How to specify the fasta path for ReportCli

[max-l]

I generate a PeptideShaker psdb from a slurm compute node, in a temporary folder (/localscratch/maxl.14009123.0)

When ReportCli is launched, this folder no longer exists (and cannot exist, because I'm on a slurm node don't even have permission in the parent folder to create the directory)

From looking at the code, ReportCli loads the path from a serialized object in the sqlite database, and it happens to be the absolute path of the fasta file used as input.

Mon Jun 08 11:21:48 EDT 2026 An error occurred while reading: /localscratch/maxl.14013444.0/local_pepshake_out.psdb.
java.io.IOException: FASTA file not found /localscratch/maxl.14009123.0/tmp/db.fasta.
at eu.isas.peptideshaker.utils.PsdbParent.loadPsdbFile(PsdbParent.java:299)
at eu.isas.peptideshaker.cmd.ReportCLI.call(ReportCLI.java:113)
at eu.isas.peptideshaker.cmd.ReportCLI.main(ReportCLI.java:508)

I

[hbarsnes]

Have you tried putting a copy of the FASTA file in the same location as the psdb file of in a folder called "data" in the same location as the psdb file? PeptideShaker should look for the file there if it cannot find it at the original location. See

peptide-shaker/src/main/java/eu/isas/peptideshaker/utils/PsdbParent.java

Line 590 in 9d0c7b4

public FastaSummary loadFastaFile(

I should also mentioned that PeptideShaker is no longer in active development, hence if you come across more issues they will most likely not be solved.