ERROR ~ Error executing process > 'DENSE_WF:DENSE:EXTRACT_CDS (18)'

[Xillanne]

I'm using fna and gff3 dowload via dataset from NCBI. Three of my genomes invoque the same issue, I don't know what to do. Can you please help me.

Caused by:
Process DENSE_WF:DENSE:EXTRACT_CDS (18) terminated with an error exit status (134)

Command executed:

chmod -R +x /home/desmarais/.nextflow/assets/i2bc/dense/bin

Use GffRead.

Need a fai index

samtools faidx Mayamaea_pseudoterrestris.fna

Keep GFF sequences that are also in the FASTA file.

awk 'BEGIN{FS=OFS=" "} {print "^"$1,""} END {print "^#"}' Mayamaea_pseudoterrestris.fna.fai | grep -f - Mayamaea_pseudoterrestris.gff3 > gff_filterA

Also remove mRNA with undefined strand and features with abnormal end

awk -F" '.next" '
FNR==NR {max[$1]=$2}
FNR!= NR && ( /^#/ || ($7 !~ /?/ && $5 <= max[$1]) )
' Mayamaea_pseudoterrestris.fna.fai gff_filterA > gff_filterB

Extract the genomic CDS.

-V discard any mRNAs with CDS having in-frame stop codons

-x : write a fasta file with spliced CDS for each GFF transcript

gffread -V -g Mayamaea_pseudoterrestris.fna -x Mayamaea_pseudoterrestris_CDS.fna gff_filterB

Remove CDS missing a terminal stop codon and get a translated version of the FASTA.

discard_CDS_missing_terminal_stop_codon.sh Mayamaea_pseudoterrestris_CDS.fna

Command exit status:
134

Command output:
(empty)

Command error:
free(): invalid next size (normal)
.command.sh: line 21: 72 Aborted gffread -V -g Mayamaea_pseudoterrestris.fna -x Mayamaea_pseudoterrestris_CDS.fna gff_filterB

Work dir:
/data/desmarais/PlastiDia/DENSE/work/88/e57bcaa319205ab5843415784d4dac

Container:
/home/desmarais/.nextflow/assets/i2bc/dense/containers/lopesi2bc-denovogenes.img

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

-- Check '.nextflow.log' file for details