blastn

[Wanli-HE]

hi!

do you know what the issue is?

Traceback (most recent call last):
File "/home/projects/ku_00041/apps/wanli/F_pipeline/db/plasforest/PlasForest.py", line 236, in
main(sys.argv[1:])
File "/home/projects/ku_00041/apps/wanli/F_pipeline/db/plasforest/PlasForest.py", line 114, in main
blast_launcher(tmp_fasta, blast_table, verbose, nthreads)
File "/home/projects/ku_00041/apps/wanli/F_pipeline/db/plasforest/PlasForest.py", line 161, in blast_launcher
stdout, stderr = blastn_cline()
File "/home/projects/ku_00041/apps/wanli/F_pipeline/conda_envs/ceb528a9/lib/python3.8/site-packages/Bio/Application/init.py", line 569, in call
raise ApplicationError(return_code, str(self), stdout_str, stderr_str)

Bio.Application.ApplicationError: Non-zero return code -11 from 'blastn -out assmebly_res/SRR2145291_contigs_1kb.fasta_blast.out -outfmt 6 -query assmebly_res/SRR2145291_contigs_1kb.fasta_tmp.fasta -db plasmid_refseq.fasta -evalue 0.001 -num_threads 30'

[Wanli-HE]

here is the command line:
python3 /home/projects/ku_00041/apps/wanli/F_pipeline/db/plasforest/PlasForest.py -i assmebly_res/SRR2145342_contigs_1kb.fasta -r -b -f --threads 30 -o linear_plasmid_genome/SRR2145342_contigs_1kb.csv

[leaemiliepradier]

Blast+ tries to detect the database plasmid_refseq.fasta in the same directory from which it is launched (this is something we will change in the future). Can you try to launch PlasForest from its directory?

If it does not work:

• Are you sure Blast+ is installed on your computer?
• Blast+ takes a temporary FASTA file that is created at the beginning of PlasForest. Can you check whether it is created? In your case, it should be assmebly_res/SRR2145291_contigs_1kb.fasta_tmp.fasta.

[Wanli-HE]

Blast+ tries to detect the database plasmid_refseq.fasta in the same directory from which it is launched (this is something we will change in the future). Can you try to launch PlasForest from its directory?

If it does not work:

• Are you sure Blast+ is installed on your computer?
• Blast+ takes a temporary FASTA file that is created at the beginning of PlasForest. Can you check whether it is created? In your case, it should be assmebly_res/SRR2145291_contigs_1kb.fasta_tmp.fasta.

hi! the problem is when i run 10 samples, 6 samples are successful, 4 are not! and the error is like above.