMsMba/TestBatch1-effects-filter.vcf.gz | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/snpEff -Xms750m -Xmx11g -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpKibk7o/tmp eff -dataDir /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/snpeff -hgvs -noLog -i vcf -o vcf -csvStats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-effects-stats.csv -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpKibk7o/TestBatch1-effects.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjmgg1i/TestBatch1-effects.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/bcftools filter -O v -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed.gz --soft-filter 'FBQualDepth' -e '(AF[0] <= 0.5 && (DP < 4 || (DP < 13 && %QUAL < 10))) || (AF[0] > 0.5 && (DP < 4 && %QUAL < 50)) || (%QUAL < 1358.0 && DP > 679 && AF[0] <= 0.5)' -m '+' /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-effects.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpR1dkBr/TestBatch1-effects-filter.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpJuX2JK/TestBatch1-effects-filter.vcf.gz | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/snpEff -Xms750m -Xmx11g -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjqqKO0/tmp eff -dataDir /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/snpeff -hgvs -noLog -i vcf -o vcf -csvStats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/TestBatch1-effects-stats.csv -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/TestBatch1-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/TestBatch1.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjqqKO0/TestBatch1-effects.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmptCuFqZ/TestBatch1-effects.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/bcftools filter -O v -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam.bed.gz --soft-filter 'stQualDepth' -e '((AC[0] / AN) <= 0.5 && DP < 4 && %QUAL < 20) || (DP < 13 && %QUAL < 10) || ((AC[0] / AN) > 0.5 && DP < 4 && %QUAL < 50)' -m '+' /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/TestBatch1-effects.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmptzXzbj/TestBatch1-effects-filter.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp4on7T6/TestBatch1-effects-filter.vcf.gz | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-grade.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpDRDGUm/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpYBOCGy/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] goleft depth --q 1 --mincov 4 --processes 1 --ordered --reference /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal-bamref.fa --prefix /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpcrImYN/VarOnly-coverage /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && export RTG_JAVA_OPTS='-Xms750m' && export RTG_MEM=2500m && rtg vcfeval --threads 1 -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/7_100326_FC6107FAAXX-grade.vcf.gz --bed-regions /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal-callable_sample.bed -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/precalled/VarOnly-precalled-effects.vcf.gz -t /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/rtg/hg19.sdf -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/rtg --vcf-score-field='GQ' | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp0Oa15L/tp-baseline-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/rtg/tp-baseline.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp0Oa15L/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpzf05Id/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmplYXEM1/tp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/rtg/tp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmplYXEM1/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpQVJo0N/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpzEu9gl/fp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/rtg/fp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpzEu9gl/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp02UlcA/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpUimQ3c/fn-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/VarOnly/precalled/rtg/fn.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpUimQ3c/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp1jGy8m/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-grade.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpsdLzvD/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpCnU4Li/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && export RTG_JAVA_OPTS='-Xms750m' && export RTG_MEM=2500m && rtg vcfeval --threads 1 -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype/7_100326_FC6107FAAXX-grade.vcf.gz --bed-regions /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample.bed -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gatk-haplotype/TestBatch1-effects-combined-gatkclean.vcf.gz -t /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/rtg/hg19.sdf -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype/rtg --vcf-score-field='GQ' | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpnsIOWm/tp-baseline-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype/rtg/tp-baseline.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpnsIOWm/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpi9uyK9/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpdx1AVy/tp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype/rtg/tp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpdx1AVy/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpISriBE/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpMlIt4J/fp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype/rtg/fp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpMlIt4J/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpfHU4g4/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjAYqzV/fn-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/gatk-haplotype/rtg/fn.