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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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ValueError: cannot convert float NaN to integer #79

Closed kfuku52 closed 2 years ago

kfuku52 commented 2 years ago 
Traceback (most recent call last):
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/bin/amalgkit", line 378, in <module>
    args.handler(args)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/bin/amalgkit", line 33, in command_getfastq
    getfastq_main(args)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/amalgkit/getfastq.py", line 774, in getfastq_main
    sra_stat = get_sra_stat(sra_id, metadata, num_bp_per_sra)
  File "/home/kfuku/.pyenv/versions/miniconda3-4.3.30/lib/python3.8/site-packages/amalgkit/util.py", line 41, in get_sra_stat
    sra_stat['spot_length'] = int(original_spot_len)
ValueError: cannot convert float NaN to integer
kfuku52 commented 2 years ago

This error is caused by an empty spot_length in the SRA metadata.