Error in Identify_P-Sites in the Riboseq Pipeline

General
1

Hello together,

upfront I have to say that I am not a coder. I was running one sample multiple times with the Riboseq-Pipeline. Everything works fine including the mapping, but every time the pipeline stops after that due to an error in the Identify_P-Sites execution. For that I have selected Ribowaltz and I am using the default settings.

This is the error:

ERROR ~ Error executing process > ‘RIBOSEQ:IDENTIFY_PSITES (null)’

Caused by:
Process `RIBOSEQ:IDENTIFY_PSITES (null)` terminated with an error exit status (134)

Command executed:

INPUT=`echo MA1024_RPF_S9_R1_001.Aligned.toTranscriptome.sorted.out.bam | sed ‘s/ /,/g’`

Rscript --vanilla /media/storage/production/executions/812898286402595711/riboseq-flow/bin/identify_psites.R $INPUT Homo_sapiens.GRCh38.109.gtf Homo_sapiens.GRCh38.fasta 26:32 50 ribowaltz 42 27 Homo_sapiens.GRCh38.109.longest_cds.transcript_info.tsv

Command exit status:
134

Command output:
(empty)

Command error:
Import genomic features from the file as a GRanges object … OK
Prepare the ‘metadata’ data frame … OK
Make the TxDb object … OK
double free or corruption (!prev)
.command.sh: line 4: 66 Aborted (core dumped) Rscript --vanilla /media/storage/production/executions/812898286402595711/riboseq-flow/bin/identify_psites.R $INPUT Homo_sapiens.GRCh38.109.gtf Homo_sapiens.GRCh38.fasta 26:32 50 ribowaltz 42 27 Homo_sapiens.GRCh38.109.longest_cds.transcript_info.tsv

Work dir:
/media/storage/production/executions/812898286402595711/work/81/20213dc00b0363954dc8bda4222402

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

– Check ‘/media/storage/production/executions/812898286402595711/.nextflow.log’ file for details
-[riboseq] Pipeline completed with errors

Does anyone know how to fix this? I would really appreciate any help!

Thank you! Rajiv

2

Hi Rajiv! yes this is an issue we were trying to figure out aha, we only recently added the riboseq pipeline – I think it’s to do with memory requirement potentially. I’ll let you know when we figure it out!

3

For now you can skip that process so that everything else runs by setting skip_psite to true.

4

Dear Charlotte,

thank you for your message!
Yes, I figured that the executions are getting completed successfully when I just skip it.

Thank you for reaching out!

Best wishes,
Rajiv

5

Hi Rajiv

We noticed also a problem with MERGE_FEATURECOUNTS not including all the samples. Maybe hang tight with your riboseq until we can confirm everything is working as expected.

Cheers

Charlotte

6

Dear Charlotte,

thanks for your message! I am just running a small set of 4 samples to get an impression of these. Once the pipeline is fixed, I would rerun all my samples with the fixed version. As of now, I noticed that the new version 1.2.0 shows an error message as soon as I start a run, at least for me. The previous version seems to work though with the known issues.

Best wishes,
Rajiv