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Arkadiy-Garber / SprayNPray

Rapid and simple taxonomic profiling of genome and metagenome contigs
GNU General Public License v3.0
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fasta file with contigs is not created #6

Open gaworj opened 1 year ago

gaworj commented 1 year ago

Hi,

Thank you for great tool!

I have encountered problem with sprayandpray.

When I run:

spray-and-pray.py -g assembly.fasta -out endosymbionts_out -cd 0.5 -L 1000000 -perc 50 -ref /BLAST_database/nr_db/nr_diamond_db -Domain Bacteria -t 40 -blast assembly.fasta.blast -fa endosymbionts.fa

endosymbionts_out dir is created with result files inside but there is no fasta file with contigs.

What I'm doing wrong? Any hints?

Bests, Jan

Arkadiy-Garber commented 1 year ago

Hi Jan,

Thanks for your interest in SprayNPray!

The issue with your command is the argument: -fa endosymbionts.fa. That is actually a flag. So you simply need to provide it with no arguments, like so:

spray-and-pray.py -g assembly.fasta -out endosymbionts_out -cd 0.5 -L 1000000 -perc 50 -ref /BLAST_database/nr_db/nr_diamond_db -Domain Bacteria -t 40 -blast assembly.fasta.blast --fa

The software will create it's own fasta files appended with 'matched' and 'unmatched'. Does that make sense? Sorry for the confusion.

Let me know if you continue to have issues or have any other questions.

Cheers, Arkadiy

gaworj commented 1 year ago

Hi,

Now it works! Thank you!

Please also add information to the instructions page that adding sprayandpray folder to the PATH is critical.

The taxmap...txt file cannot be found by the software without this step.

Bests, Jan

Arkadiy-Garber commented 1 year ago

Excellent! Glad that it works now - and I will make those changes. Are you running SprayNPray using the conda install (with the setup.sh script)? If so, the path should be set in that conda env. But I will specify this in the wiki.

Thanks! Arkadiy