Closed docxology closed 1 year ago
I updated amalgkit. Please let me know whether the latest version works fine.
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.
I'm delighted to hear the bug fix worked well!
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