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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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phyluce_assembly_parse_duplicates_file.py returns blank fasta file #199

Closed AGKizhakke closed 3 years ago

AGKizhakke commented 3 years ago

Hello, I tried using phyluce_assembly_parse_duplicates_file.py https://gist.github.com/brantfaircloth/e48e7e4eb9748854962863d104f94095 on the duplicates file that I got from phyluce_assembly_match_contigs_to_probes. The code runs with no errors but the output fasta file is blank. I have the same problem with any set of samples I use.

This is what the log file looks like:

2020-07-25 17:10:13,094 - phyluce_assembly_parse_duplicates_file - INFO - ======== Starting phyluce_assembly_parse_duplicates_file ======== 2020-07-25 17:10:13,095 - phyluce_assembly_parse_duplicates_file - INFO - Version: 1.6.8 2020-07-25 17:10:13,095 - phyluce_assembly_parse_duplicates_file - INFO - Argument --contigs: /home/krushnamegh/athulyagk/Menelaides_trial/Cleaned/MergedFiles/Assembly_output/contigs 2020-07-25 17:10:13,095 - phyluce_assembly_parse_duplicates_file - INFO - Argument --duplicates_file: /home/krushnamegh/athulyagk/Menelaides_trial/Cleaned/MergedFiles/Assembly_output/duplicates.txt 2020-07-25 17:10:13,095 - phyluce_assembly_parse_duplicates_file - INFO - Argument --exclude_cnt: 0 2020-07-25 17:10:13,095 - phyluce_assembly_parse_duplicates_file - INFO - Argument --log_path: None 2020-07-25 17:10:13,095 - phyluce_assembly_parse_duplicates_file - INFO - Argument --output: /home/krushnamegh/athulyagk/Menelaides_trial/Cleaned/MergedFiles/Assembly_output/duplicates.fasta 2020-07-25 17:10:13,095 - phyluce_assembly_parse_duplicates_file - INFO - Argument --verbosity: INFO 2020-07-25 17:10:13,112 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA757-------------- 2020-07-25 17:10:13,112 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA757 2020-07-25 17:10:20,829 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA784-------------- 2020-07-25 17:10:20,830 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA784 2020-07-25 17:10:24,545 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA785-------------- 2020-07-25 17:10:24,545 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA785 2020-07-25 17:10:30,918 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA768-------------- 2020-07-25 17:10:30,918 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA768 2020-07-25 17:10:33,570 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA781-------------- 2020-07-25 17:10:33,570 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA781 2020-07-25 17:10:35,313 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA783-------------- 2020-07-25 17:10:35,313 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA783 2020-07-25 17:10:38,661 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA771-------------- 2020-07-25 17:10:38,661 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA771 2020-07-25 17:10:41,038 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA763-------------- 2020-07-25 17:10:41,039 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA763 2020-07-25 17:10:46,923 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA764-------------- 2020-07-25 17:10:46,923 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA764 2020-07-25 17:10:52,346 - phyluce_assembly_parse_duplicates_file - INFO - ---------------Getting DUPLICATE UCE loci for AA765-------------- 2020-07-25 17:10:52,346 - phyluce_assembly_parse_duplicates_file - INFO - Parsing and renaming contigs for AA765

What could be going wrong?

brantfaircloth commented 3 years ago

It may be that that your contigs are not named in a standard way. It's not easy to say without examples of your contigs and duplicates file.

AGKizhakke commented 3 years ago

duplicates.txt

AA757_contigs.txt

I have attached my duplicates file and a contig file. I did not assemble my reads on phyluce. I used IDBA-UD and used the contigs as input for phyluce_assembly_match_contigs_to_probes. Hope there is some way to work with these contigs.

brantfaircloth commented 3 years ago

Ok - I made a small change to the script. Please download that again and give it a shot - it should work with your contigs now.

AGKizhakke commented 3 years ago

It works! Thank you so much.