Matt MacManes macmanes

About 12% faster streaming sambamba view/sort than if using samtools..

Going from 50M raw pe reads to a sorted BAM file in 15 minutes is pretty sweet.

samtools 1.2

bwa index -p index bwa.Trinity.fasta

Having an issue running GeneMark, within Braker.

Versions

perl /share/braker.pl --version
braker.pl version 1.6

perl /share/gm_et_linux_64/gmes_petap/gmes_petap.pl
# -------------------
Usage:  /share/gm_et_linux_64/gmes_petap/gmes_petap.pl  [options]  --sequence [filename]

When trying to use OPERA-LG after I have successfully mapped MP library using the included preprocessing script.

/share/OPERA-LG_v2.0.2/bin/OPERA-LG Mya.genome.v1.01.fasta lib_5kb.map 5kbopera


Step 1: Setting parameters ...
Time Taken: 0.000269 seconds
Step 2: Reading contig file ...
Analyzing 1 library: lib_5kb.map

Having problems with sleuth:

base_dir <- "~/Downloads/sleuth"
sample_id <- dir(file.path(base_dir,"results"))

sample_id

 [1] "HYB_sdE3_rep1" "HYB_sdE3_rep2" "HYB_wt_rep1"   "HYB_wt_rep2"   "ORE_sdE3_rep1"

I am having an issue with running the sample data. I can run with the -l example flag and these results match the expected results, but when I run with -l eukaryota, I get an error, which is detailed below.

python3 ../BUSCO_v1.1b1.py -o euk_test -in target.fa -l eukaryota -m genome -c 10
eukaryota
*** Running tBlastN ***


Building a new DB, current time: 06/17/2015 12:07:21

	openmpi 1.10.0
	bless V1.02
	boost header should be installed - used `sudo apt-get install libboost-all-dev`

	```
	mpicxx --version
	g++ (Ubuntu 4.8.4-2ubuntu1~14.04) 4.8.4
	```

	```

	interleave-reads.py \
	/mnt/data3/macmanes/fastq.ATTACTCG_AC730GANXX_L003_001.R1.fastq.gz \
	/mnt/data3/macmanes/fastq.ATTACTCG_AC730GANXX_L003_001.R2.fastq.gz \
	\| skewer -Q 5 -t 8 -x $SCRATCH/adapters.fa - -1 \
	\| extract-paired-reads.py -p - -s /dev/null - \
	\| bwa mem -p -t 30 jelly - \
	\| samtools view -T . -F4 -bu - \
	\| samtools sort -l 0 -O bam -T tmp -@ 8 -m 22G -o jelly.500.bam -

	interleave-reads.py file.1.fq.gz file.2.fq.gz \
	\| skewer -Q 2 -t 2 -x $HOME/Trimmomatic-0.33/adapters/TruSeq3-PE.fa - -1 \
	\| normalize-by-median.py --max-memory-usage 2e9 -C 30 -o - - \
	\| trim-low-abund.py -V -M 2e9 -o - --cutoff 2 - \
	\| split-paired-reads.py --output-orphaned orph.fq -1 stream.1.fq -2 stream.2.fq -

	Core dump with BWA ( version 0.7.12-r1039 )- only. Bowtie works just fine.

	Preprocess

	perl bin/preprocess_reads.pl test_dataset/contigs.fa test_dataset/lib_2_1.fa test_dataset/lib_2_2.fa test_dataset/lib_2.map bwa
	perl bin/preprocess_reads.pl test_dataset/contigs.fa test_dataset/lib_1_1.fa test_dataset/lib_1_2.fa test_dataset/lib_1.map bwa

	Run Opera

	bin/opera test_dataset/contigs.fa test_dataset/lib_1.map,test_dataset/lib_2.map test_dataset/results

	interleave-reads.py file.1.fq.gz file.2.fq.gz \
	\| normalize-by-median.py --max-memory-usage 8e10 -C 30 -o - - \
	\| trim-low-abund.py -M 8e10 -o 2pass.fq --cutoff 2 --gzip -