When using the test data, an error occurred. #2
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Hello,
Sorry about that. I don't use GitHub much and I didn't know that it replaced tabs with spaces if you didn't touch the drop-down menu at the top! I changed it and it works fine now.
Have a nice day,
De: "aichhhh" ***@***.***>
À: "sebc31/P-GRe" ***@***.***>
Cc: "Subscribed" ***@***.***>
Envoyé: Jeudi 25 Avril 2024 04:24:52
Objet: [sebc31/P-GRe] When using the test data, an error occurred. (Issue #2)
[ #1 | #1 ] (achhhhh) ***@***.***:~/data/ach/software/P-GRe$ ./P-GRe_pipeline.sh -f /home/xiajh2/data/ach/software/P-GRe/example/Arabidopsis_thaliana_Chromosome1_partial.fasta -g /home/xiajh2/data/ach/software/P-GRe/example/Arabidopsis_thaliana_Chromosome1_partial.gff
> Parsing: OK <<
> Filtering: OK <<
> Overlaping: OK <<
> Writing TSV: OK /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_10h_16m_40s/tmp/tblastn_results.tempfile.tsv <<
> FASTA writing: OK /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_10h_16m_40s/tmp/first_pg_set.tempfile.fasta <<
pg generation:
> BLAST parsing: OK <<
> PG generation: 0.00000% <<
pg generation: Error, check: /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_10h_16m_40s/log/PGRe_pseudogene_construct_step.err
[ #2 | #2 ] The details of the error can be found in the attachment.
[ https://github.com/sebc31/P-GRe/files/15103187/PGRe_pseudogene_construct_step.err.txt | PGRe_pseudogene_construct_step.err.txt ]
I suspect there might be an issue with your gff file, but even after I modified it using tab characters, the error persists. I would appreciate it if you could check both your test data and your code.
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I'm glad you've adjusted the format of the gff file, but I've encountered a new error when using the test data. Could you please take a look at it again? #2 The details of the error can be found in the attachment. |
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Hello,
It works fine for me. I did a pull to update the script where you add the error, maybe they were some unsaved changed. Tell me if you encounter other errors.
Have a nice day,
De: "aichhhh" ***@***.***>
À: "sebc31/P-GRe" ***@***.***>
Cc: "Sébastien Cabanac" ***@***.***>, "Comment" ***@***.***>
Envoyé: Jeudi 25 Avril 2024 08:42:25
Objet: Re: [sebc31/P-GRe] When using the test data, an error occurred. (Issue #2)
I'm glad you've adjusted the format of the gff file, but I've encountered a new error when using the test data. Could you please take a look at it again?
Here is the log of the runtime error.
[ #1 | #1 ] (achhhhh) ***@***.***:~/data/ach/software/P-GRe$ ./P-GRe_pipeline.sh -f /home/xiajh2/data/ach/software/P-GRe/example/Arabidopsis_thaliana_Chromosome1_partial.fasta -g /home/xiajh2/data/ach/software/P-GRe/example/Arabidopsis_thaliana_Chromosome1_partial.gff
> Parsing: OK <<
> Filtering: OK <<
filtering hits:Error, check: /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_14h_37m_24s/log/PGRe_BASNI_step.err
[ #2 | #2 ] The details of the error can be found in the attachment.
[ https://github.com/sebc31/P-GRe/files/15105358/PGRe_BASNI_step.err.txt | PGRe_BASNI_step.err.txt ]
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Thank you very much. I am pleased to inform you that it appears to be working now. Please see the attached output file from my run. It seems that the true_genes.id provided in your sequences was not detected. |
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There's one more bug I need to bring to your attention: the folder name "scripts" under the P-GRe directory needs to be changed to "script", otherwise it will conflict with "./P-GRe_pipeline.sh". Please find attached a screenshot of the error. |
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Thanks you. I was aware of this bug, I intended to correct it in the next big update of P-GRe (to be honest I did not think that several people would use P-GRe so quickly even though it is not yet published).
De: "aichhhh" ***@***.***>
À: "sebc31/P-GRe" ***@***.***>
Cc: "Sébastien Cabanac" ***@***.***>, "Comment" ***@***.***>
Envoyé: Jeudi 25 Avril 2024 10:04:16
Objet: Re: [sebc31/P-GRe] When using the test data, an error occurred. (Issue #2)
There's one more bug I need to bring to your attention: the folder name "scripts" under the P-GRe directory needs to be changed to "script", otherwise it will conflict with "./P-GRe_pipeline.sh". Please find attached a screenshot of the error.
