Comments (8)
Hi Tim,
There isn't a parameter that can be accessed from the main command currently. If you want a quick hack the you can modify the line below in run_PIRATE.pl to include "-t 75"
# extract sequences.
`cat $pirate_dir/genome_list.txt | parallel -k -j $threads \"perl $script_path/extract_feature_sequences.pl -s {} -d $pirate_dir -o $pirate_dir/genome_multifastas/{}.fasta $e_args >> $pirate_dir/gff_parser_log.txt 2>> $pirate_dir/gff_parser_log.txt\"`;
e.g.
# extract sequences.
`cat $pirate_dir/genome_list.txt | parallel -k -j $threads \"perl $script_path/extract_feature_sequences.pl -t 75 -s {} -d $pirate_dir -o $pirate_dir/genome_multifastas/{}.fasta $e_args >> $pirate_dir/gff_parser_log.txt 2>> $pirate_dir/gff_parser_log.txt\"`;
I am happy to add a branch with this option to the main script and include it in the next release.
All the best,
Sion
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Hi Sion - thanks for the super quick reply. Will use this hack and also would be interested in having a branch available in the next release. Tim
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When I get a spare minute I will set one up for you :)
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I don't see the nohup warnings you were getting when I created a branch with the same option. Are you still seeing them and are the outputs okay?
S
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I found an error message with link_clysters.pl but it looks like it maybe an issue of rerunning PIRATE in the same directory with different settings. When I sent outputs to a fresh directory it didn't occur. I will push to master shortly. Thank you for your help and testing.
S
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Hi @SionBayliss!
I noticed the PR for this feature was merged then reverted (#55). Are there still plans to implement this in the future?
Thanks!
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I have merged this with another commit that I wanted to push together. The revert was due to reading about the nohup errors after merging and then slightly panicking.
I have pushed them both to master now. The master branch has all of the changes that I previously reverted.
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I should have waited! Thanks Sion!
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Related Issues (20)
- Confused with terminology/output HOT 1
- extract_feature_sequences.pl failed HOT 2
- error observed during "aligning all feature sequences" HOT 2
- Missing genome in output HOT 12
- Output gene sequences to run gene alignment separately HOT 4
- PIRATE_plots.pdf created by plot_summary.R HOT 1
- Error after MCL clustering step HOT 5
- How do you tell which gene families are single-copy or multi-copy? HOT 2
- Feature request: Option to include original IDs and annotations in fasta headers for align_features_sequences script HOT 2
- Average_dose =1 is appropriate to determine whether a gene family is a single copy? HOT 1
- - ERROR: link_clusters.pl failed. HOT 1
- Undefined subroutine &main::translate called HOT 2
- Error when running PIRATE MCL process
- For some single loci, a gene family but for others not. HOT 1
- problem in installation HOT 9
- Bump version in new release HOT 4
- Missing output files and coregenom files HOT 3
- Running on large dataset HOT 2
- stuck at threshold 60 during MCL clustering HOT 3
- PIRATE.pangenome_summary.txt HOT 6
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