./feelnc_codpot_out//tmp//19973_codpot.coding_size1_kmerCounting.tmp': No such file

[csittz]

Hi, may i know if this is a bug or something wrong with my input?

FEELnc_filter.pl -i LlncRNA.detected.merged.gtf -a gencode.v49wLnc5.2.gtf -b transcript_biotype=protein_coding -p 4 --linconly -s 200 > candidates.feelnc.filt.gtf

FEELnc_codpot.pl -i candidates.feelnc.filt.gtf -a gencode.v49wLnc5.2.gtf  -g GRCh38.primary_assembly.genome.fa -b transcript_biotype=protein_coding -b transcript_status=KNOWN --mode=intergenic -p 8 -o codpot --kmer="1,2,3,6,9,12"

i tried also using "--mode=shuffle" as well as providing "-l lncipedia_5_2_hg38.gtf" but all gave me some similar error message that tmp file not found.

        Your input GTF file 'candidates.feelnc.filt.gtf' contains *183899* transcripts
        Extracting ORFs/cDNAs 183893/183899...
        Extracted '183893' ORF/cDNAs sequences on '183899'.
> Run random Forest on './feelnc_codpot_out//tmp//19973_codpot.test_rna.fa'
        1. Compute the size of each sequence and ORF
        2. Compute the kmer ratio for each kmer and put the output file name in a list
Error! Cannot open kmerFile './feelnc_codpot_out//tmp//19973_codpot.coding_size1_kmerCounting.tmp': No such file or directory at /home/FEELnc/lib/RandomForest.pm line 154.