Question: Need help with SortMeRNA error
0
gravatar for sentausa
3.9 years ago by
sentausa630
France
sentausa630 wrote:

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.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by sentausa630

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'.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by RamRS20k
1
gravatar for sentausa
3.9 years ago by
sentausa630
France
sentausa630 wrote:

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
ADD COMMENTlink written 3.9 years ago by sentausa630
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