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hallamlab / MetaPathways

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information
http://hallam.microbiology.ubc.ca/MetaPathways
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Arbitrary Limit in MetaPathways_filter_input.py #29

Closed nielshanson closed 11 years ago

nielshanson commented 11 years ago

When running long sequences sometimes the pipeline gives the following error:

shawwal:MetaPathways_1_0 kmewis$ /Users/kmewis/Desktop/MetaPathways_1_0/libs/python_scripts/MetaPathways_filter_input.py  --min_length 180 --log_file /Users/kmewis/Documents/BeaverData//Beaver_Metagenome454Reads/run_statistics//Beaver_Metagenome454Reads.nuc.stats  -i /Users/kmewis/Documents/BeaverData/GQ_12April2013/Beaver_Metagenome454Reads.fasta -o  /Users/kmewis/Documents/BeaverData//Beaver_Metagenome454Reads/preprocessed//Beaver_Metagenome454Reads.fasta -M /Users/kmewis/Documents/BeaverData//Beaver_Metagenome454Reads/preprocessed//Beaver_Metagenome454Reads.mapping.txt
Traceback (most recent call last):
  File "/Users/kmewis/Desktop/MetaPathways_1_0/libs/python_scripts/MetaPathways_filter_input.py", line 261, in <module>
    main(sys.argv[1:])
  File "/Users/kmewis/Desktop/MetaPathways_1_0/libs/python_scripts/MetaPathways_filter_input.py", line 181, in main
    length_distribution[index] += 1
KeyError: 35