search

gkno / gkno_launcher

The gkno launcher for executing tools or pipelines
MIT License
32 stars 7 forks source link

Failed task argument parsing #6

Closed CarlosBorroto closed 11 years ago

CarlosBorroto commented 11 years ago

I'm unable to specify individual task arguments when running a pipeline. Like in a similar docs example, I tried adding this argument to fastq-vcf-se pipeline:

--variant-call "--use-best-n-alleles 5"

I get this error:

Assigning command line arguments to tasks...done.
Checking the command line arguments...

ERROR:   Missing value for argument: --use-best-n-alleles (-n)

DETAILS: The argument '--use-best-n-alleles' was specified for task 'variant-call' and it
         expects a value of type 'integer', but no value was provided.  Please check the command
         line.

================================================================================================
  TERMINATED: Errors found in running gkno.  See specific error messages above for resolution.
================================================================================================

Best, Carlos

AlistairNWard commented 11 years ago

Hi Carlos,

I think that this may be a problem that has recently been fixed. The quotation marks on the command line are processed by your bash shell and not by GKNO. I modified the syntax to avoid this problem. If you do a git pull to get GKNO up to date, and then modify your command line to:

--variant-call [--use-best-n-alleles 5]

Please let me know if this works now. I only come across some of these issues by getting on different LINUX boxes, so some things creep through unnoticed!

Al

On Mon, Jun 3, 2013 at 1:57 PM, Carlos Borroto notifications@github.comwrote:

I'm unable to specify individual task arguments when running a pipeline. Like in a similar docs example, I tried adding this argument to fastq-vcf-se pipeline:

--variant-call "--use-best-n-alleles 5"

I get this error:

Assigning command line arguments to tasks...done. Checking the command line arguments...

ERROR: Missing value for argument: --use-best-n-alleles (-n)

DETAILS: The argument '--use-best-n-alleles' was specified for task 'variant-call' and it expects a value of type 'integer', but no value was provided. Please check the command line.

TERMINATED: Errors found in running gkno. See specific error messages above for resolution.

Best, Carlos

— Reply to this email directly or view it on GitHubhttps://github.com/gkno/gkno_launcher/issues/6 .

CarlosBorroto commented 11 years ago

Hi,

I just saw the recent commits where I see there was some work done on the parsing code. I can confirm after updating and switching to using [] the issue goes way.

Thanks, Carlos

AlistairNWard commented 11 years ago

Good. Glad that worked. I'm just putting a new pipeline together now that doesn't include Freebayes. Is this the only modification that you require to this pipeline?

Also, we are likely to be updating the MOSAIK alignment software very soon to be much quicker than the current version, so please keep your eyes on our blog/Twitter feed for an update soon.

Al

On Mon, Jun 3, 2013 at 2:30 PM, Carlos Borroto notifications@github.comwrote:

Hi,

I just saw the recent commits where I see there was some work done on the parsing code. I can confirm after updating and switching to using [] the issue goes way.

Thanks, Carlos

— Reply to this email directly or view it on GitHubhttps://github.com/gkno/gkno_launcher/issues/6#issuecomment-18861057 .

CarlosBorroto commented 11 years ago

Well the actual change I needed was:

--variant-call [--min-alternate-fraction 0.01]

I had to add this argument to freebayes' JSON config file. We are interested in very low frequency variants in amplicon projects with up to 10000x coverage. BTW freebayes' QUAL for these calls is extremely low. Is there anything I could do? It is not surprising freebayes is not well tuned for this corner case, but I wonder if there is something I could do. For example for this call:

g       162     .       C       A       1.6355e-12      .       AB=0.0625663;ABP=14108.7;AC=1;AF=0.5;AN=2;AO=531;CIGAR=1X;DP=8487;DPRA=0;E
PP=49.8299;EPPR=653.236;GTI=0;HWE=-0;LEN=1;MEANALT=5;MQM=23.0471;MQMR=20.2489;NS=1;NUMALT=1;ODDS=3910.62;PAIRED=0;PAIREDR=0;RO=7951;RPP=1147.39;RP
PR=17129.7;RUN=1;SAP=51.5965;SRP=646.511;TYPE=snp;XAI=0.00862855;XAM=0.00996702;XAS=0.00133847;XRI=0.00875397;XRM=0.00950692;XRS=0.000752952;techn
ology.454=1     GT:DP:RO:QR:AO:QA:GL    0/1:8487:7951:314654:531:20636:-1870.14,-1705.63,-28331.8

I'll keep an eye open for the new pipeline and MOSAIK's improvements.

Thanks, Carlos