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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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print('layout = {}; Deleting unpaired file: {}'.format(sra_stat['layout'], unpaired_file)) NameError: name 'unpaired_file' is not defined #133

Closed docxology closed 1 year ago

docxology commented 1 year ago

This is during amalgkit quant, and halts the process. Let me know what else I can try or other information to provide, thank you.

Species: Apis mellifera SRA Run ID: DRR129201 Looking for index folder in ./ Kallisto index file found: ./index/Apis_mellifera.idx Output file detected: ./quant/DRR129201/DRR129201_abundance.tsv Continued. The output will not be overwritten. If you want to overwrite the results, set "--redo yes".

Species: Apis mellifera SRA Run ID: SRR806711 Looking for index folder in ./ Kallisto index file found: ./index/Apis_mellifera.idx Output file was not detected: ./quant/SRR806711/SRR806711_abundance.tsv Traceback (most recent call last): File "/home/tet/miniconda3/bin/amalgkit", line 370, in args.handler(args) File "/home/tet/miniconda3/bin/amalgkit", line 43, in command_quant quant_main(args) File "/home/tet/miniconda3/lib/python3.9/site-packages/amalgkit/quant.py", line 191, in quant_main run_quant(args, metadata, sra_id, index) File "/home/tet/miniconda3/lib/python3.9/site-packages/amalgkit/quant.py", line 105, in run_quant ext = get_newest_intermediate_file_extension(sra_stat, work_dir=output_dir_getfastq) File "/home/tet/miniconda3/lib/python3.9/site-packages/amalgkit/util.py", line 432, in get_newest_intermediate_file_extension sra_stat = detect_layout_from_file(sra_stat) File "/home/tet/miniconda3/lib/python3.9/site-packages/amalgkit/util.py", line 475, in detect_layout_from_file print('layout = {}; Deleting unpaired file: {}'.format(sra_stat['layout'], unpaired_file)) NameError: name 'unpaired_file' is not defined

kfuku52 commented 1 year ago

I updated amalgkit. Please let me know whether the latest version works fine.

docxology commented 1 year ago

Thank you! It is running fine now and catches a few hundred samples that were previously not working. I will update this or another issue if anything comes up.

kfuku52 commented 1 year ago

I'm delighted to hear the bug fix worked well!