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjAYqzV/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpNgd3F3/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-grade.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpHpb7UV/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpzY8mOJ/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && export RTG_JAVA_OPTS='-Xms750m' && export RTG_MEM=2500m && rtg vcfeval --threads 1 -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/platypus/7_100326_FC6107FAAXX-grade.vcf.gz --bed-regions /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample.bed -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/platypus/TestBatch1-effects-filter.vcf.gz -t /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/rtg/hg19.sdf -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/platypus/rtg --vcf-score-field='GQ' | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpFf5eJw/tp-baseline-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/platypus/rtg/tp-baseline.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpFf5eJw/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpmkSGey/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpmfmlfM/tp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/platypus/rtg/tp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpmfmlfM/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpdLyYNt/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpMpgviC/fp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/platypus/rtg/fp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpMpgviC/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpuU6KV1/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpzvwVbJ/fn-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/platypus/rtg/fn.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpzvwVbJ/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpuDebjC/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-grade.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp9DO8EH/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpe1R7YS/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && export RTG_JAVA_OPTS='-Xms750m' && export RTG_MEM=2500m && rtg vcfeval --threads 1 -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/7_100326_FC6107FAAXX-grade.vcf.gz --bed-regions /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample.bed -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-effects-filter.vcf.gz -t /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/rtg/hg19.sdf -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/rtg --vcf-score-field='GQ' | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp2t7tOQ/tp-baseline-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/rtg/tp-baseline.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp2t7tOQ/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpVLVa2c/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpvqMvWs/tp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/rtg/tp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpvqMvWs/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp3tqGfB/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpd42lKm/fp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/rtg/fp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpd42lKm/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp2cQdHG/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpPOscqN/fn-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/freebayes/rtg/fn.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpPOscqN/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpGaukrm/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/data/reference_material/7_100326_FC6107FAAXX-grade.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpo2hh_w/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmppHwEMb/7_100326_FC6107FAAXX-grade.vcf.gz | |
| [2017-08-23T19:16Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && export RTG_JAVA_OPTS='-Xms750m' && export RTG_MEM=2500m && rtg vcfeval --threads 1 -b /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/samtools/7_100326_FC6107FAAXX-grade.vcf.gz --bed-regions /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-callable_sample.bed -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/samtools/TestBatch1-effects-filter.vcf.gz -t /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/rtg/hg19.sdf -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/samtools/rtg --vcf-score-field='QUAL' | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpqMJoi_/tp-baseline-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/samtools/rtg/tp-baseline.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpqMJoi_/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpWytirl/tp-baseline-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpRhFfCe/tp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/samtools/rtg/tp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpRhFfCe/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpDWJjxO/tp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpNhTB9X/fp-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/samtools/rtg/fp.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpNhTB9X/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpWqZN54/fp-context.vcf.gz | |
