Can't find cause of the error

[glitchheadgit]

AbSplice was launched with the command from tutorial python -m snakemake -j 1 --use-conda from the AbSplice container, installed strictly by instructions in READ.md

End of the output:

[Fri Feb  9 17:37:54 2024]
Error in rule mmsplice_splicemap:
    jobid: 8
    input: ../data/resources/analysis_files/vcf_files/DIV_train_all_annotated.vcf.gz, ../data/resources/downloaded_files/GRCh38.primary_assembly.genome.fa, ../data/resources/downloaded_files/splicemap_hg38/Adipose_Subcutaneous_splicemap_psi5_method=kn_event_filter=median_cutoff.csv.gz, ../data/resources/downloaded_files/splicemap_hg38/Adipose_Subcutaneous_splicemap_psi3_method=kn_event_filter=median_cutoff.csv.gz
    output: ../data/results/hg38/model_scores_from_absplice_features/DIV_train_all_annotated.vcf.gz_MMSplice_SpliceMap.csv

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete

I think that the VCF file can be the cause of the problem(despite successful annotation by SpliceAI and SPiP). It's attached below (modified extension to txt to upload it on github). DIV_train_all_annotated.txt

Can you help me to find the cause of the error? Thank you!

[neverov-am]

Dear @glitchheadgit ,

Thank you for your report. We ran AbSplice with the provided VCF file and we suspect that the issue might be in the naming of contigs. It worked for us by adding 'chr' to chromosome names. Could you provide us with the error message itself to make sure our reply matches your issue? It should be displayed above the portion you have already provided.

[glitchheadgit]

Yes, that was the case. After adding 'chr' prefix AbSplice ran with no errors. Thanks!