[BUG] IsoAnnotLite shows no transcripts were annotated despite running on provided ref gff3

[leewqa]

Is there an existing issue for this?

• I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• I have loaded the SQANTI3.env conda environment

Are you running SQANTI3 on its latest release?

• I have SQANTI3 updated to the latest release

Problem description

I am running IsoAnnotLite separately and am using the latest version of IsoAnnotLite ("2.7.3") but am getting no transcript annotation. The output of my statistical result looks like this:

 TRANSCRIPT-LEVEL SUMMARY

        ·A total of 0.00 % of transcripts in the GTF target annotation file (0 of 18016) were annotated because they matched a transcript ID in the GFF3 source annotation file (SQANTI FSM and ISM
).
        ·A total of 0.00 % of transcripts in the GTF target annotation file (0 of 18016) were not annotated because reference has no annotations.
        ·A total of 0.00 % of transcripts in the GTF target annotation file (0 of 18016) were not annotated by positional feature transference.

        ·A total of 0.00 % of transcripts in the GTF target annotation file (0 of 18016) do not match any of the transcript IDs in the GFF3 file (SQANTI novel transcripts).
            ·A total of 0.00 % novel transcripts (0 of 18016) were annotated by positional feature transference.
            ·A total of 0.00 % of novel transcripts (0 of 18016) were not annotated by any positional feature.
            ·A total of 100.00 % of novel transcripts in the GTF target annotation file (18016 of 18016) were not annotated because no gene name was returned by SQANTI output.
            ·A total of 0.00 % of novel transcripts in the GTF target annotation file (0 of 18016) were not annotated because gene ID was not found in GFF3 source annotation file.

        Global statistics:
        ·A total of 0.00 % of transcripts in the GTF target annotation file (0 of 18016) were annotated (at least one feature transferred).

I am using the TappAS gencode v39 ref (https://app.tappas.org/resources/downloads/gffs/Homo_sapiens_Gencode_v39.zip) and my sqanti3 output was ran on gencode v39 as well. I am using the sqanti3 corrected.gtf, classification.txt, and junctions.txt as stated too.

Any help would be greatly appreciated. I can email over my sqanti3 corrected.gtf file and code if that helps with debugging. Thanks a lot.

Best,
Audrey

Code sample

No response

Error

No response

Anything else?

No response

[pabloati]

Hi, I would appreciate if you could send the input files and the command you run, so I can take a look at them. Some times, isoAnnotLite gets a bit picky with the formats. Send them to pablo.atienza@csic.es

[leewqa]

I have sent the input files to your email. Thanks!