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stratust / igpipeline

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Running igpipeline #4

Open Andrea-Cavalli opened 2 years ago

Andrea-Cavalli commented 2 years ago

Hello. Unfortunately the execution of igpipeline fails after:

scripts/data_integration.py --igblast_airr /igpipeline/results/CHEMO/run1/igblast_output/CHEMO.fmt19 --igblast_fmt7 /igpipeline/results/CHEMO/run1/igblast_output/CHEMO.fmt7 --define_clones /igpipeline/results/CHEMO/run1/clones_output/CHEMO_db-pass_clone-pass.tab --corrected_regions_file /igpipeline/results/CHEMO/run1/corrected_output/CHEMO_db-pass.tab --germline_ig_v_seq database/igblast/fasta/imgt_human_ig_v.fasta --organism human --HV_primer 23 --KV_primer 21 --LV_primer 0 --correction True --output /igpipeline/results/CHEMO/run1/integration_output/CHEMO.tsv &> /igpipeline/results/CHEMO/run1/integration_output/CHEMO.log

This issue was not present in the past. Regards Andrea

stratust commented 2 years ago

Hi Andrea,

Do you mind sharing your dataset? I need to reproduce the error locally to see what is the problem.