Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

svc issue #1561

Closed
lsturm1 opened this issue Sep 17, 2016 · 8 comments
Closed

svc issue #1561

lsturm1 opened this issue Sep 17, 2016 · 8 comments

Comments

@lsturm1
Copy link

lsturm1 commented Sep 17, 2016

Hi,

I am trying to use svc on a cohort of samples. When I run it I get the following error message... does this mean I need to update something or is there some other fix? Thank you

Traceback (most recent call last):
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 50, in _setup
_logging
yield config
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py", line 362, in detec
t_sv
return ipython.zip_args(apply(structural.detect_sv, *args))
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/init.py", line 144, in detect_sv
for svdata in caller_fn(items):
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 29, in run
return _cnvkit_by_type(items, background)
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 43, in _cnvkit_by_ty
pe
return _run_cnvkit_population(items, background)
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 113, in run_cnvkit
population
out.extend(_associate_cnvkit_out(ckouts, [cur_input]))
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 57, in _associate_cn
vkit_out
ckout = _add_variantcalls_to_output(ckout, data, is_somatic)
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/cnvkit.py", line 404, in _add_variant
calls_to_output
effects_vcf, _ = effects.add_to_vcf(calls["vcf"], data, "snpeff")
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/effects.py", line 30, in add_to_vcf
ann_vrn_file, stats_file = snpeff_effects(in_file, data)
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/effects.py", line 216, in snpeff_effec
ts
return _run_snpeff(vcf_in, "vcf", data)
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/effects.py", line 304, in _run_snpeff
do.run(cmd.format(**locals()), "snpEff effects", data)
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; export PATH=/share/PI/euan/apps/bcbio/anaconda/bin:$PATH && /share/PI/euan/app
s/bcbio/anaconda/bin/snpEff -Xms4g -Xmx10g -Djava.io.tmpdir=/local-scratch/lsturm/9838413/bcbiotx/79ba2811-1ba3-4039-9513-a54
6d7ac9b5b/tmpHX7S0A/tmp eff -dataDir /share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/snpeff -noHgvs -noLog -i vcf -o vcf -s
/scratch/PI/euan/projects/elite/bcbio/projects/project_n268_svc_v1/work/structural/01_02/cnvkit/raw/01_02-dedup-call-effects
-stats.html GRCh37.75 /scratch/PI/euan/projects/elite/bcbio/projects/project_n268_svc_v1/work/structural/01_02/cnvkit/raw/01
02-dedup-call.vcf > /local-scratch/lsturm/9838413/bcbiotx/79ba2811-1ba3-4039-9513-a546d7ac9b5b/tmpHX7S0A/01_02-dedup-call-ef
fects.vcf
java.lang.RuntimeException: Database file '/share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/snpeff/GRCh37.75/snpEffectPredic
tor.bin' is not compatible with this program version:
Database version : '4.2'
Program version : '4.3'
Try installing the appropriate database.
at org.snpeff.serializer.MarkerSerializer.load(MarkerSerializer.java:158)
at org.snpeff.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:66)
at org.snpeff.snpEffect.Config.loadSnpEffectPredictor(Config.java:555)
at org.snpeff.SnpEff.loadDb(SnpEff.java:360)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:964)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:947)
at org.snpeff.SnpEff.run(SnpEff.java:1009)
at org.snpeff.SnpEff.main(SnpEff.java:155)
' returned non-zero exit status 255
[2016-09-16T20:38Z] sh-7-30.local: snpEff effects : 01_02
[2016-09-16T20:38Z] sh-7-30.local: java.lang.RuntimeException: Database file '/share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh
37/snpeff/GRCh37.75/snpEffectPredictor.bin' is not compatible with this program version:
[2016-09-16T20:38Z] sh-7-30.local: Database version : '4.2'
[2016-09-16T20:38Z] sh-7-30.local: Program version : '4.3'
[2016-09-16T20:38Z] sh-7-30.local: Try installing the appropriate database.
[2016-09-16T20:38Z] sh-7-30.local: at org.snpeff.serializer.MarkerSerializer.load(MarkerSerializer.java:158)
[2016-09-16T20:38Z] sh-7-30.local: at org.snpeff.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:66)
[2016-09-16T20:38Z] sh-7-30.local: at org.snpeff.snpEffect.Config.loadSnpEffectPredictor(Config.java:555)
[2016-09-16T20:38Z] sh-7-30.local: at org.snpeff.SnpEff.loadDb(SnpEff.java:360)
[2016-09-16T20:38Z] sh-7-30.local: at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:964)
[2016-09-16T20:38Z] sh-7-30.local: at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:947)
[2016-09-16T20:38Z] sh-7-30.local: at org.snpeff.SnpEff.run(SnpEff.java:1009)
[2016-09-16T20:38Z] sh-7-30.local: at org.snpeff.SnpEff.main(SnpEff.java:155)
[2016-09-16T20:38Z] sh-7-30.local: Uncaught exception occurred
Traceback (most recent call last):
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/share/PI/euan/apps/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; export PATH=/share/PI/euan/apps/bcbio/anaconda/bin:$PATH && /share/PI/euan/app
s/bcbio/anaconda/bin/snpEff -Xms4g -Xmx10g -Djava.io.tmpdir=/local-scratch/lsturm/9838408/bcbiotx/3d0ab058-bceb-4b2c-8f2d-81d
dc2622868/tmpAUqOOG/tmp eff -dataDir /share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/snpeff -noHgvs -noLog -i vcf -o vcf -s
/scratch/PI/euan/projects/elite/bcbio/projects/project_n268_svc_v1/work/structural/01_02/cnvkit/raw/01_02-dedup-call-effects
-stats.html GRCh37.75 /scratch/PI/euan/projects/elite/bcbio/projects/project_n268_svc_v1/work/structural/01_02/cnvkit/raw/01
02-dedup-call.vcf > /local-scratch/lsturm/9838408/bcbiotx/3d0ab058-bceb-4b2c-8f2d-81ddc2622868/tmpAUqOOG/01_02-dedup-call-ef
fects.vcf
java.lang.RuntimeException: Database file '/share/PI/euan/apps/bcbio/genomes/Hsapiens/GRCh37/snpeff/GRCh37.75/snpEffectPredic
tor.bin' is not compatible with this program version:
Database version : '4.2'
Program version : '4.3'
Try installing the appropriate database.
at org.snpeff.serializer.MarkerSerializer.load(MarkerSerializer.java:158)
at org.snpeff.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:66)
at org.snpeff.snpEffect.Config.loadSnpEffectPredictor(Config.java:555)
at org.snpeff.SnpEff.loadDb(SnpEff.java:360)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:964)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:947)
at org.snpeff.SnpEff.run(SnpEff.java:1009)
at org.snpeff.SnpEff.main(SnpEff.java:155)
' returned non-zero exit status 255
@chapmanb
Copy link
Member

