Issues with -d and -c flags (ggcat doesn't find sample in large color_mapping.in file)

[CamilaDuitama]

Hi.

I am currently running ggcat with a color_mapping.in file of 360 samples (both single and paired-end reads). The command I am running is as follows:

ggcat build -k 31 -c -d color_mapping.in -j 20 -m 600

I get the output you see on the ggcat.log file. Although ggcat finds adds the index with color per sample without problem, eventually, it throws an error as if a file was not found:

Panic: panicked at crates/io/src/sequences_stream/fasta.rs:15:14: Error while opening file /pasteur/appa/scratch/cduitama/RascovanProject/fastq_files/aOralNonHuman/SRR6877286_1.fastq.gz : Os { code: 2, kind: NotFound, message: "No such file or directory" } Backtrace: 0: <unknown> 1: <unknown> 2: <unknown> 3: <unknown> 4: <unknown> 5: <unknown> 6: <unknown> 7: <unknown> 8: <unknown> 9: <unknown> 10: <unknown> 11: <unknown> 12: <unknown> 13: <unknown> 14: <unknown> 15: <unknown> 16: <unknown> 17: __libc_start_main 18: <unknown> As an additional test, I take the sample that it's said to be not found and I create a smaller color_mapping.in file with it. Using the same parameters, ggcat runs without problem. This means for some reason ggcat finds the sample in a small color_mapping.in(2 samples) file but not on the large one (360 samples)

Thanks!

Camila ggcat.log

[CamilaDuitama]

There was an error in the filepath as there were some hidden '\s' characters at the end of each line that ggcat was interpreting as parth of the file path.