Entering edit mode
2.5 years ago
Neel
▴
20
Hi, i am trying to run PAst for pseudomonas serotyping and i encountered following error-
****./PAst.pl /home/bvs/neelam/ncbi-blast/bin /home/bvs/neelam/out /home/bvs/neelam/genome/fna /home/bvs/neelam/serotyping/OSAdb.fasta\**
>**
There are 371 files in the input directory, these are now processed by PAST.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
Warning: [blastn] Query is Empty!
- PAst encountered problems with BLAST analysis of ., please check manually.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
Warning: [blastn] Query is Empty!
- PAst encountered problems with BLAST analysis of .., please check manually.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
BLAST query error: CFastaReader: Near line 2, there's a line that doesn't look like plausible data, but it's not marked as defline or comment.
- PAst encountered problems with BLAST analysis of 7790clustout, please check manually.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
- PAst encountered problems with BLAST analysis of P_aeruginosa_1.fna, please check manually.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
Warning: [blastn] Query is Empty!
- PAst encountered problems with BLAST analysis of P_aeruginosa_1.fna.faa, please check manually.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
- PAst encountered problems with BLAST analysis of P_aeruginosa_12-4-4_59.fna, please check manually.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
- PAst encountered problems with BLAST analysis of P_aeruginosa_12939.fna, please check manually.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
- PAst encountered problems with BLAST analysis of P_aeruginosa_1334_14.fna, please check manually.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
- PAst encountered problems with BLAST analysis of P_aeruginosa_152962.fna, please check manually.
Can't exec "cd": No such file or directory at ./PAst.pl line 43.
Thank you!
what is the OS? Check all the directories exist provided as parameters and are in accessible path.
Hi, thank you for your reply but i had check it, i think there is something where i am doing mistake and i don't know how to solve it.
what is in the code of PAst at that line 43 ? (aka, can you post the code from that line?)
Hi, i am attaching here screenshot of that code-
blastn analysis is performed in terminal, output saved in $outdir
https://github.com/Sandramses/PAst/blob/master/PAst.pl
it seems the code expects the dir to exists, to cd into it...
Hi, Thank you for your reply! yeah i had dir but i don't know, why it giving this error.
as cpad0112 already mentioned here above can you double check :
the error you get indicates that one or all of the above are not correct.
Hi, Thank you so much for your time. i tried again after checking all things but it didn't work.here i am attaching output dir info.
Thank you
If your outdir is
output_sero
thenshould reference that one (in the second parameter of the command line):
Hth
Hi, actually i tried this commands and i also tried via making a different dir output_sero after giving all permission but still it didn't work.
There are 371 files in the input directory, these are now processed by PAST. Can't exec "cd": No such file or directory at ./PAst.pl line 43. Warning: [blastn] Query is Empty!
Thank you
and still the most likely cause of all this is wrong dir-name or permission issues.
can you post the output of:
and
pwd
(if you are in that /output_sero/ directory)Hi, here is the output in output_sero dir and path.
PATH-