Problems related to gffread

[spficklin]

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.

1. 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.
2. 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.