Need help with SortMeRNA error
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.
1 answer
Finally I solved the problem. I am a bit embarrassed since the culprit was only that I forgot to put spaces between the options after a newline.
/path/to/index/rfam-5.8s-db\ #right after this --reads sample1.fastq --num_alignments 1 --fastx --aligned sample1_rRNA --other sample1_non_rRNA\ #and this --log --paired_in -v
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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'.