Question

how to run freebayes in multi-thread

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5.7 years ago

marongiu.luigi ▴ 710

Dear all, I would like to run freebayes as a multi-thread application. I followed the script given as an example

freebayes-parallel < fasta_generate_regions.py ref.fa.fai 100000) 36 -f ref.fa aln.bam > out.vcf"

by writing a command:

pathTo/freebayes/scripts/frebayes-parallel <(pathTo/freebayes/scripts/fasta_generate_regions.py pathTo/ref< File >.fa.fai) 36 -f pathTo/< refFile >.fa pathTo/<alnDeduplicated>.bam > < file.vcf >

but I am getting this error:

$   File "pathTo/freebayes/scripts/fasta_generate_regions.py", line 7
    print "usage: ", sys.argv[0], " <fasta file or index file> <region size>"
                  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("usage: ", sys.argv[0], " <fasta file or index file> <region size>")?

Same thing if I use <fasta_generate_regions.py pathTo="" ref<File="">.fa.fai). frebayes-parallel is in the PATH variable but if I don't give the absolute path I get the error command not found

What would be the correct syntax for this feature?

Tx

VCF freebayes multi-thread • 8.2k views

ADD COMMENT • link updated 4 weeks ago by GenoMax 146k • written 5.7 years ago by marongiu.luigi ▴ 710

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Are you running with python 2 or 3?

ADD REPLY • link 5.7 years ago by Joe 21k

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I think the standard is Python 3.7.0 because this is what comes out if I type python on the terminal

ADD REPLY • link 5.7 years ago by marongiu.luigi ▴ 710

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Yep that makes sense. You will need to run that tool with Python2 specifically.

In python3, print commands require parentheses: print("Some string"), whereas in Python2 this wasn't strictly the case.

You can tell this from the error it gives you since it's showing you an ^ pointing (roughly) to where it was expecting to see ()

You may need to take a look at the shebang in the first line of the python script athTo/freebayes/scripts/fasta_generate_regions.py. It probably isn't specifying python2 (which it should really).

ADD REPLY • link 5.7 years ago by Joe 21k

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I ran: $ ~/src/freebayes/scripts/frebayes-parallel <(python2 ~/src/freebayes/scripts/fasta_generate_regions.py ~/refSeq/fusion/fusion38-10k.fa.fai) 36 -f ~/refSeq/fusion/fusion38-10k.fa ~/servers/chirexpsrv3_a32/LUIGI_HIPO32_nls/rslt/A1/A1-N_F-AlnSrtDed.bam > ~/Downloads/h32/rslt/A1-N_F.vcf ang got: bash: /home/gigiux/src/freebayes/scripts/frebayes-parallel: No such file or directory $ Traceback (most recent call last): File "/home/gigiux/src/freebayes/scripts/fasta_generate_regions.py", line 17, in <module> region_size = int(sys.argv[2]) IndexError: list index out of range

ADD REPLY • link 5.7 years ago by marongiu.luigi ▴ 710

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same thing when i changed the shebang to #!/usr/bin/env python2

ADD REPLY • link 5.7 years ago by marongiu.luigi ▴ 710

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I would have expected changing the shebang to work, but there may be other elements of the code that also need to change. I'll need to take a closer look. Can you provide a link to the walkthrough you're using, and some example data so we can replicate the issue?

ADD REPLY • link 5.7 years ago by Joe 21k

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marongiu.luigi are you doing the following?

Note that any of the above examples can be made parallel by using the scripts/freebayes-parallel script. If you find freebayes to be slow, you should probably be running it in parallel using this script to run on a single host, or generating a series of scripts, one per region, and run them on a cluster. Be aware that the freebayes-parallel script contains calls to other programs using relative paths from the scripts subdirectory; the easiest way to ensure a successful run is to invoke the freebayes-parallel script from within the scripts subdirectory.

ADD REPLY • link 5.7 years ago by GenoMax 146k

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I thought I did it by launching freebayes-parallel with its absolute path...

ADD REPLY • link 5.7 years ago by marongiu.luigi ▴ 710

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I will, but it might take sometimes...

ADD REPLY • link 5.7 years ago by marongiu.luigi ▴ 710

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how to add thread in freebayes?

ADD REPLY • link 4 weeks ago by skdv2522 • 0

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You have to use freebayes-parallel to execute multiple instances. It is otherwise a single threaded application.

ADD REPLY • link 4 weeks ago by GenoMax 146k

score 4 · Answer 1 · 2019-02-18

As mentioned by jrj.healey fasta_generate_regions.py must be run with python2
fasta_generate_regions.py requires two parameters:
- the reference file or its index file
- the size of the region

You are missing the size of the region in your command.

The error message you describe in this comment stated out whats wrong:

bash: /home/gigiux/src/freebayes/scripts/frebayes-parallel: No such file or directory

You are missing in e in freebayes-parallel.

(There is already a pull request to make the python scripts work in python2 and 3)