rvaser / sword Goto Github PK

Good morning, Robert.

I was wondering if there is a way to run SWORD on input fasta database target files that are compressed (*.fa.gz). I've tried process substitution to read the fa.gz database file using zcat, and it returns "No alignments found." Otherwise, running SWORD on the decompressed database file works. Is there a way to avoid the need to decompress *.fa.gz target files?

Thanks.

Any thoughts on this?

Hi Robert!
I find that when trying to run a command like:

sword -i ./Step5_align_contigs_to_database/TempFiles/Translated_step4_AbundanceFiltered_Trinity.09.fasta -t 12 -o ./Step5_align_contigs_to_database/TempFiles/Translated_step4_AbundanceFiltered_Trinity.09.result.tsv -f bm9 -j /mibi/Jon/CoMW/databases/NCyc_100.faa -c 30000

I get "Illegal instruction" as output. I got the syntax above from the script and even if I shave arguments down to just -i -o -j it gives the same error message. I have checked the -i file and they seem to be in the correct fasta-format. I have also checked lengths of sequences. The longest is just above 2200 bytes, so no problem there (checked because you recorded an issue with lengths of sequences above 65k).
Can you help with this?
Kr,
Jon

I tested a larger database
cat eggnog4.proteins.all.faa | grep ">" | wc -c
307985246

sword -i test_seq.fa -j eggnog4.proteins.all.faa -v 0.0000001 -t 8 -a 5 -c 307995246

[database][search-werk]: 29.99180 s
[database][search]: 78.24764 s
Using: lambda = 0.243, K = 0.024, H = 0.100
Segmentation fault

Any thoughts?

Hi!
I have a quite large database I am working on ~64GB with approximately 140 million protein sequences. When I try to run sword using this database I get a "segmentation fault (core dumped)" error. I can run a small test using a 10 sequence-database and a couple of sequences, which is successful as well as using a moderately large database (~264Mb and ~500000 sequences). For the larger database I am using 90GB RAM but I am still getting the same error. What would be the amount of RAM required depending on the database/threads used?
The command I used is: sword -i Test_Query.faa -j Large_DB.faa -o Test.sword -f bm8 -v 1.0 -a 1 -k 5 -c 15000 -T 0 -t 5