Problem running nextflow

[mercedes-barrero]

Hi Luca,

I am trying to run nextflow for a paired end sample with the following command:

nextflow run as_rnaseq.nf -bg -with-tower -with-singularity > log

The problem is that I constantly get errors at the first step:

**Error executing process > 'getReadLength'

Caused by: Process getReadLength terminated with an error exit status (255)

Command executed:

if [ echo NPC1_14191AAC_CGATGT_R1_001.fastq.gz | grep "gz" ]; then cat="zcat"; else cat="cat"; fi $cat NPC1_14191AAC_CGATGT_R1_001.fastq.gz | awk '{num++}{if (num%4==2){line++; sum+=length($0)} if (line==100) {printf "%.0f", sum/100; exit} }'**

My params config file is like this right now:

**params {

        reads        = "/users/bpayer/mbarrero/allele_specific_RNAseq/test/{NPC1_14191AAC_CGATGT_R1_001,NPC1_14191AAC_CGATGT_R2_001}.fastq.gz"         genome       = "/users/bpayer/mbarrero/allele_specific_RNAseq/makeAnno/filteredVCF/GRCm38_68.fa.masked.gz"         annotation   = "/users/bpayer/sequencing_analysis/pipe_data/Mus_musculus.GRCm38.68.gtf"         strandness   = "reverse"         indexfolder  = "/users/bpayer/mbarrero/allele_specific_RNAseq/index"         variants     = "/users/bpayer/mbarrero/allele_specific_RNAseq/makeAnno/filteredVCF/CAST_EiJ-129S1_SvImJ.vcf.gz"         output       = "/users/bpayer/mbarrero/allele_specific_RNAseq/output_test"         single       = "NO"         varcut       = 1         title        = "Allele specific RNAseq project PAYER_09"         subtitle     = "PAYER_09_npc1"         PI           = "Payer"         User         = "Mercedes Barrero"         UCSCgenomeID = "mm10"         email        = "mercedes.barrero@crg.eu"**

Do you know which could be the issue?

Thanks!

[lucacozzuto]

Hi, can you send me via mail the path of where you are running this?

[mercedes-barrero]

/users/bpayer/mbarrero/allele_specific_RNAseq

Thanks!

On 12 Jan 2022, at 12:51, Luca Cozzuto @.**@.>> wrote:

Hi, can you send me via mail the path of where you are running this?

— Reply to this email directly, view it on GitHubhttps://github.com/biocorecrg/allele_specific_RNAseq/issues/35#issuecomment-1010966153, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APDJALOFK5GVCE7QVUJHPJDUVVTNNANCNFSM5LYYRPFQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.Message ID: @.***>

[lucacozzuto]

Ok, so your error is related to the version of singularity used.

Command error:
  ERROR  : Unknown image format/type: /nfs/users/bpayer/mbarrero/allele_specific_RNAseq/singularity/biocorecrg-asrnaseq-0.3.img
  ABORT  : Retval = 255

The image is done the version 3.2.1. If you use an older version it won't work. You can add to your .bashrc the following code

module use /software/as/el7.2/EasyBuild/CRG/modules/all
module load Singularity/3.2.1

And then source again it

source $HOME/.bashrc

[mercedes-barrero]

Thanks!