[ https://github.com/sebc31/P-GRe/assets/99796066/9d9cfe38-8e36-4808-8ff1-3b9bdfead1cf | error.jpg (view on web) ]
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Ha ha, I just happened to come across your software and it seems to fit my needs perfectly, as I am currently working on pseudogene identification in eukaryotes. There's one question you haven't answered yet: do you think the output file I obtained using your test data is okay? Are there any issues with it? |
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Looks good. The example data only contains one pseudogene that I found on A. thaliana, as it was an "interesting" case with multiple frameshift, a start and a stop codon.
De: "aichhhh" ***@***.***>
À: "sebc31/P-GRe" ***@***.***>
Cc: "Sébastien Cabanac" ***@***.***>, "Comment" ***@***.***>
Envoyé: Jeudi 25 Avril 2024 10:43:43
Objet: Re: [sebc31/P-GRe] When using the test data, an error occurred. (Issue #2)
Thanks you. I was aware of this bug, I intended to correct it in the next big update of P-GRe (to be honest I did not think that several people would use P-GRe so quickly even though it is not yet published). De: "aichhhh" @ . > À: "sebc31/P-GRe" @ . > Cc: "Sébastien Cabanac" @ . >, "Comment" @ . > Envoyé: Jeudi 25 Avril 2024 10:04:16 Objet: Re: [sebc31/P-GRe] When using the test data, an error occurred. (Issue [ #2 | #2 ] ) There's one more bug I need to bring to your attention: the folder name "scripts" under the P-GRe directory needs to be changed to "script", otherwise it will conflict with "./P-GRe_pipeline.sh". Please find attached a screenshot of the error. [ [ https://github.com/sebc31/P-GRe/assets/99796066/9d9cfe38-8e36-4808-8ff1-3b9bdfead1cf | https://github.com/sebc31/P-GRe/assets/99796066/9d9cfe38-8e36-4808-8ff1-3b9bdfead1cf ] | error.jpg (view on web) ] — Reply to this email directly, [ [ #2 (comment) | #2 (comment) ] | view it on GitHub ] , or [ [ https://github.com/notifications/unsubscribe-auth/A6QCFGBOS7X573JI5K47NTDY7C2IBAVCNFSM6AAAAABGX7S2B6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZWGYYDKOJXGU | https://github.com/notifications/unsubscribe-auth/A6QCFGBOS7X573JI5K47NTDY7C2IBAVCNFSM6AAAAABGX7S2B6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZWGYYDKOJXGU ] | unsubscribe ] . You are receiving this because you commented. Message ID: @ .***>
Ha ha, I just happened to come across your software and it seems to fit my needs perfectly, as I am currently working on pseudogene identification in eukaryotes.
There's one question you haven't answered yet: do you think the output file I obtained using your test data is okay? Are there any issues with it?
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I apologize for bothering you again. My previous work with the test data proceeded without any issues, but now I encounter errors when using my own data. Please see the attached file for the details of these errors. If necessary, I can also send you a copy of my data so that you might examine it and identify the root cause of these problems. It is worth mentioning that my GFF3 file was annotated using BRAKER. |
#1 (achhhhh) xiajh2@xiajh2:~/data/ach/software/P-GRe$ ./P-GRe_pipeline.sh -f /home/xiajh2/data/ach/software/P-GRe/example/Arabidopsis_thaliana_Chromosome1_partial.fasta -g /home/xiajh2/data/ach/software/P-GRe/example/Arabidopsis_thaliana_Chromosome1_partial.gff
>> Parsing: OK <<
>> Filtering: OK <<
>> Overlaping: OK <<
>> Writing TSV: OK /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_10h_16m_40s/tmp/tblastn_results.tempfile.tsv <<
>> FASTA writing: OK /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_10h_16m_40s/tmp/first_pg_set.tempfile.fasta <<
pg generation:
>> BLAST parsing: OK <<
>> PG generation: 0.00000% <<
pg generation: Error, check: /home/xiajh2/data/ach/software/P-GRe/example/PGRe_25_04_2024_10h_16m_40s/log/PGRe_pseudogene_construct_step.err
#2 The details of the error can be found in the attachment.
PGRe_pseudogene_construct_step.err.txt
I suspect there might be an issue with your gff file, but even after I modified it using tab characters, the error persists. I would appreciate it if you could check both your test data and your code.
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