"IndexError: list index out of range" exception in run_genemapper_mp

[Zuulira]

Got this error when trying to use a .vcf file created using VarScan somatic following this tutorial (https://usegalaxy.eu/training-material/topics/variant-analysis/tutorials/somatic-variants/tutorial.html#variant-calling-and-classification) using galaxy build in reference genome hg38 (2013).

2022/09/20 22:02:44 cravat C:\Program Files (x86)\open-cravat\python-3.7.2.amd64\Scripts\oc run C:\open-cravat\jobs\default\220920-220241\Galaxy35-[VarScan_somatic_on_data_34_and_data_32].vcf -a cancer_genome_interpreter cancer_hotspots cgc cgl civic civic_gene cosmic_gene cscape_coding dbcid mutpanning oncokb target -l hg38 --skip reporter --temp-files 2022/09/20 22:02:44 cravat started: Tue Sep 20 22:02:44 2022 2022/09/20 22:02:44 cravat input files: C:\open-cravat\jobs\default\220920-220241\Galaxy35-[VarScan_somatic_on_data_34_and_data_32].vcf 2022/09/20 22:02:44 cravat input assembly: hg38 2022/09/20 22:02:44 cravat version: open-cravat 2.2.7 C:\Program Files (x86)\open-cravat\python-3.7.2.amd64\lib\site-packages\cravat 2022/09/20 22:02:44 cravat version: cancer_genome_interpreter 1.3.0 C:\open-cravat\modules\annotators\cancer_genome_interpreter 2022/09/20 22:02:44 cravat version: cancer_hotspots 1.2.1 C:\open-cravat\modules\annotators\cancer_hotspots 2022/09/20 22:02:44 cravat version: cgc 85.0.12 C:\open-cravat\modules\annotators\cgc 2022/09/20 22:02:44 cravat version: cgl 1.1.0 C:\open-cravat\modules\annotators\cgl 2022/09/20 22:02:44 cravat version: civic 1.0.16 C:\open-cravat\modules\annotators\civic 2022/09/20 22:02:44 cravat version: civic_gene 1.0.10 C:\open-cravat\modules\annotators\civic_gene 2022/09/20 22:02:44 cravat version: cosmic_gene 94.0.0 C:\open-cravat\modules\annotators\cosmic_gene 2022/09/20 22:02:44 cravat version: cscape_coding 1.0.0 C:\open-cravat\modules\annotators\cscape_coding 2022/09/20 22:02:44 cravat version: dbcid 1.0.1 C:\open-cravat\modules\annotators\dbcid 2022/09/20 22:02:44 cravat version: mutpanning 1.0.0 C:\open-cravat\modules\annotators\mutpanning 2022/09/20 22:02:44 cravat version: oncokb 1.1.3 C:\open-cravat\modules\annotators\oncokb 2022/09/20 22:02:44 cravat version: target 3.1.0 C:\open-cravat\modules\annotators\target 2022/09/20 22:02:44 cravat version: hg38 1.10.2 C:\open-cravat\modules\mappers\hg38 2022/09/20 22:02:44 cravat.converter started: Tue Sep 20 22:02:44 2022 2022/09/20 22:02:44 cravat.converter Input file(s): C:\open-cravat\jobs\default\220920-220241\Galaxy35-[VarScan_somatic_on_data_34_and_data_32].vcf 2022/09/20 22:02:46 cravat.converter input format: vcf 2022/09/20 22:02:58 cravat.converter error lines: 0 2022/09/20 22:02:58 cravat.converter finished: Tue Sep 20 22:02:58 2022 2022/09/20 22:02:58 cravat.converter num input lines: 115206 2022/09/20 22:02:58 cravat.converter runtime: 12.814 2022/09/20 22:02:58 cravat num_workers: 23 2022/09/20 22:02:58 cravat input line chunksize=5008 total number of input lines=115206 number of chunks=23 2022/09/20 22:03:06 cravat An unexpected exception occurred. Traceback (most recent call last): File "C:\Program Files (x86)\open-cravat\python-3.7.2.amd64\lib\site-packages\cravat\cravat_class.py", line 539, in main self.run_genemapper_mp() File "C:\Program Files (x86)\open-cravat\python-3.7.2.amd64\lib\site-packages\cravat\cravat_class.py", line 1323, in run_genemapper_mp fn = fns[0] IndexError: list index out of range 2022/09/20 22:03:06 cravat finished with an exception: Tue Sep 20 22:03:06 2022 2022/09/20 22:03:06 cravat runtime: 22.381s

[Zuulira]

somehow fixed it by renaming the vcf files

[kmoad]

Yup, it was a filename issue. The [] characters were causing errors with filename globs. The fix will be in the next release. Thanks for finding both a problem and a solution here.