Issue with vcfanno

Moiz Bootwalla

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Jul 3, 2018, 5:59:19 PM7/3/18

to biovalidation

Hello bcbio team,

I am trying to run a workflow through bcbio and it keeps stalling at the vcfanno part. I have been trying to figure out what the issue might be and it seems like a combination of couple of things. Before I list what I found here's the error log from bcbio:

Traceback (most recent call last):

File "/shared/software/bcbio_nextgen/1.0.9/bin/bcbio_nextgen.py", line 241, in <module>

main(**kwargs)

File "/shared/software/bcbio_nextgen/1.0.9/bin/bcbio_nextgen.py", line 46, in main

run_main(**kwargs)

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 53, in run_main

fc_dir, run_info_yaml)

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 89, in _run_toplevel

for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 164, in variant2pipeline

samples = run_parallel("postprocess_variants", samples)

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipython.py", line 137, in run

for data in view.map_sync(fn, items, track=False):

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/ipyparallel/client/view.py", line 344, in map_sync

return self.map(f,*sequences,**kwargs)

File "<decorator-gen-137>", line 2, in map

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/ipyparallel/client/view.py", line 52, in sync_results

ret = f(self, *args, **kwargs)

File "<decorator-gen-136>", line 2, in map

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/ipyparallel/client/view.py", line 37, in save_ids

ret = f(self, *args, **kwargs)

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/ipyparallel/client/view.py", line 1114, in map

return pf.map(*sequences)

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/ipyparallel/client/remotefunction.py", line 299, in map

return self(*sequences, __ipp_mapping=True)

File "<decorator-gen-119>", line 2, in __call__

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/ipyparallel/client/remotefunction.py", line 80, in sync_view_results

return f(self, *args, **kwargs)

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/ipyparallel/client/remotefunction.py", line 285, in __call__

return r.get()

File "/gpfs/fs1/data/bcbio_data_1.0.9/anaconda/lib/python2.7/site-packages/ipyparallel/client/asyncresult.py", line 169, in get

raise self.exception()

ipyparallel.error.CompositeError: one or more exceptions from call to method: postprocess_variants

[9:apply]: CalledProcessError: Command 'set -o pipefail; /gpfs/fs1/data/bcbio_data_1.0.9/anaconda/bin/vcfanno -p 16 -lua /gpfs/fs1/data/bcbio_data_1.0.9/genomes/Hsapiens/hs37d5/config/vcfanno/gemini.lua -base-path /gpfs/fs1/data/bcbio_data_1.0.9/genomes/Hsapiens/hs37d5 /gpfs/fs1/data/bcbio_data_1.0.9/genomes/Hsapiens/hs37d5/config/vcfanno/gemini.conf /gpfs/fs1/SES/Validation_HiSeq/180410_K00187_0035_AHMFM3BBXX/bcbio_20180410/work/mutect2/CPM00004824-F-D_20171030-annotated.vcf.gz | bgzip -c > /gpfs/fs1/SES/Validation_HiSeq/180410_K00187_0035_AHMFM3BBXX/bcbio_20180410/work/bcbiotx/tmp_jeUXd/CPM00004824-F-D_20171030-annotated-annotated-gemini.vcf.gz

=============================================

vcfanno version 0.2.8 [built with go1.8]

see: https://github.com/brentp/vcfanno

=============================================

vcfanno.go:112: [Flatten] unable to open file: /gpfs/fs1/data/bcbio_data_1.0.9/genomes/Hsapiens/hs37d5//gpfs/fs1/data/bcbio_data_1.0.9/genomes/Hsapiens/hs37d5/ExAC.r0.3.sites.vep.tidy.vcf.gz in /gpfs/fs1/data/bcbio_data_1.0.9/genomes/Hsapiens/hs37d5

' returned non-zero exit status 1

It looks like vcfanno is looking for annotation files under the genomes/Hsapiens/GENOME directory but all these annotation files are under bcbio_data_1.0.9/gemini_data directory. Can you kindly help me fix this error?

Thanks,

Moiz

Brad Chapman

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Jul 4, 2018, 11:25:06 AM7/4/18

to Moiz Bootwalla, biovalidation

Moiz;
Thanks for the detailed report and apologies about the issue. It looks like
you're using a custom installed human build 37 genome (hs37d5) and bcbio isn't
correctly detecting it's build 37 to insert the location of the gemini data.
GEMINI in hg19/GRCh37 gets treated specially, while in hg38 it's more a
standard part of the integration.

I've pushed a fix that I hope will resolve this expanding the current checks
(which just look for genome names) to also include looking for any of the hg19
or GRCh37 specific GL contigs within the reference.

If you update to the latest development (`bcbio_nextgen.py upgrade -u
development`) and re-run I hope this will correctly insert the gemini_data
directory as part of the vcfanno run.

Thanks again,
Brad

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Moiz Bootwalla

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Jul 6, 2018, 5:14:24 PM7/6/18

to Brad Chapman, biovalidation

Hi Brad,

Thank you for providing the fix so quickly. I restarted my job and it looks like the fix is working. The job is still running. I will report back if it runs into any further errors.

Best Regards,

Moiz

Moiz Bootwalla

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Jul 9, 2018, 2:49:48 PM7/9/18

to biovalidation

Hi Brad,

Following up on this. The fix you implemented worked great. The annotation and prioritization steps worked perfectly and I was able to get the final output as well. I was going through the logs and I kept seeing the following error/warning from vcfanno over and over again and am trying to figure out what this means. I'm pasting the output below:

[2018-07-06T21:04Z] chla-cpm-cn11.chla-cpm.cluster: vcfanno.go:115: found 49 sources from 17 files

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: =============================================

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: vcfanno version 0.2.8 [built with go1.8]

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: see: https://github.com/brentp/vcfanno

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: =============================================

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: vcfanno.go:115: found 49 sources from 17 files

[2018-07-06T21:04Z] chla-cpm-cn05.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn02.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn01.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn10.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn07.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn05.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn11.chla-cpm.cluster: vcfanno.go:187: Info Error: max_aaf_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn11.chla-cpm.cluster: vcfanno.go:187: Info Error: clinvar_sig not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn03.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn03.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn10.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn01.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn05.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn12.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn06.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn06.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn07.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: vcfanno.go:187: Info Error: clinvar_sig not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: vcfanno.go:187: Info Error: max_aaf_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn11.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn11.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: vcfanno.go:187: Info Error: af_esp_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn02.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn12.chla-cpm.cluster: vcfanno.go:187: Info Error: af_1kg_all not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn10.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn03.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn07.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn02.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn12.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn06.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn09.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn11.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

[2018-07-06T21:04Z] chla-cpm-cn01.chla-cpm.cluster: vcfanno.go:187: Info Error: af_adj_exac_sas not found in INFO >> this error/warning may occur many times. reporting once here...

Any idea as to what this error/warning means?

Thanks,

Moiz

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Brad Chapman

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Jul 9, 2018, 4:34:36 PM7/9/18

to Moiz Bootwalla, biovalidation

Moiz;
Glad to hear it worked for you. Sorry for any confusion with the warnings.
Those are expected warnings for positions where a variant does not overlap
with ESP, 1000 genomes or other resources. There is a post annotation,
`max_aaf_all` that looks for all these and reports the maximum. This is useful
as a general metric, but unfortunately makes vcfanno noisy. So, nothing to
worry about here and sorry about the noise,
Brad

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Moiz Bootwalla

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Jul 9, 2018, 4:35:31 PM7/9/18

to Brad Chapman, biovalidation

That is perfect.

Thank You,

Moiz

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