Question: Using parallel with Mem
0
gravatar for always_learning
4.9 years ago by
Doha, Qatar
always_learning960 wrote:

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

bwa parallel mem • 2.9k views
ADD COMMENTlink modified 12 months ago by Korsocius100 • written 4.9 years ago by always_learning960

show us the cmd-line please.

ADD REPLYlink written 4.9 years ago by Pierre Lindenbaum117k

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

ADD REPLYlink modified 4.9 years ago by Michael Dondrup45k • written 4.9 years ago by always_learning960

but how do you invoke parallel ?

ADD REPLYlink written 4.9 years ago by Pierre Lindenbaum117k

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
ADD REPLYlink modified 3 days ago by Kevin Blighe39k • written 4.9 years ago by always_learning960
4
gravatar for Matt Shirley
4.9 years ago by
Matt Shirley8.9k
Cambridge, MA
Matt Shirley8.9k wrote:

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

ADD COMMENTlink modified 3 days ago by Kevin Blighe39k • written 4.9 years ago by Matt Shirley8.9k

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.

ADD REPLYlink written 4.3 years ago by Ron880
0
gravatar for Korsocius
12 months ago by
Korsocius100
Korsocius100 wrote:

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/ =}'
ADD COMMENTlink written 12 months ago by Korsocius100
1

ask this as a new question please.

ADD REPLYlink written 12 months ago by Pierre Lindenbaum117k

Paralle bwa mem - problem with -R argument for ID and SM

ADD REPLYlink written 12 months ago by Korsocius100
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