nfcorernaseq05102020

130 dnanexus@job-Fpqyjj0014vg89F98195yqxP:~/RNA-Seq⟫ sudo ~/nextflow run nf-core/rnaseq -profile docker --aligner hisat2 -r 1.4.2 --pseudo_aligner salmon --reads 'data/*_{1,2}.fastq' --reverseStranded --fasta Homo_sapiens.GRCh38.dna_sm.primary_assembly_withBKV.fa.gz --gtf Homo_sapiens.GRCh38.90_withBKV.gtf.gz --max_memory 30GB
N E X T F L O W  ~  version 20.04.1
Launching `nf-core/rnaseq` [sick_hamilton] - revision: 3b6df9bd10 [1.4.2]
Extracting transcript fastas from genome fasta + gtf/gff
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  nf-core/rnaseq v1.4.2
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Pipeline Release  : 1.4.2
Run Name          : sick_hamilton
Reads             : data/*_{1,2}.fastq
Data Type         : Paired-End
Strandedness      : Reverse
Trimming          : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0 / NextSeq Trim: 0
Aligner           : HISAT2
Fasta Ref         : Homo_sapiens.GRCh38.dna_sm.primary_assembly_withBKV.fa.gz
Pseudo Aligner    : Salmon
GTF Annotation    : Homo_sapiens.GRCh38.90_withBKV.gtf.gz
Remove Ribosomal RNA: false
Biotype GTF field : gene_biotype
Save prefs        : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No
Max Resources     : 30GB memory, 16 cpus, 10d time per job
Container         : docker - nfcore/rnaseq:1.4.2
Output dir        : ./results
Launch dir        : /home/dnanexus/RNA-Seq
Working dir       : /home/dnanexus/RNA-Seq/work
Script dir        : /home/dnanexus/.nextflow/assets/nf-core/rnaseq
User              : root
Config Profile    : docker
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executor >  local (14)
executor >  local (26)
[2f/76d739] process > get_software_versions                                                           [100%] 1 of 1 ✔
[58/faf0d6] process > gunzip_genome_fasta (Homo_sapiens.GRCh38.dna_sm.primary_assembly_withBKV.fa.gz) [100%] 1 of 1 ✔
[81/3a5d26] process > gunzip_gtf (Homo_sapiens.GRCh38.90_withBKV.gtf.gz)                              [100%] 1 of 1 ✔
[e9/3454e8] process > makeBED12 (Homo_sapiens.GRCh38.90_withBKV.gtf)                                  [100%] 1 of 1 ✔
[96/13b911] process > makeHisatSplicesites (Homo_sapiens.GRCh38.90_withBKV.gtf)                       [100%] 1 of 1 ✔
[d8/8e9560] process > makeHISATindex (Homo_sapiens.GRCh38.dna_sm.primary_assembly_withBKV.fa)         [100%] 1 of 1 ✔
[64/4a1d86] process > transcriptsToFasta (Homo_sapiens.GRCh38.dna_sm.primary_assembly_withBKV.fa)     [100%] 1 of 1 ✔
[25/e38971] process > makeSalmonIndex (transcripts.fa)                                                [100%] 1 of 1 ✔
[a5/bcc2b0] process > fastqc (SRR11074360)                                                            [100%] 1 of 1 ✔
[de/96df9c] process > trim_galore (SRR11074360)                                                       [100%] 1 of 1 ✔
[9e/d55d91] process > hisat2Align (SRR11074360)                                                       [100%] 1 of 1 ✔
[ac/469112] process > hisat2_sortOutput (SRR11074360_1)                                               [100%] 1 of 1 ✔
[de/e027c0] process > rseqc (SRR11074360_1)                                                           [100%] 1 of 1 ✔
[08/dab211] process > preseq (SRR11074360_1)                                                          [100%] 1 of 1 ✔
[08/db7525] process > markDuplicates (SRR11074360_1)                                                  [100%] 1 of 1 ✔
[f8/7cb2a9] process > qualimap (SRR11074360_1.sorted)                                                 [100%] 1 of 1 ✔
[61/2cebce] process > dupradar (SRR11074360_1)                                                        [100%] 1 of 1 ✔
[b2/96513e] process > featureCounts (SRR11074360_1)                                                   [100%] 1 of 1 ✔
[68/4bb669] process > merge_featureCounts (SRR11074360_1_gene.featureCounts)                          [100%] 1 of 1 ✔
[d2/f6d397] process > stringtieFPKM (SRR11074360_1)                                                   [100%] 1 of 1 ✔
[-        ] process > sample_correlation                                                              -
[ee/416d88] process > salmon (SRR11074360)                                                            [100%] 1 of 1 ✔
[10/448259] process > salmon_tx2gene (1)                                                              [100%] 1 of 1 ✔
[14/e6a8de] process > salmon_tximport (1)                                                             [100%] 1 of 1 ✔
[bb/95d17b] process > salmon_merge (1)                                                                [100%] 1 of 1 ✔
[b1/e06f09] process > multiqc                                                                         [100%] 1 of 1 ✔
[dc/5eedd5] process > output_documentation                                                            [100%] 1 of 1 ✔
[0;35m[nf-core/rnaseq] Pipeline completed successfully
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Completed at: 10-May-2020 17:25:10
Duration    : 5h 13m 42s
CPU hours   : 27.4
Succeeded   : 26