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sebc31 / P-GRe

P-GRe is a software allowing the prediction of the positions of pseudogenes and their structures on a genome scale.
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When using the test data, an error occurred. #2

Closed chhhhai closed 6 months ago

chhhhai commented 6 months ago

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.

sebc31 commented 6 months ago

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)

[ https://github.com/sebc31/P-GRe/issues/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 [ https://github.com/sebc31/P-GRe/issues/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.

— Reply to this email directly, [ https://github.com/sebc31/P-GRe/issues/2 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/A6QCFGFXUSFG5C6WZSNCS3TY7BSPJAVCNFSM6AAAAABGX7S2B6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGI3DENJQGU3TIMI | unsubscribe ] . You are receiving this because you are subscribed to this thread. Message ID: @.***>

chhhhai commented 6 months ago

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 (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 <<

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 The details of the error can be found in the attachment.

PGRe_BASNI_step.err.txt

sebc31 commented 6 months ago

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. [ https://github.com/sebc31/P-GRe/issues/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

[ https://github.com/sebc31/P-GRe/issues/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 ]

— Reply to this email directly, [ https://github.com/sebc31/P-GRe/issues/2#issuecomment-2076478990 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/A6QCFGHNO2W7BNQWTGZ75NTY7CQVDAVCNFSM6AAAAABGX7S2B6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZWGQ3TQOJZGA | unsubscribe ] . You are receiving this because you commented. Message ID: @.***>

chhhhai commented 6 months ago

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. PGRe_25_04_2024_15h_50m_00s.zip

chhhhai commented 6 months ago

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. error

sebc31 commented 6 months ago

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) ]

— Reply to this email directly, [ https://github.com/sebc31/P-GRe/issues/2#issuecomment-2076605975 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/A6QCFGBOS7X573JI5K47NTDY7C2IBAVCNFSM6AAAAABGX7S2B6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZWGYYDKOJXGU | unsubscribe ] . You are receiving this because you commented. Message ID: @.***>

chhhhai commented 6 months ago

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) ] — Reply to this email directly, [ #2 (comment) | view it on GitHub ] , or [ 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?

sebc31 commented 6 months ago

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 [ https://github.com/sebc31/P-GRe/issues/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, [ [ https://github.com/sebc31/P-GRe/issues/2#issuecomment-2076605975 | #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?

— Reply to this email directly, [ https://github.com/sebc31/P-GRe/issues/2#issuecomment-2076674989 | view it on GitHub ] , or [ https://github.com/notifications/unsubscribe-auth/A6QCFGFVNM6QFMSVV4TBHDLY7C637AVCNFSM6AAAAABGX7S2B6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZWGY3TIOJYHE | unsubscribe ] . You are receiving this because you commented. Message ID: < @.*** >

chhhhai commented 6 months ago

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. PGRe_pseudogene_construct_step.err.txt error