| [2017-08-23T19:16Z] vcfanno /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpUKxhQM/fn-context.toml /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/validate/Test1/samtools/rtg/fn.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpUKxhQM/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpD7cI5m/fn-context.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/sambamba depth region -t 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/variant_regions-bam-seq2cclean.bed -F "not unmapped and not mate_is_unmapped and not secondary_alignment and not failed_quality_control and not duplicate" -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpmopamv/sv_regions_regions_depth.bed | |
| [2017-08-23T19:16Z] sort -V -k4,4 -k1,1 /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/rnaseq/ref-transcripts.bed > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp20vjbe/ref-transcripts-transcripts_w10000-sortprep.bed | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/ref-transcripts-transcripts_w10000.bed | sort -V -k1,1 -k2,2n | bedtools merge -i - -c 4 -o distinct > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp6YxQCG/ref-transcripts-transcripts_w10000-sortmerge.bed | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/ref-transcripts-transcripts_w10000-sortmerge-noexclude.bed | grep -v ^track | grep -v ^browser | grep -v ^# | /usr/local/bin/py -x 'bcbio.variation.bedutils.remove_bad(x)' | sort -V -k1,1 -k2,2n > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpyYseLz/ref-transcripts-transcripts_w10000-sortmerge-noexclude.bed | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/ref-transcripts-transcripts_w10000-sortmerge-noexclude.bed | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp719RU8/ref-transcripts-transcripts_w10000-sortmerge-noexclude.bed.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmppcVMxe/ref-transcripts-transcripts_w10000-sortmerge-noexclude.bed.gz | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/ref-transcripts-transcripts_w10000-sortmerge-noexclude.bed | sort -V -k1,1 -k2,2n | bedtools merge -i - -c 4 -o distinct > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpUfEmvO/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge.bed | |
| [2017-08-23T19:16Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge.bed | grep -v ^track | grep -v ^browser | grep -v ^# | sort -V -k1,1 -k2,2n | bedtools closest -g <(cut -f1,2 /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa.fai | sort -V -k1,1 -k2,2n) -d -t all -a - -b <(sort -V -k1,1 -k2,2n /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/rnaseq/ref-transcripts.bed) | awk -F$'\t' -v OFS='\t' '{if ($NF > 10000) $8 = "."} {print}' | cut -f 1-9 | bedtools merge -i - -c 4,8 -o distinct,distinct -delim ',' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpk0zkuW/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated.bed | |
| [2017-08-23T19:16Z] export TMPDIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp8L6BhY && /usr/local/share/bcbio_nextgen/anaconda/bin/coverage_bin_size.py /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam -m wgs -t /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated.bed -g /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge.bed > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp8L6BhY/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated-TestBatch1-bin_estimate.txt | |
| [2017-08-23T19:16Z] export TMPDIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp9E2Y5X && /usr/local/share/bcbio_nextgen/anaconda/bin/cnvkit.py target /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated.bed --split -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp9E2Y5X/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated-TestBatch1.target.bed | |
| [2017-08-23T19:16Z] export TMPDIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpuMGFjt && /usr/local/share/bcbio_nextgen/anaconda/bin/cnvkit.py antitarget -g /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated-TestBatch1.target.bed -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpuMGFjt/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated-TestBatch1.antitarget.bed | |
| [2017-08-23T19:16Z] export TMPDIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpRwaNbA && /usr/local/share/bcbio_nextgen/anaconda/bin/cnvkit.py coverage -p 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated-TestBatch1.target.bed -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpRwaNbA/Test1-sort-recal-TestBatch1.targetcoverage.cnn | |
| [2017-08-23T19:16Z] export TMPDIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpSr02T4 && /usr/local/share/bcbio_nextgen/anaconda/bin/cnvkit.py coverage -p 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated-TestBatch1.antitarget.bed -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpSr02T4/Test1-sort-recal-TestBatch1.antitargetcoverage.cnn | |
| [2017-08-23T19:16Z] export TMPDIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpw0A51F && /usr/local/share/bcbio_nextgen/anaconda/bin/cnvkit.py reference -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpw0A51F/flat_background.cnn -t /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated-TestBatch1.target.bed -a /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/ref-transcripts-transcripts_w10000-sortmerge-noexclude-sortmerge-annotated-TestBatch1.antitarget.bed | |
| [2017-08-23T19:16Z] export TMPDIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpqIwzjW && /usr/local/share/bcbio_nextgen/anaconda/bin/cnvkit.py fix -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpqIwzjW/Test1-sort-recal-TestBatch1.cnr /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.targetcoverage.cnn /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.antitargetcoverage.cnn /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/flat_background.cnn | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp3WMEbW/TestBatch1-effects-filter-Test1.vcf.gz | |
