search

kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
7 stars 1 forks source link

AssertionError: None of expected extensions (.amalgkit.fastq.gz .rename.fastq.gz .fastp.fastq.gz .fastq.gz) found #45

Closed kfuku52 closed 3 years ago

kfuku52 commented 3 years ago

fixed in https://github.com/kfuku52/amalgkit/commit/feca4a6fe0f317e7fafd93fc1493f3d2352322f9

Traceback (most recent call last):
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/bin/amalgkit", line 326, in <module>
    args.handler(args)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/bin/amalgkit", line 43, in command_quant
    quant_main(args)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/amalgkit/quant.py", line 78, in quant_main
    ext = get_newest_intermediate_file_extension(sra_stat, work_dir=output_dir_getfastq)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/amalgkit/util.py", line 51, in get_newest_intermediate_file_extension
    assert 'ext_out' in locals(), 'None of expected extensions ('+' '.join(extensions)+') found in '+work_dir
AssertionError: None of expected extensions (.amalgkit.fastq.gz .rename.fastq.gz .fastp.fastq.gz .fastq.gz) found in /lustre6/home/lustre1/kfuku/my_project/daniel_friedman/20210402_amalgkit/amalgkit_out/getfastq/SRR584147