Error during Transdecoder.Predict #207

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1. brianjohnhaas commented on Mar 3, 2026

   

   brianjohnhaas

   on Mar 3, 2026 via email

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   hi, my guess is that it ran out of RAM. You might need a greater RAM allocation for it.

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   On Tue, Mar 3, 2026 at 4:19 PM desmodus1984 ***@***.***> wrote: *desmodus1984* created an issue (TransDecoder/TransDecoder#207) <#207> Hi I am interested in refining my genome annotation, and I am using mikado, and it needs Transdecoder output. I installed it in conda, I ran TransDecoder.LongOrfs and it finished, TransDecoder.LongOrfs -t mikado_prepared.fasta -m 30 Then, I ran TransDecoder.Predict , and it mentioned an error, but it produced the bed and pep files. TransDecoder.Predict -t mikado_prepared.fasta --retain_long_orfs_length 30 * [Sun Mar 1 20:07:57 2026] Running CMD: /home/jpac1984/miniconda3/envs/annotation/bin/util/gff3_file_to_proteins.pl --gff3 /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.gff3 --fasta mikado_prepared.fasta --genetic_code Universal > /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.pep Making pep file: /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.pep Killed Error, cmd: /home/jpac1984/miniconda3/envs/annotation/bin/util/gff3_file_to_proteins.pl --gff3 /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.gff3 --fasta mikado_prepared.fasta --genetic_code Universal > /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.pep died with ret 35072 No such file or directory at /home/jpac1984/miniconda3/envs/annotation/bin/PerlLib/Pipeliner.pm line 187. Pipeliner::run(Pipeliner=HASH(0x5e078b76f340)) called at /home/jpac1984/miniconda3/envs/annotation/bin/TransDecoder.Predict line 369 I ran it on Linux tty. There are a bed and a pep, any way to check if those files are okay? Any reason why this happened and how to fix this? — Reply to this email directly, view it on GitHub <#207>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX4N4CONEH3PYGIODNL4O5D65AVCNFSM6AAAAACWF5LKSSVHI2DSMVQWIX3LMV43ASLTON2WKOZUGAYTQNZVGU3DAOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

   -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
2. desmodus1984 commented on Mar 3, 2026

   

   desmodus1984

   on Mar 3, 2026 via email

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   The file I was running has ~169.3K sequences, min length 200 and Max 1.5M. Could you tell how much memory it would require? I ran in on a workstation with 32 GB RAM. Thanks Juan Pablo

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   ________________________________ From: Brian Haas ***@***.***> Sent: Tuesday, March 3, 2026 5:19:42 PM To: TransDecoder/TransDecoder ***@***.***> Cc: Aguilar Cabezas, Juan Pablo ***@***.***>; Author ***@***.***> Subject: [External] Re: [TransDecoder/TransDecoder] Error during Transdecoder.Predict (Issue #207) Use caution with links and attachments. [https://avatars.githubusercontent.com/u/7542111?s=20&v=4]brianjohnhaas left a comment (TransDecoder/TransDecoder#207)<#207 (comment)> hi, my guess is that it ran out of RAM. You might need a greater RAM allocation for it.

   On Tue, Mar 3, 2026 at 4:19 PM desmodus1984 ***@***.***> wrote: *desmodus1984* created an issue (TransDecoder/TransDecoder#207) <#207> Hi I am interested in refining my genome annotation, and I am using mikado, and it needs Transdecoder output. I installed it in conda, I ran TransDecoder.LongOrfs and it finished, TransDecoder.LongOrfs -t mikado_prepared.fasta -m 30 Then, I ran TransDecoder.Predict , and it mentioned an error, but it produced the bed and pep files. TransDecoder.Predict -t mikado_prepared.fasta --retain_long_orfs_length 30 * [Sun Mar 1 20:07:57 2026] Running CMD: /home/jpac1984/miniconda3/envs/annotation/bin/util/gff3_file_to_proteins.pl --gff3 /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.gff3 --fasta mikado_prepared.fasta --genetic_code Universal > /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.pep Making pep file: /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.pep Killed Error, cmd: /home/jpac1984/miniconda3/envs/annotation/bin/util/gff3_file_to_proteins.pl --gff3 /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.gff3 --fasta mikado_prepared.fasta --genetic_code Universal > /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.pep died with ret 35072 No such file or directory at /home/jpac1984/miniconda3/envs/annotation/bin/PerlLib/Pipeliner.pm line 187. Pipeliner::run(Pipeliner=HASH(0x5e078b76f340)) called at /home/jpac1984/miniconda3/envs/annotation/bin/TransDecoder.Predict line 369 I ran it on Linux tty. There are a bed and a pep, any way to check if those files are okay? Any reason why this happened and how to fix this? — Reply to this email directly, view it on GitHub <#207>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX4N4CONEH3PYGIODNL4O5D65AVCNFSM6AAAAACWF5LKSSVHI2DSMVQWIX3LMV43ASLTON2WKOZUGAYTQNZVGU3DAOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

