svc issue

[lsturm1]

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 _runcnvkit\ 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 effectsvcf, = 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/0102/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/0102/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]

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]

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]

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]

Hi,

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

Luke

[chapmanb]

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]

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]

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]

Thank you! That worked!