dummy_data file issue - Singularity

[njm-data]

Hi! I'm trying to run the example data (testrun) in Finder on an HPC using Singularity (v 3.7.1). In the main testrun.error file the error that starts the error series was cat: /scratch1/njmello/Finder-finder_v1.1.0/example/testrun/alignments/dummy_data1_round2_SJ.out.tab: No such file or directory

I then went to the progress.log file and saw that the mapping rate for the dummy variables were 0. I went to the alignments folder for the dummy_data1_round1.error and saw

EXITING because of fatal input ERROR: could not open readFilesIn=/home/ubuntu/Finder/example/raw_data//dummy_data1.fastq

Jan 11 13:05:49 ...... FATAL ERROR, exiting

I went to the raw data file and saw this:

[njmello@login001 raw_data]$ pwd
/scratch1/njmello/Finder-finder_v1.1.0/example/raw_data
[njmello@login001 raw_data]$ ls
dummy_data1.fastq  dummy_data2.fastq.gz

I think the double '//' that I saw in the dummy_data1_round1.error is potentially the key to the problem, as I know that the dummy1 fastq file is present. I'll upload the testrun.error file and the progress.log file too if that helps. If there's anything I should try, please let me know. Thank you!! testrun.error.log progress.log