| [2017-08-23T19:16Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpvauIV5/TestBatch1-effects-combined-gatkclean-Test1.vcf.gz | |
| [2017-08-23T19:16Z] unset R_HOME && unset R_LIBS && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && export TMPDIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpIXB5ML && /usr/local/share/bcbio_nextgen/anaconda/bin/cnvkit.py segment -p 1 -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpIXB5ML/Test1-sort-recal-TestBatch1.cns /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.cnr --threshold 0.00001 | |
| [2017-08-23T19:16Z] /usr/local/bin/cnvkit.py export seg -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpY9zihx/Test1-sort-recal-TestBatch1.seg /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.cns | |
| [2017-08-23T19:16Z] /usr/local/bin/cnvkit.py gainloss -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.cns -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpiUPBjf/Test1-sort-recal-TestBatch1-gainloss.txt /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.cnr | |
| [2017-08-23T19:16Z] /usr/local/bin/cnvkit.py segmetrics --ci --pi -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.cns -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpHIQ42l/Test1-sort-recal-TestBatch1-segmetrics.txt /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.cnr --alpha 0.1 --bootstrap 50 | |
| [2017-08-23T19:16Z] /usr/local/bin/cnvkit.py call --filter cn --ploidy 2 -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpLEiv2F/Test1-sort-recal-TestBatch1-call.cns /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.cns -v /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-effects-filter-Test1.vcf.gz -m clonal | |
| [2017-08-23T19:17Z] /usr/local/bin/cnvkit.py export bed --sample-id Test1 --ploidy 2 -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpkZZiUZ/Test1-sort-recal-TestBatch1-call.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1-call.cns | |
| [2017-08-23T19:17Z] /usr/local/bin/cnvkit.py export vcf --sample-id Test1 --ploidy 2 -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpgh_p7U/Test1-sort-recal-TestBatch1-call.vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1-call.cns | |
| [2017-08-23T19:17Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1-call.bed | grep -v ^track | grep -v ^browser | grep -v ^# | sort -V -k1,1 -k2,2n | bedtools closest -g <(cut -f1,2 /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa.fai | sort -V -k1,1 -k2,2n) -d -t all -a - -b <(sort -V -k1,1 -k2,2n /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/rnaseq/ref-transcripts.bed) | awk -F$'\t' -v OFS='\t' '{if ($NF > 10000) $9 = "."} {print}' | cut -f 1-10 | bedtools merge -i - -c 4,5,9 -o distinct,distinct,distinct -delim ',' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpxNfzHf/Test1-sort-recal-TestBatch1-call-annotated.bed | |
| [2017-08-23T19:17Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/snpEff -Xms750m -Xmx11g -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpfNdmy7/tmp eff -dataDir /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/snpeff -hgvs -noLog -i vcf -o vcf -csvStats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1-call-effects-stats.csv -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1-call-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1-call.vcf > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpfNdmy7/Test1-sort-recal-TestBatch1-call-effects.vcf | |
| [2017-08-23T19:17Z] sed 1d /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.cnr | cut -f1,2,3,5 > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpp3HBAE/Test1-sort-recal-TestBatch1.cnr.bedgraph | |
| [2017-08-23T19:17Z] sed 1d /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/cnvkit/raw/Test1-sort-recal-TestBatch1.cnr | cut -f1,2,3,4,5 > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpeH_ieI/Test1-sort-recal-TestBatch1.cnr.bed | |
| [2017-08-23T19:17Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && cov2lr.pl -a /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/seq2c/mapping_reads.txt /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/seq2c/sample_coverages.txt | lr2gene.pl > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/seq2c/calls_combined.tsv | |
| [2017-08-23T19:17Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/seq2c/Test1-calls.vcf | grep -v ^##contig | bcftools annotate -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpW9qR1C/Test1-calls-prep-header.txt | vt sort -m full -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpW9qR1C/Test1-calls-prep.vcf.gz - | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpRh0krO/Test1-calls-prep.vcf.gz | |
| [2017-08-23T19:17Z] export OMP_NUM_THREADS=1 && export LC_ALL=C && delly call -n -t DEL -g /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp2JdgFf/Test1-sort-recal-TestBatch1-svs-chrM-DEL.bcf -x /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chrM-DEL-exclude-chrM-delly.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T19:17Z] bcftools view /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chrM-DEL.bcf | sed 's/\.,\.,\././' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmptAiwDN/Test1-sort-recal-TestBatch1-svs-chrM-DEL.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpnlnH3c/Test1-sort-recal-TestBatch1-svs-chrM-DEL.vcf.gz | |
