Entering edit mode
9.6 years ago
sentausa
▴
650
Dear all,
I am using SortMeRNA version 2.0 to filter out rRNAs from my metatranscriptomics data and I got an error message:
ERROR: '1' is not one of the options.
I run the program using sbatch in our lab's cluster and the bash script looks like this:
#!/bin/bash source /etc/profile.d/modules.sh module add sortmerna sortmerna --ref\ /path/to/rRNA_databases/silva-bac-16s-id90.fasta,\ /path/to/index/silva-bac-16s-db:\ /path/to/rRNA_databases/silva-bac-23s-id98.fasta,\ /path/to/index/silva-bac-23s-db:\ /path/to/rRNA_databases/silva-arc-16s-id95.fasta,\ /path/to/index/silva-arc-16s-db:\ /path/to/rRNA_databases/silva-arc-23s-id98.fasta,\ /path/to/index/silva-arc-23s-db:\ /path/to/rRNA_databases/silva-euk-18s-id95.fasta,\ /path/to/index/silva-euk-18s-db:\ /path/to/rRNA_databases/silva-euk-28s-id98.fasta,\ /path/to/index/silva-euk-28s:\ /path/to/rRNA_databases/rfam-5s-database-id98.fasta,\ /path/to/index/rfam-5s-db:\ /path/to/rRNA_databases/rfam-5.8s-database-id98.fasta,\ /path/to/index/rfam-5.8s-db\ --reads sample1.fastq --num_alignments 1 --fastx --aligned sample1_rRNA --other sample1_non_rRNA\ --log --paired_in -v echo "sample1 done...."
At first I suspected that the error came from the "--num_alignments 1" option, but it still came even I deleted this option.
Does anyone here have any idea on how I could fix this? I will really appreciate your kind help.
Do you see any stack trace? Any cpp source file name maybe? main.cpp or indexed.cpp would be possible locations. Somewhere, the command line parser is encountering a '-1' or a '--1'.