Phyluce unable to recognize Galaxy-assembled .fasta file
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16 months ago
kacollier • 0

My apologies if this is a trivial question; I'm new to working in bioinformatics. I'm attempting to use Phyluce to get match counts for a reference sequence I've assembled on Galaxy. The particular file opens in MEGA and has been called successfully to create a data matrix earlier in the pipeline using the line "--contigs gavia-stellata-refseq-fasta/gavia-stellata-Galaxy-assembled/ \". However, in this particular function, the shell simply won't recognize that the file is still present in the directory. If anyone here has an idea about why that might be the case (or if more information is needed), I'd appreciate any guidance you could give in figuring this out.

This is what I'm running:

phyluce_assembly_get_fastas_from_match_counts \ --contigs gavia-stellata-refseq-fasta/gavia-stellata-Galaxy-assembled/ \ --locus-db gavia-stellata-uce-search-results/probe.matches.sqlite \ --match-count-output gavia-stellata-reference.conf \ --output gavia-stellata-refseq-fasta/gavia-stellata_reference.fasta

And this is the output:

2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - ===== Starting phyluce_assembly_get_fastas_from_match_counts ==== 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Version: git fatal: not a git repository: '//anaconda2/lib/python2.7/site-packages/.git' 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Argument --contigs: /Users/catharus2018/KC-MS-Project/Species-pipelines/gavia-stellata/gavia-stellata-SNP-calling-pipeline/gavia-stellata-refseq-fasta 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Argument --extend_locus_contigs: None 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Argument --extend_locus_db: None 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Argument --incomplete_matrix: False 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Argument --locus_db: /Users/catharus2018/KC-MS-Project/Species-pipelines/gavia-stellata/gavia-stellata-SNP-calling-pipeline/gavia-stellata-uce-search-results/probe.matches.sqlite 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Argument --log_path: None 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Argument --match_count_output: /Users/catharus2018/KC-MS-Project/Species-pipelines/gavia-stellata/gavia-stellata-SNP-calling-pipeline/gavia-stellata-reference.conf 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Argument --output: /Users/catharus2018/KC-MS-Project/Species-pipelines/gavia-stellata/gavia-stellata-SNP-calling-pipeline/gavia-stellata-refseq-fasta/gavia-stellata_reference.fasta 2020-06-10 15:28:39,947 - phyluce_assembly_get_fastas_from_match_counts - INFO - Argument --verbosity: INFO 2020-06-10 15:28:39,964 - phyluce_assembly_get_fastas_from_match_counts - INFO - There are 1 taxa in the match-count-config file named gavia-stellata-reference.conf 2020-06-10 15:28:39,971 - phyluce_assembly_get_fastas_from_match_counts - INFO - There are 3296 shared UCE loci in a COMPLETE matrix 2020-06-10 15:28:39,971 - phyluce_assembly_get_fastas_from_match_counts - INFO - ---Getting UCE loci for gavia_stellata_Galaxy_assembled_refseq--- Traceback (most recent call last): File "//anaconda2/bin/phyluce_assembly_get_fastas_from_match_counts", line 263, in <module> main() File "//anaconda2/bin/phyluce_assembly_get_fastas_from_match_counts", line 212, in main reads = find_file(args.contigs, name) File "//anaconda2/bin/phyluce_assembly_get_fastas_from_match_counts", line 140, in find_file ', '.join(extensions) ValueError: Cannot find the a fasta file for gavia-stellata-Galaxy-assembled-refseq with any of the extensions (.fa, .fasta, .contigs.fasta, .contigs.fa, .gz, .fasta.gz, .fa.gz)

phyluce Galaxy contigs ValueError .fasta • 342 views
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