Error executing process > 'FEELnc_filter (1)'

[wjdiniz]

Hi!

I'm new using Nextflow, and I had some issues
when trying to run the lncRNA-Annotation-nf pipeline using the test dataset. Maybe you can guide me on that.

I’m using an HPC server.

module load singularity

singularity pull docker://cbcrg/lncrna_annotation

This was the command to run Nextflow

module load singularity

module load java/jdk

/gpfs1/home/w.dasilvadiniz/nextflow run skptic/lncRNA-Annotation-nf -with-singularity /gpfs1/home/w.dasilvadiniz/lnc_test/lncrna_annotation_latest.sif

Below follows the output

N E X T F L O W ~ version 20.04.1
Launching skptic/lncRNA-Annotation-nf [jolly_sinoussi] - revision: 047c3f1 [master]
lncRNA Annotation - N F ~ version 0.1

name : lncRNA_Pig_RNA-Seq
genome : /gpfs1/home/w.dasilvadiniz/.nextflow/assets/skptic/lncRNA-Annotation-nf/tutorial/genome/genome_chr38.fa
reads : /gpfs1/home/w.dasilvadiniz/.nextflow/assets/skptic/lncRNA-Annotation-nf/tutorial/reads/*_{1,2}.fastq
annotation : /gpfs1/home/w.dasilvadiniz/.nextflow/assets/skptic/lncRNA-Annotation-nf/tutorial/annotation/annotation_chr38.gtf
STAR overhang : 99
output : results/

[- ] process > index -
[- ] process > index -
[- ] process > mapping -
executor > local (1)
[62/8cbc04] process > index [ 0%] 0 of 1
executor > local (6)
[62/8cbc04] process > index [100%] 1 of 1 ✔
[d9/03c6fe] process > mapping (reads: sampleA) [100%] 1 of 1 ✔
[9b/20b0e5] process > cufflinks (1) [100%] 1 of 1 ✔
[bc/ae811c] process > cufflinks_postprocess (1) [100%] 1 of 1 ✔
[bf/19298e] process > cuffmerge (1) [100%] 1 of 1 ✔
[6f/ae7db2] process > FEELnc_filter (1) [ 0%] 0 of 1
[- ] process > FEELnc_codpot -
[- ] process > FEELnc_classifier -
Error executing process > 'FEELnc_filter (1)'

Caused by:
Process FEELnc_filter (1) terminated with an error exit status (2)

Command executed:

mkdir FEELnc_filter

FEELnc_filter.pl --infile CUFFMERGE/merged.gtf --mRNAexecutor > local (6)
[62/8cbc04] process > index [100%] 1 of 1 ✔
[d9/03c6fe] process > mapping (reads: sampleA) [100%] 1 of 1 ✔
[9b/20b0e5] process > cufflinks (1) [100%] 1 of 1 ✔
[bc/ae811c] process > cufflinks_postprocess (1) [100%] 1 of 1 ✔
[bf/19298e] process > cuffmerge (1) [100%] 1 of 1 ✔
[6f/ae7db2] process > FEELnc_filter (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > FEELnc_codpot -
[- ] process > FEELnc_classifier -
Error executing process > 'FEELnc_filter (1)'

Caused by:
Process FEELnc_filter (1) terminated with an error exit status (2)

Command executed:

mkdir FEELnc_filter

FEELnc_filter.pl --infile CUFFMERGE/merged.gtf --mRNAfile annotation_chr38.gtf --biotype transcript_biotype=protein_coding \ --monoex -1 \ --proc 1 > FEELnc_filter/merged_filtered.gtf

Command exit status:
2

Command output:
(empty)

Command error:
Possible precedence issue with control flow operator at /usr/local/share/perl/5.20.2/Bio/DB/IndexedBase.pm line 791.
Unknown option: 1
Usage:
FEELnc_filter.pl -i candidate.gtf -a mRNA.gtf > candidate_lncRNA.gtf

Work dir:
/gpfs1/home/w.dasilvadiniz/lnc_test/work/6f/ae7db246096135d72b0ed76046b27f

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

Thanks,

Wellison