Need help with SortMeRNA error

Question

[sentausa]

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.

[Ram]

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'.

Answer 1

[sentausa]

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