cdna_alignment_orf_to_genome_orf.pl - Error ... couldn't be fully propagated

[sjfleck]

I have a problem that's somewhat similar to the error in #110

my command is: cdna_alignment_orf_to_genome_orf.pl \ Trinity.fasta.transdecoder.gff3 \ Trinity.gff3 \ $TRINITY > $SAMPLE.fasta.transdecoder.genome.gff3

Because I needed to generate a gff3 for Trinity (only provides a fasta), I used PASA to create one: process_GMAP_alignments_gff3_chimeras_ok.pl \ --CPU 16 \ --genome $GENOME \ --transcripts $TRINITY > Trinity.gff3

Ultimately, $SAMPLE.fasta.transdecoder.genome.gff3 was generated (166.7 MB) and looks similar to when I did the same thing with HISAT2/StringTie when I look at each file side by side (HISAT2/StringTie did not generate any of the same error for cdna_alignment_orf_to_genome_orf.pl). I'll attach an example of the the error in a txt file.

Any help would be greatly appreciated. Thanks!

error.txt

[brianjohnhaas]

hi,

Was this a fatal error, or did it end up generating your final output?

I'm pretty sure this should be a warning and not a fatal error, even though it says 'error' in the message. You'll see these errors for any transcripts that contain orfs where the orf-containing part isn't within the aligned region of the transcript sequence.

best,

~b

On Mon, Oct 4, 2021 at 7:28 PM sjfleck @.***> wrote:

I have a problem that's somewhat similar to the error in #110 https://github.com/TransDecoder/TransDecoder/issues/110

my command is: cdna_alignment_orf_to_genome_orf.pl Trinity.fasta.transdecoder.gff3 Trinity.gff3 $TRINITY > $SAMPLE.fasta.transdecoder.genome.gff3

Because I needed to generate a gff3 for Trinity (only provides a fasta), I used PASA to create one: process_GMAP_alignments_gff3_chimeras_ok.pl --CPU 16 --genome $GENOME --transcripts $TRINITY > Trinity.gff3

Ultimately, $SAMPLE.fasta.transdecoder.genome.gff3 was generated (166.7 MB) and looks similar to when I did the same thing with HISAT2/StringTie when I look at each file side by side (HISAT2/StringTie did not generate any of the same error for cdna_alignment_orf_to_genome_orf.pl). I'll attach an example of the the error in a txt file.

Any help would be greatly appreciated. Thanks!

error.txt https://github.com/TransDecoder/TransDecoder/files/7281824/error.txt

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/TransDecoder/TransDecoder/issues/139, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX2C62J35HGVWTVRMGTUFI2CLANCNFSM5FKPCGNA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

[sjfleck]

It did produce my final output, $SAMPLE.fasta.transdecoder.genome.gff3. I just wanted to make sure I could trust this output. When I did a similar run using the output of HISAT2/StringTie, I only got errors like these:

StringTie: Warning [5295], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry STRG.9996.2.p1.

Trinity: Warning [46857], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry TRINITY_DN9_c0_g1_i89.p1.

While using the StringTie input, it only had 5,295 of these errors, the Trinity input gave me 46,857 of them. Trinity also gave 501 errors like: No paths found for TRINITY_DN57039_c0_g1_i1

and 4,684 of the type of error I attached to my original message.

I'm sure it won't be useful, but just in case it is, I attached all the alignment errors to this message. Thanks! error_all.txt

[brianjohnhaas]

I think it should be fine. It's just very noisy when it runs.

On Tue, Oct 5, 2021, 10:12 AM sjfleck @.***> wrote:

It did produce my final output, $SAMPLE.fasta.transdecoder.genome.gff3. I just wanted to make sure I could trust this output. When I did a similar run using the output of HISAT2/StringTie, I only got errors like these:

StringTie: Warning [5295], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry STRG.9996.2.p1.

Trinity: Warning [46857], shouldn't have a minus-strand ORF on a spliced transcript structure. Skipping entry TRINITY_DN9_c0_g1_i89.p1.

While using the StringTie input, it only had 5,295 of these errors, the Trinity input gave me 46,857 of them. Trinity also gave 501 errors like: No paths found for TRINITY_DN57039_c0_g1_i1

and 4,684 of the type of error I attached to my original message.

I'm sure it won't be useful, but just in case it is, I attached all the alignment errors to this message. Thanks! error_all.txt https://github.com/TransDecoder/TransDecoder/files/7286558/error_all.txt

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/TransDecoder/TransDecoder/issues/139#issuecomment-934451909, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3TK445IM4UVXNZTHDUFMBWJANCNFSM5FKPCGNA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.