allowable characters in the genome fasta ID? #54
Description
Hi!
I've been getting a consistent error with one batch of genome files when I run the "genome" command with a concatenated set of the genomes:
coverm genome \
--reference ~/binned_dRepd/ \
-s "-" \
-m relative_abundance \
--interleaved /home/GLBRCORG/trina.mcmahon/lake_data_general/Mendota_metaGs_renamed/*.fastq \
--bam-file-cache-directory bam_cache \
--min-read-aligned-percent 0.75 \
--min-read-percent-identity 0.95 \
--min-covered-fraction 0 \
-x fasta -t 20 &> relative_abundance_output.txt &
The error is:
thread 'main' panicked at 'index out of bounds: the len is 0 but the index is 4294967295', src/genome.rs:811:23
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
But if I run "genome" with the individual files, it works fine.
coverm genome \
--genome-fasta-directory ~/binned_dRepd/ \
-m relative_abundance \
--interleaved /home/GLBRCORG/trina.mcmahon/lake_data_general/Mendota_metaGs_renamed/*.fastq \
--bam-file-cache-directory bam_cache \
--min-read-aligned-percent 0.75 \
--min-read-percent-identity 0.95 \
--min-covered-fraction 0 \
-x fa -t 20 &> relative_abundance_output.txt &
I am wondering if it is a formatting problem with my fasta ID (I've done some other debugging that makes me think this).
Are there any forbidden characters that we should not use to separate the genome name from the contig name? I suspect it's the "-" but want to confirm.
Example fasta ID:
ME_SAG_rebinned_metabat1_bin.1-2739367620_Contig_60
thanks,
trina