Over 150 genomes failed on the last run of pynome. On inspecting one of them (./2792677/ASM1369444v1-ncbi), there were problems creating the cDNA FASTA file.
- The genome assembly FASTA index file with extension
.fa.fai did not have the sequence names in the first column. Not sure what caused that.
- The cDNA file could not be created. Using the
gffread utility on Kamiak I got the following message Error: no ID found for GFF record start. It turns out there is a transcript_id = ""; entry in the gene feature of the GTF file. When I manually removed that entry for each gene the cDNA was built just fine.
Over 150 genomes failed on the last run of pynome. On inspecting one of them (./2792677/ASM1369444v1-ncbi), there were problems creating the cDNA FASTA file.
.fa.faidid not have the sequence names in the first column. Not sure what caused that.gffreadutility on Kamiak I got the following messageError: no ID found for GFF record start. It turns out there is atranscript_id = "";entry in thegenefeature of the GTF file. When I manually removed that entry for each gene the cDNA was built just fine.