Error in renaming and classification

[drwazeem]

I'm facing the problem (likely related to grep (Discussed here probably: #41 (comment) ) as an empty file is generated) since a few days. Could you please have a look and check if everything is okay. The commands and the output are given below:

Error executing process > 'Summary_renaming_and_classification (1)'

Caused by:
 Process `Summary_renaming_and_classification (1)` terminated with an error exit status (1)

Command executed:

 set -o pipefail
 gffcompare -G -o filter                     -r know_lnc.gtf                     -p 3 novel.lncRNA.stringent.gtf
 awk '$3 =="u"||$3=="x"{print $5}' filter.novel.lncRNA.stringent.gtf.tmap |sort|uniq|                     perl /media/wazeem/82346450346448ED/lncpipe/LncPipe/bin/extract_gtf_by_name.pl novel.lncRNA.stringent.gtf - > novel.lncRNA.stringent.filter.gtf
 
 #rename lncRNAs according to neighbouring protein coding genes
 awk '$3 =="gene"{print }' known_coding.gtf | perl -F'\t' -lane '$F[8]=~/gene_id "(.*?)";/ && print join qq{\t},@F[0,3,4],$1,@F[5,6,1,2,7,8,9]' - |             sort-bed - > gencode.protein_coding.gene.bed
 gtf2bed < novel.lncRNA.stringent.filter.gtf |sort-bed - > novel.lncRNA.stringent.filter.bed
 gtf2bed < know_lnc.gtf |sort-bed - > known.lncRNA.bed
 perl /media/wazeem/82346450346448ED/lncpipe/LncPipe/bin/rename_lncRNA_2.pl non_human_mod.gtf
 # mv lncRNA.final.v2.gtf all_lncRNA_for_classifier.gtf
 grep -v 'gene_id "NA-' lncRNA.final.v2.gtf > all_lncRNA_for_classifier.gtf
 perl /media/wazeem/82346450346448ED/lncpipe/LncPipe/bin/rename_proteincoding.pl known_coding.gtf> protein_coding.final.gtf
 cat all_lncRNA_for_classifier.gtf protein_coding.final.gtf > final_all.gtf
 gffread final_all.gtf -g GRCm38.primary_assembly.chr_only.fa -w final_all.fa -W
 gffread all_lncRNA_for_classifier.gtf -g GRCm38.primary_assembly.chr_only.fa -w lncRNA.fa -W
 gffread protein_coding.final.gtf -g GRCm38.primary_assembly.chr_only.fa -w protein_coding.fa -W
 #classification 
 perl /media/wazeem/82346450346448ED/lncpipe/LncPipe/bin/lincRNA_classification.pl all_lncRNA_for_classifier.gtf known_coding.gtf lncRNA_classification.txt

Command exit status:
 1

Command output:
 (empty)

Command error:
   18856 reference transcripts loaded.
   74 duplicate reference transcripts discarded.
   655 query transfrags loaded.

Work dir:
 /media/wazeem/82346450346448ED/lncpipe/LncPipe/work/22/39af242ea431e3e89321040f827330

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` 
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