Closed lsturm1 closed 8 years ago
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.
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
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.
Hi,
I checked the python-packages.yaml and weirdly, there is no entry for snpeff listed at all. What should I do?
Luke
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.
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?
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.
Thank you! That worked!
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