| [2017-08-23T19:17Z] export OMP_NUM_THREADS=1 && export LC_ALL=C && delly call -n -t DUP -g /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpy3MyPc/Test1-sort-recal-TestBatch1-svs-chrM-DUP.bcf -x /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chrM-DUP-exclude-chrM-delly.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T19:17Z] bcftools view /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chrM-DUP.bcf | sed 's/\.,\.,\././' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp_GM1VQ/Test1-sort-recal-TestBatch1-svs-chrM-DUP.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpm5uu1m/Test1-sort-recal-TestBatch1-svs-chrM-DUP.vcf.gz | |
| [2017-08-23T19:17Z] export OMP_NUM_THREADS=1 && export LC_ALL=C && delly call -n -t DEL -g /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp4kNqnP/Test1-sort-recal-TestBatch1-svs-chr22-DEL.bcf -x /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chr22-DEL-exclude-chr22-delly.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T19:17Z] bcftools view /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chr22-DEL.bcf | sed 's/\.,\.,\././' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpo1SLlj/Test1-sort-recal-TestBatch1-svs-chr22-DEL.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpEA8X9Q/Test1-sort-recal-TestBatch1-svs-chr22-DEL.vcf.gz | |
| [2017-08-23T19:17Z] export OMP_NUM_THREADS=1 && export LC_ALL=C && delly call -n -t DUP -g /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjA0ouD/Test1-sort-recal-TestBatch1-svs-chr22-DUP.bcf -x /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chr22-DUP-exclude-chr22-delly.bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T19:17Z] bcftools view /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chr22-DUP.bcf | sed 's/\.,\.,\././' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp1EayVo/Test1-sort-recal-TestBatch1-svs-chr22-DUP.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjHGki8/Test1-sort-recal-TestBatch1-svs-chr22-DUP.vcf.gz | |
| [2017-08-23T19:17Z] unset JAVA_HOME && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/share/bcbio_nextgen/anaconda/bin/gatk-framework -Xms750m -Xmx2500m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp24T2m0 -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpSzR7yK -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpSzR7yK/Test1-sort-recal-TestBatch1-svs.vcf.gz --variant:v0 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chrM-DEL.vcf.gz --variant:v1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chrM-DUP.vcf.gz --variant:v2 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chr22-DEL.vcf.gz --variant:v3 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-chr22-DUP.vcf.gz --rod_priority_list v0,v1,v2,v3 --genotypemergeoption PRIORITIZE --suppressCommandLineHeader --setKey null | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpwEnuS0/Test1-sort-recal-TestBatch1-svs-Test1.vcf.gz | |
| [2017-08-23T19:17Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/delly/Test1-sort-recal-TestBatch1-svs-Test1-filter.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp7FKyQO/Test1-sort-recal-TestBatch1-svs-Test1-filter.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjymvrP/Test1-sort-recal-TestBatch1-svs-Test1-filter.vcf.gz | |
| [2017-08-23T19:17Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && gridss -Xms750m -Xmx2500m -XX:+UseSerialGC -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp24T2m0 -Dsamjdk.create_index=true -Dsamjdk.use_async_io_read_samtools=true -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=true gridss.CallVariants THREADS=1 TMP_DIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpwEXgwh WORKING_DIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpwEXgwh OUTPUT=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpwEXgwh/TestBatch1-gridss.sv.vcf ASSEMBLY=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpwEXgwh/TestBatch1-gridss.gridss.assembly.bam REFERENCE_SEQUENCE=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpwEXgwh/bwa/hg19.fa BLACKLIST=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/gridss/TestBatch1-gridss.sv-exclude.bed INPUT=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam INPUT_LABEL=Test1 | |
| [2017-08-23T19:17Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/gridss/TestBatch1-gridss.sv.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpcvg6Rx/TestBatch1-gridss.sv.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpgEPXJd/TestBatch1-gridss.sv.vcf.gz | |
| [2017-08-23T19:17Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/snpEff -Xms750m -Xmx11g -Djava.io.tmpdir=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpOo5q6h/tmp eff -dataDir /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/snpeff -hgvs -noLog -i vcf -o vcf -csvStats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/gridss/TestBatch1-gridss.sv-effects-stats.csv -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/gridss/TestBatch1-gridss.sv-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/gridss/TestBatch1-gridss.sv.vcf.gz | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpOo5q6h/TestBatch1-gridss.sv-effects.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpxEAqNl/TestBatch1-gridss.sv-effects.vcf.gz | |
| [2017-08-23T19:17Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-cnvkit-prioritize.vcf | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpJjgI24/Test1-cnvkit-prioritize.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp1BXS0n/Test1-cnvkit-prioritize.vcf.gz | |
