Comments (2)
The "E: 8_extractSamples.pl" error occurs because that script received an empty file as input. I fixed the code to produce a clear error message instead of the two obscure "Use of uninitialized value $header..." messages, but this is just cosmetic.
Logging "8_extractSamples.pl - ALL DONE, completed successfully!" instead of aborting with an error message when the step actually failed is also a mistake, it has now been fixed.
The same goes for 8_extractTranscripts.pl, and I fixed it as well.
But your real issue happens upstream from these steps - they should not be receiving empty files as input, some step upstream must have failed.
Your sampleCLN.xlsx looks fine, and if it wasn't you would get early error messages about it: all metadata files get thoroughly sanity-checked before anything else happens.
Please do the following:
git pull
to refresh your codebase. You should not make changes to any files from the repo, the only customizations should be in a copy of grexomeTIMCsec_config.pm (copied somewhere and edited). For example if you don't use subCohorts you should just modify &subCohorts() in your copy of grexomeTIMCsec_config.pm so it returns an empty hash.- Run
grexome-TIMC-secondary.pl
- If the logfile still contains E or W lines, and/or if the results are still empty, please post the full command-line that you used and attach the full logfile.
- Also please post the result of
zgrep -m 1 '#CHROM' [your GVCF.gz file]
(it should end with the sample IDs, including at least all the sampleID values in sampleCLN.xlsx , I thought the code checked this but your test VEP output from test.zip doesn't have anything after INFO, seems strange)
from grexome-timc-secondary.
@ntm
Thanks for your great work!! It runs successfully after refreshing the git.
Cheers,
Chris
from grexome-timc-secondary.
Related Issues (7)
- use CADD v1.6 (AKA CADD-Splice) for upgrading splice variants HOT 1
- dbNSFP VEP plugin error "transcript_match parameter specified but..." -> due to corrupt dbNSFP4.3a.zip HOT 3
- generate updated list of canonical transcripts HOT 2
- debug mode on, step3 failed: 256 at sec_.pl line 283. HOT 5
- How to edit &subCohorts() in config.pm? W grexome-TIMC-secondary.pl: sub-cohort file defined in &subCohorts() but this file doesn't exist. Skipping this sub-cohort HOT 2
- command line for 0_coverage.pl HOT 2
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from grexome-timc-secondary.