Thank you for the response. I got some question regarding your answer. I paste the command at my terminal but it looks like it missing something as I get a blinking ">" Did I have to remove the \ or I have to run the code in different way?. I m sorry for that but I am still learning bash
Blast in parallel with edible outfmt
Hello Biostars
I know that I can run blast with with "edible" output by using this command:
blastp -query -FASTA.faa - db MYDATABASE -evalue 1e-5 -outfmt "6 sseqid pident evalue bitscore staxids"
If I want to run the same command in parallel, i am using
ls *.fna| parallel -a - blastp -query {} -db MYDATABASE -evalue 1e-5 -outfmt 6 -out {.}.txt
My issue is when I am trying to combine the outfmt in parallel I got an error and I want to know if I can combine those two commands in one?
I tried:
ls *.fna| parallel -a - blastp -query {} -db MYDATABASE -evalue 1e-5 -outfmt "6 sseqid pident evalue bitscore staxids sscinames sskingdoms stitle" -out {.}.txt
This gives me:
Error: Too many positional arguments (1), the offending value: evalue Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: evalue
sorry for my terminology, but I'm a new kid on the block
Thank you in advance
1 answer
I second the other suggestions of conflicts with how parallel and bash interpret quotations. I generally find it best to write a function for the command and then feed the function into parallel, avoiding exactly what you experience. I do not see a reason to use -a so leaving it out here (untested, based on your code, I do not know the blast syntax):
function blasty {
blastp \
-query "${1}" \
-out "${1%.fna}".txt \
-db MYDATABASE -evalue 1e-5 -outfmt "6 sseqid pident evalue bitscore staxids sscinames sskingdoms stitle"
}; export -f blasty
ls *.fna | parallel blasty {}
MYDATABASE is worth checking as well, is this a variable or in this case simply a spaceholder for the actual path to the file (or whatever it is, as said not a blast user myself)?
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I suspect this is just a matter of how bash and parallel are handling the
"differently. Have you tried hard-quoting instead with'?I did but doesnt work either :-(, but thanks for your response anyhow!!!
I did but doesnt work either :-(, but thanks for your response anyhow!!!
does the cmdline using only
-outfmt 6work ? (== the problem starts when you add the"6 ...."part ? )on a side note: I don't see any immediate advantage in using
parallelhere (if you want to speed it up somehow, run it on multiple threads)Yes with -outfmt 6 works perfectly!!! My issue starts when I am editing the out format
This is almost certainly a quirk of how parallel is treating
"I would think, but I can't spot the issue off hand.I tried almost everything before posting my issue. Also I realised that I cannot increase the
-num_threadsas I am doing in the "normal" blast search, so I guess that it is a bag of the parallel command than a mistake during my typing.see if this is populating correct queries and then try removing
dry-runAlso check your parallel version.
Works too!!! thank you very much!