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