Thanks for the report, it looks like you updated snpEff to version 4.3 but not the databases. You can do this with:

bcbio_nextgen.py upgrade --data

Hope this helps, feel free to re-open this issue if you run into other problems.

@lsturm1
Copy link
Author

lsturm1 commented Sep 24, 2016

Hi Brad,

I successfully updated using bcbio_nextgen.py upgrade --data. However, after rerunning the test, I still get the same error. The update seemed to update a bunch of gemini_data, but I don't believe it updated bcbio/genomes/Hsapiens/GRCh37/snpeff/GRCh37.75/snpEffectPredictor.bin. How can I update the snpEff database?

Thank you,
Luke

chapmanb added a commit that referenced this issue Sep 26, 2016
@chapmanb
Avoid getting older program versions from brew
07051d1 
Now that we install everything with conda packages, avoid potentially
pulling in old versions for things like snpEff from older brew
installs. #1561
@chapmanb
Copy link
Member

Luke;
Sorry about the issue, I'm not positive why it wouldn't upgrade snpEff as well. If you look at /path/to/bcbio/manifest/python-packages.yaml and search for snpeff, what version is listed? It should have been updated with 4.3 which is where the installers pulls from to know it needs an update. If this is an older installation I pushed a fix to avoid pulling old versions from brew installs which might also help. Hope one of these two ideas helps resolve the problem.

@lsturm1
Copy link
Author

lsturm1 commented Sep 26, 2016

Hi,

I checked the python-packages.yaml and weirdly, there is no entry for snpeff listed at all. What should I do?

Luke

@chapmanb
Copy link
Member

Luke;
That's strange it should get updated and reported there on any successful run of an install/upgrade, if you run:

bcbio_nextgen.py upgrade -u development --tools

does it finish cleanly and update the manifest file? Hopefully that fixes it and you can then run the data update command afterwards.

@lsturm1
Copy link
Author

lsturm1 commented Sep 26, 2016

I wasn't able to do that update do to a previous issue. I somehow got into a state where conda wasn't in the right place. Specifically bcbio/anaconda/bin/conda doesn't exist. I tried to reinstall conda, but that path still doesn't exist. Any thoughts on how to fix that?

@chapmanb
Copy link
Member

Luke;
You'll probably need to remove the broken anaconda directory (rm -rf /path/to/bcbio/anaconda) and re-run the installer to recreate conda and the installed packages:

http://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html#automated

You should use the same tool and data directories as previously to avoid re-downloading the data. Hopefully this will get your installation working cleanly again.

@lsturm1
Copy link
Author

lsturm1 commented Sep 30, 2016

Thank you! That worked!

vladsavelyev pushed a commit to vladsavelyev/bcbio-nextgen that referenced this issue Oct 24, 2016
@chapmanb
Avoid getting older program versions from brew
bf039ce 
Now that we install everything with conda packages, avoid potentially
pulling in old versions for things like snpEff from older brew
installs. bcbio#1561
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@chapmanb @lsturm1