Can't exec "cd": No such file or directory at ./PAst.pl line 43

Question

[Neel]

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!

[cpad0112]

what is the OS? Check all the directories exist provided as parameters and are in accessible path.

[Neel]

./PAst.pl help

Program:    PAst (Pseudomonas aeruginosa serotyper)
Version:    1.0 (using NCBI blast+ 2.2.29)

Usage:      ./PAst.pl <path/to/BLASTbin> <path/to/output/directory> <path/to/input/directory> <path/to/OSAdatabase>

BLAST bin:  Path to the bin containing blasts executables (ex. /usr/bin/ncbi-blast-2.2.29+/bin/)
Output dir: Directory where blast reports, OSA multifasta files and result summary (serotyping.txt) are placed
Input dir:  Directory containing assembled input genomes in multifasta format (and nothing else)
OSA database:   Path to OSA database file (downloadable from Github)

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.

[lieven.sterck]

what is in the code of PAst at that line 43 ? (aka, can you post the code from that line?)

[Neel]

Hi, i am attaching here screenshot of that code-

blastn analysis is performed in terminal, output saved in $outdir

43 system("cd $outdir");

44 system("$BLASTbin/blastn -query $inputdir/$file -subject $db -out $outdir/BLAST$file"); 45 46#information about OSA clusters (sequence and length) is extracted from blastn output my %data = &extractBLAST_sub($file);

[patrickdm]

https://github.com/Sandramses/PAst/blob/master/PAst.pl

foreach my $file (@IDs) {

    #blastn analysis is performed in terminal, output saved in $outdir
    system("cd $outdir");
    system("$BLASTbin/blastn -query $inputdir/$file -subject $db -out $outdir/BLAST$file");

it seems the code expects the dir to exists, to cd into it...

[Neel]

Hi, Thank you for your reply! yeah i had dir but i don't know, why it giving this error.

[lieven.sterck]

as cpad0112 already mentioned here above can you double check :

1. if the directory you specify as output path exists
2. if that directory is accessible for you?
3. the permission to access & write are set OK for that directory.

the error you get indicates that one or all of the above are not correct.

[Neel]

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.

drwxrwxrwx 2 bvs bvs 4096 Apr 28 09:33 output_sero

Thank you

[patrickdm]

If your outdir is output_sero then

./PAst.pl /home/bvs/neelam/ncbi-blast/bin /home/bvs/neelam/out /home/bvs/neelam/genome/fna /home/bvs/neelam/serotyping/OSAdb.fasta

should reference that one (in the second parameter of the command line):

./PAst.pl /home/bvs/neelam/ncbi-blast/bin /home/bvs/neelam/output_sero /home/bvs/neelam/genome/fna /home/bvs/neelam/serotyping/OSAdb.fasta

Hth

[Neel]

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.

./PAst.pl /home/bvs/neelam/ncbi-blast/bin/ /home/bvs/neelam/output_sero/ /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.

Thank you

[lieven.sterck]

and still the most likely cause of all this is wrong dir-name or permission issues.

can you post the output of:

ls -l  /home/bvs/neelam/output_sero/

and

pwd (if you are in that /output_sero/ directory)

[Neel]

Hi, here is the output in output_sero dir and path.

ls -l /home/bvs/neelam/output_sero/

total 2772
-rw-rw-r-- 1 bvs bvs      0 Apr 28 15:20 BLAST.
-rw-rw-r-- 1 bvs bvs      0 Apr 28 15:20 BLAST..
-rw-rw-r-- 1 bvs bvs    318 Apr 28 15:20 BLAST7790clustout
-rw-rw-r-- 1 bvs bvs 186290 Apr 28 09:32 BLASTP_aeruginosa_12-4-4_59.fna
-rw-rw-r-- 1 bvs bvs 193237 Apr 28 09:33 BLASTP_aeruginosa_12939.fna
-rw-rw-r-- 1 bvs bvs 205557 Apr 28 09:33 BLASTP_aeruginosa_1334_14.fna
-rw-rw-r-- 1 bvs bvs 205421 Apr 28 09:33 BLASTP_aeruginosa_152962.fna
-rw-rw-r-- 1 bvs bvs 188465 Apr 28 09:33 BLASTP_aeruginosa_1811-13R031.fna
-rw-rw-r-- 1 bvs bvs 188465 Apr 28 09:33 BLASTP_aeruginosa_1811-18R001.fna
-rw-rw-r-- 1 bvs bvs 181269 Apr 28 09:33 BLASTP_aeruginosa_1903031130.fna
-rw-rw-r-- 1 bvs bvs 243939 Apr 28 15:20 BLASTP_aeruginosa_1.fna
-rw-rw-r-- 1 bvs bvs      0 Apr 28 09:32 BLASTP_aeruginosa_1.fna.faa
-rw-rw-r-- 1 bvs bvs 178441 Apr 28 09:33 BLASTP_aeruginosa_2020HL-00861.fna
-rw-rw-r-- 1 bvs bvs 181260 Apr 28 09:33 BLASTP_aeruginosa_243931.fna
-rw-rw-r-- 1 bvs bvs 181270 Apr 28 09:33 BLASTP_aeruginosa_24Pae112.fna
-rw-rw-r-- 1 bvs bvs 179496 Apr 28 09:33 BLASTP_aeruginosa_268.fna
-rw-rw-r-- 1 bvs bvs 238031 Apr 28 09:33 BLASTP_aeruginosa_401853.fna
-rw-rw-r-- 1 bvs bvs 202100 Apr 28 09:33 BLASTP_aeruginosa_519119.fna
-rw-rw-r-- 1 bvs bvs  39507 Apr 28 09:34 serotyping.txt

PATH-

/home/bvs/neelam/output_sero