Closed yocra3 closed 3 years ago
@yocra3 I can see that you're trying things out. I'm sorry that you're running into issues, but I'll help you out.
I'll try the same command to see if I can reproduce the issue.
Which sarek version did you run?
I am using nf-core/sarek v2.6.1.
Can you give me the full .command.err
and .command.sh
from the work directory in which this process failed?
Here you have:
.command.err
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'ann'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'null'
00:00:00 Reading config file: /home/genetica/Carlos/sarek_test/work/8e/415451e58c50279088367b8233bbc4/snpEff.config
00:00:00 Reading config file: /opt/conda/envs/nf-core-sarek-2.6.1/share/snpeff-4.3.1t-3/snpEff.config
java.lang.RuntimeException: Property: 'null.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:106)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1000)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:01 Logging
00:00:03 Done.
.command.sh
#!/bin/bash -euo pipefail
snpEff -Xmx7g null -csvStats HaplotypeCaller_1234N.g_snpEff.csv -nodownload -dataDir ${PWD}/cache -canon -v HaplotypeCaller_1234N.g.vcf.gz > HaplotypeCaller_1234N.g_snpEff.ann.vcf
mv snpEff_summary.html HaplotypeCaller_1234N.g_snpEff.html
ok, this is very weird.
It seems that the params snpeff_db
is not set up when you're using --tools merge
.
I definitively did not managed to reproduce that.
Can you try the dev branch (-r dev
) to see if the issue remain?
I'll try to do more digging to understand where this could be coming from.
Other idea would be to try to add this params to the command line --snpeff_db GRCh37.75
other idea, can you try --tools snpeff,vep,merge
I have tried both things.
--snpeff_db GRCh37.75
runs snpEff successfully but not VEP, so the pipeline fails.--tools snpeff,vep,merge
runs both tools and the merging step, so the pipeline runs successfully. Therefore, I close the issue.
Good morning,
I am testing your sarek pipeline and I am experiencing some problems with the annotation step. Until now, I am just using the test dataset.
After the whole pipeline failed to annotate my variants, I tried to only run the annotation steps, using the commands from
annotation.md
. First, I downloaded the snpEff and VEP cache files. Then I tried to annotate a VCF (one of the files generated with the test dataset) using different tools. If I annotate with snpEff or VEP alone, the pipeline works without any error:However, if I try to use the merge option,
Snpeff
process fails to execute:When examining the .command.log:
This error is not happening when runing snpEff alone. Do you have any idea of how can this be solved?
Thanks,