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Using parallel with Mem

Hi All.

We are trying to us MEM with GNU parallel with paired fastQ files, but its saying that can't accept more then one file. What could be the possible reasons? What if we concatante both file as single one and then use that with mem? Does Mem command support multi threading too ?

Thanks

Syed

mem parallel bwa
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updated by Ram Ram • written by always_learning always_learning

this exact commant we are using:

${bwa} mem -t 8 -R \\"@RG\\tID:${ursId}_pairend\\tSM:${sampleName}\\tLB:${libraryId}\\tPL:${platform}\\" ${refGenomeFastaFile} \${seqReadsDir}/${ursId}_pairend1.fastq.gz ${seqReadsDir}/${ursId}_pairend2.fastq.gz

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updated by Michael Dondrup Michael Dondrup • written by always_learning always_learning

Sorry as I didn't able to post complete command. Here it goes as we are trying to convert SAM files to BAM files at same time only

${bwa} mem -t 8 -R "@RG\\tID:${ursId}_pairend\\tSM:${sampleName}\\tLB:${libraryId}\\tPL:${platform}" ${refGenomeFastaFile} \
${seqReadsDir}/${ursId}_pairend1.fastq.gz ${seqReadsDir}/${ursId}_pairend2.fastq.gz | ${samtools} view -bhS - > ${bamDir}/${ursId}.bam" > \
${seqReadsDir}/${ursId}_pairend.txt; parallel -a ${seqReadsDir}/${ursId}_pairend.txt&#39
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updated by Kevin Blighe Kevin Blighe • written by always_learning always_learning

2 answers

This command is telling bwa mem to use 8 threads (`-t`) so you will have some level of parallelism. Your command above does not invoke GNU parallel, and to do so you would use something like:

parallel bwa mem -t 8 -R "@RG\t@ID:blahblahblah" reference.fasta {1} {2} > {1.}.sam ::: *R1.fastq.gz ::: *R2.fastq.gz

See here: https://www.gnu.org/software/parallel/man.html#example__use_multiple_inputs_in_one_command and here: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them

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updated by Kevin Blighe Kevin Blighe • written by Matt Shirley Matt Shirley

Hi Matt,

I am using gnu parallel as explained by you for cufflinks.Here is my post.

Cufflinks output with filename prefix

I want to add the prefix to my cufflink output files using filenames from bam samples.

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written by Ron Ron

There is snytax for parallel with bwa mem, but I can't load ID and SM from INPUT. Do you know, where could be a problem? 

ls *R1_001.fastq | parallel 'bwa mem -k 19 -A 1 -B 4 -O 6 -L 5 -R '@RG\tID:'{.}'\tSM:'{.}'\tLB:'Trusight_custom_amplicon_CARR'\tPL:'ILLUMINA'\tPI:150' $REFERENCE {} {= s/_R1_001/_R2_001/ =} > {= s/_R1_001.fastq/.sam/ =}'
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written by Korsocius Korsocius

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