FATAL ERROR for pigeon sort about pbbioconda

[armintoepfer]

Please post all commands that you ran to reproduce this bug.

[oucstar]

conda activate PacBio
lima ../E.ccs.bam ../primers.fasta E.fl.bam --isoseq --peek-guess
lima ../M.ccs.bam ../primers.fasta M.fl.bam --isoseq --peek-guess
lima ../N.ccs.bam ../primers.fasta N.fl.bam --isoseq --peek-guess
lima ../P.ccs.bam ../primers.fasta P.fl.bam --isoseq --peek-guess
lima ../Z.ccs.bam ../primers.fasta Z.fl.bam --isoseq --peek-guess
ls E.fl.NEB_5p--NEB_Clontech_3p.bam M.fl.NEB_5p--NEB_Clontech_3p.bam N.fl.NEB_5p--NEB_Clontech_3p.bam P.fl.NEB_5p--NEB_Clontech_3p.bam Z.fl.NEB_5p--NEB_Clontech_3p.bam > all.fofn
isoseq3 refine all.fofn ../primers.fasta flnc.bam --require-polya --log-level DEBUG
isoseq3 cluster flnc.bam clustered.bam --use-qvs --verbose
pbmm2 align --preset ISOSEQ --sort outs1/clustered.bam shrimp.genome.fa mapped.bam
isoseq3 collapse --do-not-collapse-extra-5exons mapped.bam collapsed.gff
pigeon sort collapsed.gff -o sorted.gff
| 20230215 12:09:29.024 | FATAL | pigeon sort ERROR: 1 - could not read GFF file

[oucstar]

Thank you very much for your reply

[oucstar]

@armintoepfer ,
Sorry to bother you, I have a very confusing question. I used pigeon in isoseq3 to get the gtf file after the sorted isoforms, sorted.filtered_lite.gff file. But now I want to compare the length and numbers of transcripts between this output file and the gtf annotation file I input in terms of completeness. Do you have supporting software or parameters? Hope to get your reply, thank you very much!

[oucstar]

@armintoepfer @jmattick ,Sorry to bother you, but we have a question that has been bothering us for a long time. We have consulted a lot of data but failed to get an answer. I hope to get some effective reply here. It was obvious that there were new genes and transcripts identified by the pacbio full-length transcriptome, but I wanted to align this annotated file with the reference annotated file to make the genetic structure annotations more complete, but there was no evidencemodeler to do that. Unfortunately, evm did not retain these variable splicing bodies, which is a pity. Do you have any suggestions? Thank you very much for your help!

[armintoepfer]

@jmattick please have a look

[oucstar]

@jmattick ,Could you please answer my question

[armintoepfer]

We will get to it, when time allows.

[oucstar]

@armintoepfer ,Sorry to bother you, but we have a question that has been bothering us for a long time. We have consulted a lot of data but failed to get an answer. I hope to get some effective reply here. It was obvious that there were new genes and transcripts identified by the pacbio full-length transcriptome, but I wanted to align this annotated file with the reference annotated file to make the genetic structure annotations more complete, but there was no evidencemodeler to do that. Unfortunately, evm did not retain these variable splicing bodies, which is a pity. Do you have any suggestions? Thank you very much for your help!