Converting to GFF3 Format fails

[Ghanizadeh1980]

Hi Brian,

I have followed the steps outlined in "https://evidencemodeler.github.io/", however, when I execute the command "convert_EVM_outputs_to_GFF3.pl", this error message pops up:

// Processing contig_11083, /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083
Error, cannot open /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083/evm.out
Error, cmd /home/dieter/EVidenceModeler-1.1.1/EvmUtils/EVM_to_GFF3.pl /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083/evm.out contig_11083 > /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083/evm.out.gff3 died with ret 512 at ./convert_EVM_outputs_to_GFF3.pl line 64.

The EMV.out.log file corresponding to contig_11083 says :
"-successfully changed directories to /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)
-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)
-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -) -no exons in range 1 - 17347"

Can you please help me with this? Thanks.

Cheers,

Hossein.

[brianjohnhaas]

Hi, That is peculiar. You'd expect to have at least an empty output file if there's no result. You can try: touch /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083/evm.out and then rerun the conversion script and see if that helps. best, ~b

…

On Tue, Oct 25, 2022 at 5:49 AM Ghanizadeh1980 ***@***.***> wrote: Hi Brian, I have followed the steps outlined in "https://evidencemodeler.github.io/", however, when I execute the command "convert_EVM_outputs_to_GFF3.pl", this error message pops up: // Processing contig_11083, /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083 Error, cannot open /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083/evm.out Error, cmd /home/dieter/EVidenceModeler-1.1.1/EvmUtils/EVM_to_GFF3.pl /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083/evm.out contig_11083 > /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083/evm.out.gff3 died with ret 512 at ./convert_EVM_outputs_to_GFF3.pl line 64. The EMV.out.log file corresponding to contig_11083 says : "-successfully changed directories to /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_11083 -reading genomic sequence. ** Processing features (+) -finding all potential splice sites, looking for GT/GC donors and AG acceptors. -finding all potential starts and stops. (strand: +) -loading gene prediction evidence. (strand: +) -loading the search evidence (protein and EST search results, strand: +) -scoring exons (strand: +) ** Processing features (-) -finding all potential splice sites, looking for GT/GC donors and AG acceptors. -finding all potential starts and stops. (strand: -) -loading gene prediction evidence. (strand: -) -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -) -no exons in range 1 - 17347" Can you please help me with this? Thanks. Cheers, Hossein. — Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX4MPEU7SVUPUPGHBT3WE6UI5ANCNFSM6AAAAAARNZJF6I> . 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>

[Ghanizadeh1980]

Hi Brian,

Thanks for your reply. There is an empty output in the folder corresponding to that contig. I followed your instruction, and now I get the same error for another contig (see below , please):
"./convert_EVM_outputs_to_GFF3.pl --partitions /home/dieter/GB/partitions_list.out --output evm.out --genome /home/dieter/GB/medaka/consensus.fasta
// Processing contig_10017, /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017
Error, cannot open /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/evm.out
Error, cmd /home/dieter/EVidenceModeler-1.1.1/EvmUtils/EVM_to_GFF3.pl /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/evm.out contig_10017 > /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/evm.out.gff3 died with ret 512 at ./convert_EVM_outputs_to_GFF3.pl line 64."

If I repeatedly execute the command, I end up with the same error message for some other contigs with no exons. There is also an empty output in the folder corresponding to the contigs with no exons.

Could this be a bug?

Cheers,

Hossein.

[brianjohnhaas]

I wonder if something happened when running the individual commands. Are you sure that all the commands completed successfully? I'd also think it was a bug, but the code hasn't changed in years and there haven't been other reports, but lots of successful uses. best, ~b

