Dear Community
I have a very annoying problem. In our laboratory we’re going to launch automated BLAST-searches. Therefore we’re using BLAST+ and its output-files. We have chosen the old XML-Format (-outfmt 5). Everything worked fine until we started searching for a “max_target_seqs” value higher than 50. In this case the “<hsp>” - sections were so numerous that our Java-Software (while reading >80k lines) crashed. Is there a possibility to limited the <hsp> results per hit? May be one hsp per hit?
Our command for blast+ is something like that:
…\blastn.exe -db nt -remote -task blastn-short -outfmt 5 -max_target_seqs 500 -evalue 10.00 -word_size 7 -gapopen 5 -gapextend 2 -reward 1 -penalty -3 -out xml.gb -query seq.fas
Greetings from Germany
Jesfreric
I have a very annoying problem. In our laboratory we’re going to launch automated BLAST-searches. Therefore we’re using BLAST+ and its output-files. We have chosen the old XML-Format (-outfmt 5). Everything worked fine until we started searching for a “max_target_seqs” value higher than 50. In this case the “<hsp>” - sections were so numerous that our Java-Software (while reading >80k lines) crashed. Is there a possibility to limited the <hsp> results per hit? May be one hsp per hit?
Our command for blast+ is something like that:
…\blastn.exe -db nt -remote -task blastn-short -outfmt 5 -max_target_seqs 500 -evalue 10.00 -word_size 7 -gapopen 5 -gapextend 2 -reward 1 -penalty -3 -out xml.gb -query seq.fas
Greetings from Germany
Jesfreric
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