report_gff_intron_and_intergenic_stats.py error message Detected assembly with undefined or 0 length

[cmccracken]

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]

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.