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On Tue, Oct 25, 2022 at 1:43 PM Ghanizadeh1980 ***@***.***> wrote: Hi Brian, Thanks for your reply. There is an empty output in the folder corresponding to that contig. I followed your instruction, and now I get the same error for another contig (see below , please): "./convert_EVM_outputs_to_GFF3.pl --partitions /home/dieter/GB/partitions_list.out --output evm.out --genome /home/dieter/GB/medaka/consensus.fasta // Processing contig_10017, /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017 Error, cannot open /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/evm.out Error, cmd /home/dieter/EVidenceModeler-1.1.1/EvmUtils/EVM_to_GFF3.pl /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/evm.out contig_10017 > /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/evm.out.gff3 died with ret 512 at ./convert_EVM_outputs_to_GFF3.pl line 64." If I repeatedly execute the command, I end up with the same error message for some other contigs with no exons. There is also an empty output in the folder corresponding to the contigs with no exons. Could this be a bug? Cheers, Hossein. — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX73SI6NYXAQZJ72VBDWFAL3LANCNFSM6AAAAAARNZJF6I> . You are receiving this because you commented.Message ID: ***@***.***>

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

[Ghanizadeh1980]

Below is the log for the contig_10017 as an example. I assume a "zero" means success and the command completed successfully.

#18062 0 /home/dieter/EVidenceModeler-1.1.1/EvmUtils/.././evidence_modeler.pl -G consensus.fasta -g newGB2.gff3 -w /home/dieter/GB/weight.txt -e GBPASA.gff3 --exec_dir /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017 > /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/EVM.out 2> /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/EVM.out.log

[brianjohnhaas]

Yes, zero would be success. That command should be writing to the output file EVM.out. Is that one of the files that was missing?

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On Tue, Oct 25, 2022 at 1:58 PM Ghanizadeh1980 ***@***.***> wrote: Below is the log for the contig_10017 as an example. I assume a "zero" means success and the command completed successfully. #18062 0 /home/dieter/EVidenceModeler-1.1.1/EvmUtils/.././evidence_modeler.pl -G consensus.fasta -g newGB2.gff3 -w /home/dieter/GB/weight.txt -e GBPASA.gff3 --exec_dir /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017 > /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/EVM.out 2> /home/dieter/EVidenceModeler-1.1.1/EvmUtils/contig_10017/EVM.out.log — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas

[Ghanizadeh1980]

The file is not missing, but it is empty. Can you please take a look at my commands and let me know if anything is missing?

./partition_EVM_inputs.pl --genome /home/dieter/GB/medaka/consensus.fasta --gene_predictions /home/dieter/GB/GFF/newGB2.gff3 --transcript_alignments /home/dieter/GB/PASA/GBPASA.gff3 --segmentSize 1000000 --overlapSize 200000 --partition_listing /home/dieter/GB/partitions_list.out

./write_EVM_commands.pl --genome /home/dieter/GB/repeatmasker1/consensus.fasta --weights /home/dieter/GB/weight.txt --gene_predictions /home/dieter/GB/GFF/newGB2.gff3 --transcript_alignments /home/dieter/GB/PASA/GBPASA.gff3 --output_file_name EVM.out --partitions /home/dieter/GB/partitions_list.out > /home/dieter/GB/GBEvidencemodeller/GBnanocommands.list

./execute_EVM_commands.pl /home/dieter/GB/GBEvidencemodeller/GBnanocommands.list | tee run.log

./recombine_EVM_partial_outputs.pl --output_file_name EVM.out --partitions /home/dieter/GB/partitions_list.out

./convert_EVM_outputs_to_GFF3.pl --partitions /home/dieter/GB/partitions_list.out --output evm.out --genome /home/dieter/GB/medaka/consensus.fasta

[Ghanizadeh1980]

Aha, I fixed it. It was a foolish mistake. the "--output" option in the last command line, and it should read "--output EVM.out". Sorry for that.

Thanks, Brian.

[brianjohnhaas]

Glad you figured it out. Best of luck! ~brian

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On Tue, Oct 25, 2022 at 3:01 PM Ghanizadeh1980 ***@***.***> wrote: Aha, I fixed it. It was a foolish mistake. the "--output" option in the last command line, and it should read "--output EVM.out". Sorry for that. Thanks, Brian. — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX5SAKURQNALWAPDDOLWFAVB7ANCNFSM6AAAAAARNZJF6I> . You are receiving this because you commented.Message ID: ***@***.***>

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