SortMeRNA outputting empty files

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1

I’m new to Galaxy, but I am trying to use SortMeRNA v 2.1b.6 to filter rRNA out of paired metagenome datasets. I am using default parameters, all available reference databases, paired-out, and I am including unaligned/rejected reads in the output. Unfortunately the output files for both aligned and unaligned reads are completely empty. This is the standard error output I get:

/usr/local/bin/merge-paired-reads.sh: line 54: perl: command not found
/usr/local/bin/merge-paired-reads.sh: line 56: perl: command not found
/usr/local/bin/merge-paired-reads.sh: line 58: paste: command not found
The input reads file or reference file is empty, or the reads file is not in FASTA or FASTQ format, no analysis could be made.
/usr/local/bin/unmerge-paired-reads.sh: line 49: perl: command not found
/usr/local/bin/unmerge-paired-reads.sh: line 51: perl: command not found
/usr/local/bin/unmerge-paired-reads.sh: line 49: perl: command not found
/usr/local/bin/unmerge-paired-reads.sh: line 51: perl: command not found

I think these missing commands cause the file data to be lost and the output to be empty. Has anyone had this problem before, and if so, what did you do? I’ve tried other versions of SortMeRNA and have run into the same problem. Running my data as single reads through SortMeRNA works but the workflow I am trying to replicate does not do this.

2

Hi @vrm39,

What Galaxy server do you use?

Thank you!

Igor

3

Hi Igor,

Thank you for your response! I’m using usegalaxy eu.

4

Hi @vrm39,

It seems output depends on database(s) used. I tried SortMeRNA on Galaxy Europe with test data and got empty output for the default rfam-5s-database-id98 database. The same files returned many reads when the job was submitted against all six available silva databases.

I guess at this point we need an input from an expert who understand what is going under the hood.

Hi @jennaj, why SortMRNA output varies so much between databases? Is it normal?

In the shared history the first job (datasets 3-4) was submitted with the default rfam-s5 db and returned empty files, the second job (datasets 24-25) was submitted against all silva dbs and returned many sequences.

Kind regards,

Igor