Sortmerna not running with error showing -m

Question

[boydmm6]

Using ubuntu 16.04 LTS 62.8 GiB

We downloaded the data files with no problem but when trying to run the samples through the program we are getting an error message each time.

I am entering the code directly from the manual for sortmerna as so;

time ./sortmerna --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db:\
./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-db:\
./rRNA_databases/silva-arc-16s-id95.fasta,./index/silva-arc-16s-db:\
./rRNA_databases/silva-arc-23s-id98.fasta,./index/silva-arc-23s-db:\
./rRNA_databases/silva-euk-18s-id95.fasta,./index/silva-euk-18s-db:\
./rRNA_databases/silva-euk-28s-id98.fasta,./index/silva-euk-28s:\
./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-db:\
./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s-db\
--reads file_name_rRNA --sam --num_alignments 1 --fastx --aligned SRR105861_rRNA\
--other file_name_non_rRNA --log -v

The error message that is coming up says ERROR: -m [INT] must be a positive integer value (in Mbytes)

We have tried adding -m of various integers to the end of the code but the same error message still comes up.

Any idea what this error code means and how to fix it?

[GenoMax]

What value for -m did you use and how did you enter the value? (e.g. -m 1024 at end of the command above)

Did you copy and paste that command from the PDF file? You may have copied some non-printable characters in the process. Something to check into.

[boydmm6]

We tried entering -m 1024 and other various numbers that we saw in the manual. I copied and pasted from the PDF file into a text editor. I don't think it's a non-printable error as I even tried once by just entering in the entire code.

Answer 1

[h.mon]

I suspect the error is quite subtle: after the last db item, you add a backlash without a space:

./index/rfam-5.8s-db\

Try adding a space:

./index/rfam-5.8s-db \

The same after the --aligned parameter:

--aligned SRR105861_rRNA\

Try adding a space:

--aligned SRR105861_rRNA \

However, the backlashes to break the crazy long db name should not contain spaces. You could set a variable to make your command more readable:

CRAZYDB=./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db:\
./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-db:\
./rRNA_databases/silva-arc-16s-id95.fasta,./index/silva-arc-16s-db:\
./rRNA_databases/silva-arc-23s-id98.fasta,./index/silva-arc-23s-db:\
./rRNA_databases/silva-euk-18s-id95.fasta,./index/silva-euk-18s-db:\
./rRNA_databases/silva-euk-28s-id98.fasta,./index/silva-euk-28s:\
./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-db:\
./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s-db

time ./sortmerna --ref $CRAZYDB --other file_name_non_rRNA --log -v \
    --reads file_name_rRNA --sam --num_alignments 1 --fastx --aligned SRR105861_rRNA

[boydmm6]

Thank you!! It was the spacing issue. All is resolved now

[GenoMax]

I moved @h.mon's comment to an answer. You should mark it as accepted.