SortMeRNA starts, pauses, never finishes

Question

[Katie D]

Hi,

I'm using SortMeRNA to remove rRNA reads from my RNA-seq data. I successfully used the program on multiple transcriptomes, but it just will not work for one of my files. It starts to run normally, and eventually pauses and never finishes. Eventually it just gets killed.

Has anyone run into this before? Any insight?

Thank you,

Katie

[Shahzad]

please share the command you are using and also if you get and "verbose" which appear while running the tool.

[Katie D]

./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 JRYH001K_merge.fastq --fastx --aligned JRYH001K_rRNA.fastq --other JRYH001K_mRNA.fastq --paired_in --log -v

That's the command I used which worked for other files. I'm a bit confused by the second part of your comment - I did use the option -v for verbose in my command if that is what you are asking