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jorvis / biocode

Bioinformatics code libraries and scripts
MIT License
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report_gff_intron_and_intergenic_stats.py error message Detected assembly with undefined or 0 length #22

Closed cmccracken closed 10 years ago

cmccracken commented 10 years ago

When I run this script, I get a message that I'm not sure how to troubleshoot.

$ /home/cmccracken/biocode/gff/report_gff_intron_and_intergenic_stats.py -i final_annotation_bmi_20140606.fixed.newIDs.gff3 /usr/local/packages/Python-3.2.3/lib/python3.2/subprocess.py:389: RuntimeWarning: The _posixsubprocess module is not being used. Child process reliability may suffer if your program uses threads. "program uses threads.", RuntimeWarning) Traceback (most recent call last): File "/home/cmccracken/biocode/gff/report_gff_intron_and_intergenic_stats.py", line 212, in main() File "/home/cmccracken/biocode/gff/report_gff_intron_and_intergenic_stats.py", line 91, in main raise Exception("ERROR: Detected assembly with undefined or 0 length: {0}".format(assembly.id)) Exception: ERROR: Detected assembly with undefined or 0 length: ChromosomeIII_BmicrotiR1

jorvis commented 10 years ago

Do you know if your input file had embedded FASTA residues? If not, I suspect that's because you didn't use the --fasta option to specify the FASTA input data?

Please re-open and submit an example file if this is still an issue.