Entering edit mode
4.5 years ago
kacollier
▴
30
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)