| [2017-08-23T19:17Z] simple_sv_annotation.py --known_fusion_pairs /usr/local/share/bcbio_nextgen/anaconda/share/simple_sv_annotation-2017.02.17-0/fusion_pairs.txt --gene_list /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-cnvkit-prioritize-genes.txt -o - /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-cnvkit-prioritize.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpp4gETQ/Test1-cnvkit-simple.vcf.gz | |
| [2017-08-23T19:17Z] zcat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-cnvkit-simple.vcf.gz | grep -v ^##contig | bcftools annotate -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpK5SDFT/Test1-cnvkit-simple-prep-header.txt | vt sort -m full -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpK5SDFT/Test1-cnvkit-simple-prep.vcf.gz - | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpuJ1abQ/Test1-cnvkit-simple-prep.vcf.gz | |
| [2017-08-23T19:17Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && zcat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-cnvkit-simple-prep.vcf.gz | vawk -v SNAME=Test1 -v CALLER=cnvkit '{if (($7 == "PASS" || $7 == ".") && (S$Test1$GT != "0/0")) print CALLER,SNAME,$1,$2,I$END,I$SVTYPE=="BND" ? I$SVTYPE":"$3":"I$MATEID : I$SVTYPE,I$LOF,I$SIMPLE_ANN,S$Test1$SR,S$Test1$PE,S$Test1$PR}' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpl0BOz_/Test1-cnvkit-prioritize.tsv | |
| [2017-08-23T19:17Z] simple_sv_annotation.py --known_fusion_pairs /usr/local/share/bcbio_nextgen/anaconda/share/simple_sv_annotation-2017.02.17-0/fusion_pairs.txt --gene_list /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-seq2c-prioritize-genes.txt -o - /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-seq2c-prioritize.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpBoGDWY/Test1-seq2c-simple.vcf.gz | |
| [2017-08-23T19:17Z] zcat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-seq2c-simple.vcf.gz | grep -v ^##contig | bcftools annotate -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpqDtSsS/Test1-seq2c-simple-prep-header.txt | vt sort -m full -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpqDtSsS/Test1-seq2c-simple-prep.vcf.gz - | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpm3DKPM/Test1-seq2c-simple-prep.vcf.gz | |
| [2017-08-23T19:17Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && zcat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-seq2c-simple-prep.vcf.gz | vawk -v SNAME=Test1 -v CALLER=seq2c '{if (($7 == "PASS" || $7 == ".") && (S$Test1$GT != "0/0")) print CALLER,SNAME,$1,$2,I$END,I$SVTYPE=="BND" ? I$SVTYPE":"$3":"I$MATEID : I$SVTYPE,I$LOF,I$SIMPLE_ANN,S$Test1$SR,S$Test1$PE,S$Test1$PR}' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpe5vyg5/Test1-seq2c-prioritize.tsv | |
| [2017-08-23T19:17Z] simple_sv_annotation.py --known_fusion_pairs /usr/local/share/bcbio_nextgen/anaconda/share/simple_sv_annotation-2017.02.17-0/fusion_pairs.txt --gene_list /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-gridss-prioritize-genes.txt -o - /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-gridss-prioritize.vcf.gz | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpAQHEUK/Test1-gridss-simple.vcf.gz | |
| [2017-08-23T19:17Z] zcat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-gridss-simple.vcf.gz | grep -v ^##contig | bcftools annotate -h /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpLZsrYw/Test1-gridss-simple-prep-header.txt | vt sort -m full -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpLZsrYw/Test1-gridss-simple-prep.vcf.gz - | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp3LZ0Fi/Test1-gridss-simple-prep.vcf.gz | |
| [2017-08-23T19:17Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && zcat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-gridss-simple-prep.vcf.gz | vawk -v SNAME=Test1 -v CALLER=gridss '{if (($7 == "PASS" || $7 == ".") && (S$Test1$GT != "0/0")) print CALLER,SNAME,$1,$2,I$END,I$SVTYPE=="BND" ? I$SVTYPE":"$3":"I$MATEID : I$SVTYPE,I$LOF,I$SIMPLE_ANN,S$Test1$SR,S$Test1$PE,S$Test1$PR}' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp4Sn5Sj/Test1-gridss-prioritize.tsv | |
| [2017-08-23T19:17Z] { echo 'caller sample chrom start end svtype lof annotation split_read_support paired_support_PE paired_support_PR'; cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-cnvkit-prioritize.tsv /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-seq2c-prioritize.tsv /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/structural/Test1/prioritize/Test1-gridss-prioritize.tsv | sort -V -T /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpKr2GK7 -k3,3 -k4,4n; } > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpKr2GK7/Test1-prioritize.tsv | |
| [2017-08-23T19:17Z] /usr/local/bin/vcfanno -p 1 -lua /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.lua -base-path /usr/local/share/bcbio_nextgen/gemini_data /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-platypus.vcf.gz | sed -e 's/Number=A/Number=1/g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpmSKbaw/TestBatch1-platypus-annotated-gemini.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpyXeWyc/TestBatch1-platypus-annotated-gemini.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/vcfanno -p 1 -lua /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.lua -base-path /usr/local/share/bcbio_nextgen/gemini_data /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-samtools.vcf.gz | sed -e 's/Number=A/Number=1/g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmp1JVEmq/TestBatch1-samtools-annotated-gemini.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpXSgU7x/TestBatch1-samtools-annotated-gemini.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/vcfanno -p 1 -lua /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.lua -base-path /usr/local/share/bcbio_nextgen/gemini_data /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-freebayes.vcf.gz | sed -e 's/Number=A/Number=1/g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpSb4lAn/TestBatch1-freebayes-annotated-gemini.