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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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sys.stderr.write('ERROR: could not find fastq file(s) in:', output_dir_getfastq) #113

Closed kfuku52 closed 1 year ago

kfuku52 commented 1 year ago

@Hego-CCTB I'll fix this.

Traceback (most recent call last):
  File "/home/kfuku/miniconda3/bin/amalgkit", line 361, in <module>
    args.handler(args)
  File "/home/kfuku/miniconda3/bin/amalgkit", line 35, in command_quant
    quant_main(args)
  File "/home/kfuku/miniconda3/lib/python3.9/site-packages/amalgkit/quant.py", line 194, in quant_main
    run_quant(args, metadata, sra_id, index)
  File "/home/kfuku/miniconda3/lib/python3.9/site-packages/amalgkit/quant.py", line 108, in run_quant
    sys.stderr.write('ERROR: could not find fastq file(s) in:', output_dir_getfastq)
kfuku52 commented 1 year ago

@Hego-CCTB Around line 108, you seem to have tried to catch FileNotFoundError raised by get_newest_intermediate_file_extension(), but it's redundant. If there is something to do with the error, we should do that in the function that raises the error, rather than trying to catch it later. I moved the codes around line 108 in run_quant() to get_newest_intermediate_file_extension().