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issue with add_names #123

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SrichandanPadhi opened this issue May 23, 2024 · 0 comments
Open

issue with add_names #123

SrichandanPadhi opened this issue May 23, 2024 · 0 comments

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@SrichandanPadhi
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Hi, hoe this message finds you in good health.

I run the following script lines for adding names to abundance text files, however, returned errors. Please suggest any modification with the script.

CAT_pack add_names -i /scratch/srichandanp/CAT_pack/RAT_45/ST-FNFP_2_S104_RAT/out.RAT.complete.abundance.txt -o complete_abundance_with_names.txt -t /scratch/srichandanp/CAT_pack/20231120_CAT_gtdb/tax/

CAT_pack add_names -i /scratch/srichandanp/CAT_pack/RAT_45/ST-FNFP_2_S104_RAT/out.RAT.contig.abundance.txt -o contig_abundance_with_names.txt -t /scratch/srichandanp/CAT_pack/20231120_CAT_gtdb/tax/

CAT_pack add_names -i /scratch/srichandanp/CAT_pack/BAT_45/ST-FNFP_2_S104_BAT/out.BAT.bin2classification.txt -o bin_abundance_with_names.txt -t /scratch/srichandanp/CAT_pack/20231120_CAT_gtdb/tax/

Following errors displayed.

CAT_pack v6.0.

[2024-05-23 10:47:02] Loading file /scratch/srichandanp/CAT_pack/20231120_CAT_gtdb/tax/nodes.dmp.
[2024-05-23 10:47:03] Loading file /scratch/srichandanp/CAT_pack/20231120_CAT_gtdb/tax/names.dmp.
Traceback (most recent call last):
File "/scratch/srichandanp/CAT_pack/CAT_pack-6.0/CAT_pack/CAT_pack", line 101, in
main()
File "/scratch/srichandanp/CAT_pack/CAT_pack-6.0/CAT_pack/CAT_pack", line 87, in main
add_names.run()
File "/scratch/srichandanp/CAT_pack/CAT_pack-6.0/CAT_pack/add_names.py", line 80, in run
taxid2name = tax.import_names(args.names_dmp, args.log_file, args.quiet)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/scratch/srichandanp/CAT_pack/CAT_pack-6.0/CAT_pack/tax.py", line 39, in import_names
if line[6] == "scientific name":
~~~~^^^
IndexError: list index out of range

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