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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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postprocessing of vcf file error - #3615

Open Priyankanator opened 2 years ago

Priyankanator commented 2 years ago

Hi I am running the variant calling pipeline with vardict and mutect2..After calling variants and during the annotation process I get this error - 

[2022-02-09T12:12Z] Calculating variation effects for T-ag_1, vardict
[2022-02-09T12:28Z] Annotate VCF file: T-ag_1, vardict
[2022-02-09T12:30Z] Filtering for T-ag_1, vardict
[2022-02-09T12:30Z] Prioritization for T-ag_1, vardict
[2022-02-09T12:30Z] Uncaught exception occurred

Traceback (most recent call last):
  File "/project/rdrapkinlab/WGS_bcbio/anaconda/lib/python3.7/site-packages/bcbio/provenance/do.py", line 26, in run
    _do_run(cmd, checks, log_stdout, env=env)
  File "/project/rdrapkinlab/WGS_bcbio/anaconda/lib/python3.7/site-packages/bcbio/provenance/do.py", line 106, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; /project/rdrapkinlab/WGS_bcbio/anaconda/bin/vcfanno -p 1 -lua /project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/vardict/T-ag_1-effects-annotated-annotated-gemini-combine.lua  /project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/vardict/T-ag_1-effects-annotated-annotated-gemini-combine.conf /project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/vardict/T-ag_1-effects-annotated.vcf.gz |  bgzip -c > /project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/bcbiotx/tmp4bx5xqyr/T-ag_1-effects-annotated-annotated-gemini.vcf.gz
=============================================
vcfanno version 0.3.3 [built with go1.16.5]
see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:116: found 69 sources from 7 files
vcfanno.go:157: falling back to non-bgzip
panic: runtime error: slice bounds out of range [28:27]
goroutine 5 [running]:
github.com/brentp/bix.NewCSI(0x86ff20, 0xc0001f6b00, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
    /home/brentp/go/go/pkg/mod/github.com/brentp/bix@v0.0.0-20190718140914-00aa7a7f205d/csi.go:122 +0x3a5
github.com/brentp/bix.New(0xc000026240, 0x52, 0xc005587f78, 0x1, 0x1, 0x0, 0x0, 0x0)
    /home/brentp/go/go/pkg/mod/github.com/brentp/bix@v0.0.0-20190718140914-00aa7a7f205d/bix.go:124 +0x12bf
github.com/brentp/vcfanno/api.(*Annotator).Setup.func1(0xc0001b5810, 0x7, 0x7, 0xc0027c10f0, 0x1, 0xc000026240, 0x52)
    /home/brentp/src/vcfanno/api/api.go:792 +0x231
created by github.com/brentp/vcfanno/api.(*Annotator).Setup
    /home/brentp/src/vcfanno/api/api.go:783 +0x170
' returned non-zero exit status 2.

What could be the reason ? I am running this on HPC cluster..

Thanks

naumenko-sa commented 2 years ago

Hi @Priyankanator !

What is your project yaml file? What kind of annotations were applied?

Sergey

Priyankanator commented 2 years ago

Hi Sergey, Here is the project yaml file - details:

I used the variant2 pipeline and I think it is getting stuck while annotating with vcfanno..

Thanks Priyanka

naumenko-sa commented 2 years ago

Hi @Priyankanator !

Thanks for providing more details!

We need to dig into this command:

/project/rdrapkinlab/WGS_bcbio/anaconda/bin/vcfanno \
-p 1 \
-lua /project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/vardict/T-ag_1-effects-annotated-annotated-gemini-combine.lua  \
/project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/vardict/T-ag_1-effects-annotated-annotated-gemini-combine.conf \
/project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/vardict/T-ag_1-effects-annotated.vcf.gz |  bgzip -c > \
T-ag_1-effects-annotated-annotated-gemini.vcf.gz

Could you please try running it outside of bcbio, and provide your combine.lua and combine.conf?

Sergey

Priyankanator commented 2 years ago

Hi Sergey, I ran the command and get the same results-

(base) [prawat@consign rdrapkinlab]$ /project/rdrapkinlab/WGS_bcbio/anaconda/bin/vcfanno \
> -p 1 \
> -lua /project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/vardict/T-ag_1-effects-annotated-annotated-gemini-combine.lua  \
> /project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/vardict/T-ag_1-effects-annotated-annotated-gemini-combine.conf \
> /project/rdrapkinlab/WGS_bcbio/config/FT_cell/work/vardict/T-ag_1-effects-annotated.vcf.gz |  bgzip -c > \
> T-ag_1-effects-annotated-annotated-gemini.vcf.gz

=============================================
vcfanno version 0.3.3 [built with go1.16.5]

see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:116: found 69 sources from 7 files
vcfanno.go:157: falling back to non-bgzip
panic: runtime error: slice bounds out of range [28:27]

goroutine 8 [running]:
github.com/brentp/bix.NewCSI(0x86ff20, 0xc0000ecb00, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, ...)
    /home/brentp/go/go/pkg/mod/github.com/brentp/bix@v0.0.0-20190718140914-00aa7a7f205d/csi.go:122 +0x3a5
github.com/brentp/bix.New(0xc0000222a0, 0x52, 0xc003345f78, 0x1, 0x1, 0x0, 0x0, 0x0)
    /home/brentp/go/go/pkg/mod/github.com/brentp/bix@v0.0.0-20190718140914-00aa7a7f205d/bix.go:124 +0x12bf
github.com/brentp/vcfanno/api.(*Annotator).Setup.func1(0xc0057ec8c0, 0x7, 0x7, 0xc003114ac0, 0x1, 0xc0000222a0, 0x52)
    /home/brentp/src/vcfanno/api/api.go:792 +0x231
created by github.com/brentp/vcfanno/api.(*Annotator).Setup
/home/brentp/src/vcfanno/api/api.go:783 +0x170

T-ag_1-effects-annotated-annotated-gemini-combine_conf.txt T-ag_1-effects-annotated-annotated-gemini-combine_lua.txt

I have attached the lua and conf file as in txt format.

Thanks Priyanka

naumenko-sa commented 2 years ago

Hi @Priyankanator !

My run finishes ok with a similar config and hg19 reference. Not sure, why do you have gemini annotations is in your vcfanno? gemini is not specified in the yaml. Are you providing the complete yaml?

If you want to use gemini annotations, you need to install gemini files: bcbio_nextgen.py upgrade -u skip --genomes hg19 --datatarget gemini By default gemini annotations are off, to turn on: tools_on: gemini.

Sergey

Priyankanator commented 2 years ago

Hi Sergey, I have provided complete yaml file. I was also not sure that why I have gemini annotations. I did also tried with tools on option and installed gemini files but still it is giving me the same error. Do you think it is vcfanno specific error as described in this page- https://github.com/brentp/vcfanno/issues/64

Thanks Priyanka

naumenko-sa commented 2 years ago

No, I think it is not related. Could you please try to install gemini as outlined above?