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I ran shorah.py in my data and got the following error. I also got a bunch of empty .fas files as my output. How can I resolve this issue? Thanks.
wld28@william:~/SG1/2$ python ~/shorah_0.8/shora…
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This is the command I extracted from error messages. When reruning the command manually with samtools 0.1.19, it gave "floating point exception" error.
``` python
/usr/local/bin/samtools mpileup\
…
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Calls to `gmt analysis coverage bam-readcount` fail because this module has this hard coding in it:
``` perl
my $cmd = "java -jar /gsc/scripts/lib/java/VarScan/VarScan.v2.2.9.jar readcounts $tempdir/…
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Hi Brad/Rory/John,
I've been trying out bcbio_vm on AWS (tumor/normal calling on a couple BAMs from s3 bucket). I was able to set up and start a cluster, and ssh into the head-node to start the run. …
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I am trying to use bcbio to do somatic variants calling with either Mutect or FreeBayes, but I am not sure how performance they are between Mutect and FreeBayes. For example, how long Mutect and FreeB…
ghost updated
10 years ago
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Unlike MuTect or other software, VarScan (when doing somatic mutation calling) adds a `SS` (Somatic Status) field to the VCFs it produces, using this code:
- 0 - reference
- 1 - germline
- 2 - somatic…
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Master from a couple of days ago.
Traceback:
``` python
Traceback (most recent call last):
File "/usr/local/bin/bcbio_nextgen.py", line 8, in
execfile(__file__)
File "/mnt/data/software/bc…
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Hi Brad,
I run bcbio-nextgen with -n 32 for gatk variant template. However, I see that the system consistently runs on only 2 CPUs !! Is it a bug or it's something that I don't understand.
Thanks,
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While the GATK is quite useful for analysis and recalibration, at least in some occasions in the pipeline (for example VarScan 2 paired calling) it is called repeatedly just to join the SNPs and indel…
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The clonality analysis step within ClinSeq fails on Obi's box with this error,
2014-01-21 23:27:27-0600 GGM: ERROR RUNNING COMMAND. Exit code 1 from: R --vanilla --slave < /opt/gms/AUIS907/fs/AUIS9…