Error in rRNAfilter and sortmerna

[dpaz-corals]

Hi @rivera10 ,

I have problems removing rRNA using --rRNAfilter (sortmerna) and --rRNAdb (database of 12.2 GB) options. I hope you can point me in the right direction to resolve this issue. I was able to run TransPi, and all the steps were good when the rRNA removal step was skipped.

Here is my script

./nextflow run TransPi.nf --all --reads '/All_reads/LP_ALL_R[1,2].fastq.gz' \ --k 25,41,53 --maxReadLen 75 -profile conda \ --allBuscos --rescueBusco --buscoDist \ --rRNAfilter --rRNAdb "/LSU_SSU/LSU_SSU.fasta" \ --outdir Results_LP2 -w LP2_work

and here is what I got [c7/479987] process > remove_rrna (LP_ALL_R) [ 0%] 0 of 1 . . . [48/1fe9d5] process > get_run_info [100%] 1 of 1 ✔ Error executing process > 'remove_rrna (LP_ALL_R)'

Caused by: Process remove_rrna (LP_ALL_R) terminated with an error exit status (135)

Command executed:

sortmerna --ref /LSU_SSU/LSU_SSU.fasta --reads left-LP_ALL_R.filter.fq --reads right-LP_ALL_R.filter.fq --threads 15 --aligned rRNAreads --other nonrRNAreads --paired_in --out2 --fastx --workdir . mv rRNAreads.log LP_ALL_R_remove_rRNA.log mv rRNAreads_fwd LP_ALL_R_rRNA_reads.R1.fq mv rRNAreads_rev LP_ALL_R_rRNA_reads.R2.fq mv nonrRNAreads_fwd LP_ALL_R_no_rRNA.R1.fq mv nonrRNAreads_rev LP_ALL_R_no_rRNA.R2.fq v=$( sortmerna -version | grep "SortMeRNA version" | awk '{print $3}' ) echo "SortMeRNA: $v" >sortmerna.version.txt

Command exit status: 135

Command output: [pop:108] read_queue Popped read number: 92990059 [pop:108] write_queue Popped read number: 92990062 . . . [pop:108] write_queue Popped read number: 94140063 [pop:108] read_queue Popped read number: 94190059 [pop:108] write_queue Po

Command error: .command.sh: line 2: 21691 Bus error sortmerna --ref /LSU_SSU/LSU_SSU.fasta --reads left-LP_ALL_R.filter.fq --reads right-LP_ALL_R.filter.fq --threads 15 --aligned rRNAreads --other nonrRNAreads --paired_in --out2 --fastx --workdir .

Work dir: /LP2_work/c7/4799873eae6b2df5b8c5ffeffc3aba

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

Saludos! David Paz