Pigeon classify fails about pbbioconda

[sojichld]

found error

[armintoepfer]

It would be helpful if you document what was your problem and how you've fixed it.

[sojichld]

It was missing the gene_name field. In the example posted to the isoseq.how, while it begins similarly to my file, there is indeed a gene_name field in column 9, just a few entries farther down. The gtf that I was using did not have this field, and I overlooked that this is mentioned as one of the three required fields.

I used the following awk script to add a gene_name field, identical to what is listed in the transcript id field (subfield of $9) to each line of my file, and I was able to proceed after that:

awk 'BEGIN{FS=OFS="\t"} {if (split($9, arr, "transcript_id \"") > 1) {split(arr[2], id, "\""); $9 = $9 " gene_name \"" id[1] "\"";} print;}' input.gtf > output.gtf