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpjYOd7q/TestBatch1-freebayes-annotated-gemini.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/vcfanno -p 1 -lua /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.lua -base-path /usr/local/share/bcbio_nextgen/gemini_data /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/config/vcfanno/gemini.conf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/TestBatch1-gatk-haplotype.vcf.gz | sed -e 's/Number=A/Number=1/g' | bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bcbiotx/tmpQK7Od5/TestBatch1-gatk-haplotype-annotated-gemini.vcf.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p vcf /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp_KbDkD/TestBatch1-gatk-haplotype-annotated-gemini.vcf.gz | |
| [2017-08-23T19:17Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/fastqc -d /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpAQo4ox -t 1 --extract -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpAQo4ox -f bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T19:17Z] unset DISPLAY && export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && /usr/local/bin/qualimap bamqc -bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam -outdir /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpV2ej5X/Test1 --skip-duplicated --skip-dup-mode 0 -nt 1 --java-mem-size=1G -gd HUMAN -gff /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/Test1/qualimap/cov-coverage_transcripts-bam-merged-bed6.bed | |
| [2017-08-23T19:17Z] sed -i 's/bam file = .*/bam file = Test1.bam/' /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpV2ej5X/Test1/genome_results.txt | |
| [2017-08-23T19:17Z] /usr/local/bin/samtools stats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpMQQwbN/Test1.txt | |
| [2017-08-23T19:17Z] /usr/local/bin/sambamba depth region -t 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/cov-coverage_transcripts-bam-merged.bed -F "not unmapped and not mate_is_unmapped and not secondary_alignment and not failed_quality_control and not duplicate" -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpIp6YvS/coverage_regions_depth.bed | |
| [2017-08-23T19:17Z] /usr/local/bin/samtools stats /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpllBlBE/Test1.txt | |
| [2017-08-23T19:17Z] /usr/local/bin/sambamba view -c -t 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/cov-coverage_transcripts-bam-merged.bed -F "not unmapped and not mate_is_unmapped and not secondary_alignment and not failed_quality_control and not duplicate" > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmppxT_BO/num_not_unmapped_and_not_mate_is_unmapped_and_not_secondary_alignment_and_not_failed_quality_control_and_not_duplicate_on_coverage | |
| [2017-08-23T19:17Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/cov-coverage_transcripts-bam.bed | grep -v ^track | grep -v ^browser | grep -v ^# | iconv -c -f utf-8 -t ascii | sed 's/ //g' | /usr/local/bin/py -x 'bcbio.variation.bedutils.remove_bad(x)' | sort -V -k1,1 -k2,2n > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpRHlIkx/cov-cov-coverage_transcripts-bam.bed | |
| [2017-08-23T19:17Z] cat /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/cov-cov-coverage_transcripts-bam.bed | /usr/local/bin/bgzip -c > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpWq67BA/cov-cov-coverage_transcripts-bam.bed.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/tabix -f -p bed /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpFVwRvl/cov-cov-coverage_transcripts-bam.bed.gz | |
| [2017-08-23T19:17Z] /usr/local/bin/sambamba depth region -t 1 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam -L /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/bedprep/cov-cov-coverage_transcripts-bam.bed -T1 -T5 -T10 -T20 -T50 -T100 -T250 -T500 -T1000 -T1136 -T5000 -T10000 -T50000 -F "not unmapped and not mate_is_unmapped and not secondary_alignment and not failed_quality_control and not duplicate" | sed 's/# chrom/chrom/' > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpvohqgc/Test1_coverage.bed | |
| [2017-08-23T19:17Z] goleft indexcov --directory /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpWZhVho/Test1 -- /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T19:17Z] gunzip -c /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/Test1/coverage/indexcov/Test1-indexcov.bed.gz > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmp0O97Fo/Test1-indexcov.tsv | |
| [2017-08-23T19:17Z] /usr/local/bin/bcftools stats -s Test1 -f PASS /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/TestBatch1-effects-filter.vcf.gz > /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpri2W3b/orig_Test1_bcftools_stats.txt | |
| [2017-08-23T19:17Z] export PATH=/usr/local/share/bcbio_nextgen/anaconda/bin:$PATH && export TMPDIR=/home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest && /usr/local/bin/multiqc -f -l /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/qc/multiqc/list_files.txt -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpaFGAvl | |
| [2017-08-23T19:17Z] /usr/local/bin/samtools view -T /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -@ 1 -C -x BD -x BI -o /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpYV2DIX/Test1-sort-recal.cram /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1-sort-recal.bam | |
| [2017-08-23T19:17Z] samtools index /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/tmptest/tmpKjcy7k/Test1-sort-recal.cram |
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