   -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> — Reply to this email directly, view it on GitHub<#207 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AJWD2VLDLDPLK4Y2XH7G2R34O5K6VAVCNFSM6AAAAACWF5LKSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSOJTHEZDENBXGQ>. You are receiving this because you authored the thread.
3. brianjohnhaas commented on Mar 3, 2026

   

   brianjohnhaas

   on Mar 3, 2026 via email

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   Hi Juan Pablo, I suspect the issue is related to the length of your sequences. TransDecoder expects transcript sequences as input, and any sequence around a megabase is unlikely to be a transcript. Additionally, using a short minimum ORF length of 30 residues will likely compound the problem and increase memory requirements. Best regards, Brian On Tue, Mar 3, 2026 at 5:24 PM desmodus1984 ***@***.***> wrote:

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   *desmodus1984* left a comment (TransDecoder/TransDecoder#207) <#207 (comment)> The file I was running has ~169.3K sequences, min length 200 and Max 1.5M. Could you tell how much memory it would require? I ran in on a workstation with 32 GB RAM. Thanks Juan Pablo ________________________________ From: Brian Haas ***@***.***> Sent: Tuesday, March 3, 2026 5:19:42 PM To: TransDecoder/TransDecoder ***@***.***> Cc: Aguilar Cabezas, Juan Pablo ***@***.***>; Author ***@***.***> Subject: [External] Re: [TransDecoder/TransDecoder] Error during Transdecoder.Predict (Issue #207) Use caution with links and attachments. [https://avatars.githubusercontent.com/u/7542111?s=20&v=4]brianjohnhaas left a comment (TransDecoder/TransDecoder#207)< #207 (comment)> hi, my guess is that it ran out of RAM. You might need a greater RAM allocation for it. On Tue, Mar 3, 2026 at 4:19 PM desmodus1984 ***@***.***> wrote: > *desmodus1984* created an issue (TransDecoder/TransDecoder#207) > <#207> > > Hi > > I am interested in refining my genome annotation, and I am using mikado, > and it needs Transdecoder output. > I installed it in conda, I ran TransDecoder.LongOrfs and it finished, > > TransDecoder.LongOrfs -t mikado_prepared.fasta -m 30 > > Then, I ran TransDecoder.Predict , and it mentioned an error, but it > produced the bed and pep files. > > TransDecoder.Predict -t mikado_prepared.fasta --retain_long_orfs_length 30 > > * [Sun Mar 1 20:07:57 2026] Running CMD: /home/jpac1984/miniconda3/envs/annotation/bin/util/ gff3_file_to_proteins.pl --gff3 /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.gff3 --fasta mikado_prepared.fasta --genetic_code Universal > /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.pep > Making pep file: /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.pep > Killed > Error, cmd: /home/jpac1984/miniconda3/envs/annotation/bin/util/ gff3_file_to_proteins.pl --gff3 /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.gff3 --fasta mikado_prepared.fasta --genetic_code Universal > /home/jpac1984/Lwed/mikado/mikado_prepared.fasta.transdecoder.pep died with ret 35072 No such file or directory at /home/jpac1984/miniconda3/envs/annotation/bin/PerlLib/Pipeliner.pm line 187. > Pipeliner::run(Pipeliner=HASH(0x5e078b76f340)) called at /home/jpac1984/miniconda3/envs/annotation/bin/TransDecoder.Predict line 369 > > I ran it on Linux tty. > There are a bed and a pep, any way to check if those files are okay? > Any reason why this happened and how to fix this? > > — > Reply to this email directly, view it on GitHub > <#207>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABZRKX4N4CONEH3PYGIODNL4O5D65AVCNFSM6AAAAACWF5LKSSVHI2DSMVQWIX3LMV43ASLTON2WKOZUGAYTQNZVGU3DAOI> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> — Reply to this email directly, view it on GitHub< #207 (comment)>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AJWD2VLDLDPLK4Y2XH7G2R34O5K6VAVCNFSM6AAAAACWF5LKSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSOJTHEZDENBXGQ>. You are receiving this because you authored the thread. — Reply to this email directly, view it on GitHub <#207 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX326JAC7253V5GM65L4O5LQJAVCNFSM6AAAAACWF5LKSSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTSOJTHE2DCMJXGI> . You are receiving this because you commented.Message ID: ***@***.***>

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