Error: Invalid parameter count for option '--tmpdir'
lhxaurora opened this issue · 3 comments
Greeting!
I am trying to run Diamond (version=2.1.9) via the cluster, I smoothly created the database, but cannot avoid "Error: Invalid parameter count for option '--tmpdir'" problem no matter how did I set this parameter. here is the command I have tried:
diamond blastp -threads 20 -q C0_6_aa.fasta -d nr.dmnd -o C0_6_aa_vs_nr_blt.txt --max-target-seqs 10 -evalue 1e-5 --outfmt 6 qseqid qlen sseqid stitle slen pident length mismatch gapopen qstart qend sstart send evalue bitscore -t ./tmp
diamond blastp -threads 20 -q C0_6_aa.fasta -d nr.dmnd -o C0_6_aa_vs_nr_blt.txt --max-target-seqs 10 -evalue 1e-5 --outfmt 6 qseqid qlen sseqid stitle slen pident length mismatch gapopen qstart qend sstart send evalue bitscore
diamond blastp -threads 20 -q C0_6_aa.fasta -d nr.dmnd -o C0_6_aa_vs_nr_blt.txt --max-target-seqs 10 -evalue 1e-5 --outfmt 6 qseqid qlen sseqid stitle slen pident length mismatch gapopen qstart qend sstart send evalue bitscore -t /dev/shm
I have already checked that for each of the dictionary, there are enough space (>100G), could anyone kindly help me with solving this problem, thanks so much!
The problem is -evalue should be --evalue
Greeting!
I am trying to run Diamond (version=2.1.9) via the cluster, I smoothly created the database, but cannot avoid "Error: Invalid parameter count for option '--tmpdir'" problem no matter how did I set this parameter. here is the command I have tried:
diamond blastp -threads 20 -q C0_6_aa.fasta -d nr.dmnd -o C0_6_aa_vs_nr_blt.txt --max-target-seqs 10 -evalue 1e-5 --outfmt 6 qseqid qlen sseqid stitle slen pident length mismatch gapopen qstart qend sstart send evalue bitscore -t ./tmp diamond blastp -threads 20 -q C0_6_aa.fasta -d nr.dmnd -o C0_6_aa_vs_nr_blt.txt --max-target-seqs 10 -evalue 1e-5 --outfmt 6 qseqid qlen sseqid stitle slen pident length mismatch gapopen qstart qend sstart send evalue bitscore diamond blastp -threads 20 -q C0_6_aa.fasta -d nr.dmnd -o C0_6_aa_vs_nr_blt.txt --max-target-seqs 10 -evalue 1e-5 --outfmt 6 qseqid qlen sseqid stitle slen pident length mismatch gapopen qstart qend sstart send evalue bitscore -t /dev/shm
I have already checked that for each of the dictionary, there are enough space (>100G), could anyone kindly help me with solving this problem, thanks so much!
The problem is -d nr.dmnd, you should not use nr.dmnd directly, you can use that like this: /data3/durui/database/nr_db/nr(right)；nor /data3/durui/database/nr_db/nr.dmnd(wrong)