bbuchfink
Error: Invalid parameter count for option '--tmpdir'
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!
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)
I have fixed this problem by downgrading the version of conda : conda install -c bioconda conda=24.3.0; Hope this method can be work for others!!!
在 2024-10-20 21:58:01，"Benjamin Buchfink" @.***> 写道：
Closed #803 as completed.
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