Input file error

[HTaekOppa]

Dear Drs,

Hope this email finds you well.

I think I have followed the steps from the github but the outcome file contains a bit of error message.

Please see the attached file for more info
scanPAV_Taek.zip
.

File not in the working directory or the used command not recognised!
Input presence file: /work/MGRF_NGS/Nbenth_SolG_ISO_gDNA/Nbenth_EU/Nb_LAB_Chromosome/ReName_DB/NbV1Ch_Final/scanPAV/PBN47S_Corrected_RN.fasta
File not in the working directory or the used command not recognised!
Input absence file: /work/MGRF_NGS/Nbenth_SolG_ISO_gDNA/Nbenth_EU/Nb_LAB_Chromosome/ReName_DB/NbV1Ch_Final/scanPAV/NbV1ChF.fasta
Calling /work/MGRF_NGS/Nbenth_SolG_ISO_gDNA/Nbenth_EU/Nb_LAB_Chromosome/ReName_DB/NbV1Ch_Final/scanPAV/PBN47S_Corrected_RN.fasta /work/MGRF_NGS/Nbenth_SolG_ISO_gDNA/Nbenth_EU/Nb_LAB_Chromosome/ReName_DB/NbV1Ch_Final/scanPAV/NbV1ChF.fasta pavs_absnt_NbV1Ch.fasta smalt
cat align.sam | awk '($2<100)&&($5>=0){print $1,$2,$3,$4,$5,$13}' | egrep -v '^@' > align-1.dat

I can see that the input file “Input presence file: /work/MGRF_NGS/Nbenth_SolG_ISO_gDNA/Nbenth_EU/Nb_LAB_Chromosome/ReName_DB/NbV1Ch_Final/scanPAV/PBN47S_Corrected_RN.fasta” file is in the same working directory (/work/MGRF_NGS/Nbenth_SolG_ISO_gDNA/Nbenth_EU/Nb_LAB_Chromosome/ReName_DB/NbV1Ch_Final/scanPAV).

Does it have to be in /work/waterhouse_team/apps/scanPAV/scanPAV/src/scanPAV?

Or did I miss something?

Despite this, it has generated two files (pavs_absnt_PBN_Scf47.fasta and pavs_absnt_PBN_Scf47.fasta.fasta).

Looking forward to your reply!

Best regards,

Taek

[phloz]

I launch a scanPAV job through my system scheduler and it crashed. When I ran scanPAV on the command line, I received the same error output "File not in the working directory or the used command not recognised!" but it did generate an output. Taek's error was independently reproduced but I'm not sure whether my initial crash is related.