empty output files in dataprep stage

[villegmb]

Hello. I am having problems with the output file from the dataprep stage. This is the code I am running:

xpore dataprep \
--eventalign /ibex/tmp/c2078/Heat_stress_analysis/xpore/data/25rep1/eventalign.txt \
--out_dir /ibex/tmp/c2078/Heat_stress_analysis/xpore/data/25rep1/dataprep \
--gtf_or_gff /ibex/tmp/c2078/Heat_stress_analysis/xpore/Ahem_transcriptome_with_reference.gtf \
--transcript_fasta /ibex/tmp/c2078/Heat_stress_analysis/scripts/transcripts_util_names_edited.fasta \
--genome \
--n_processes 24

This is my eventalign.txt file:

This is my gtf:

My Fasta:

And my dataprep directory looks like this:

Empty:

data.json: empty

This is from the running process:

Can you please tell me what am I doing wrong?

[yuukiiwa]

Hi @villegmb,

Can you try removing the sample column in your eventalign.txt file and run xpore dataprep again, please?

Thanks!

Best wishes,
Yuk Kei

[villegmb]

Hi @villegmb,

Can you try removing the sample column in your eventalign.txt file and run xpore dataprep again, please?

Thanks!

Best wishes, Yuk Kei

Hello, I did it, but the outcome did not change. I got exactly the same.

[yuukiiwa]

Hi @villegmb,

I suspect that this has to do with how the gene_id (STRG.8) and transcript_id (STRG.446.1) look like in your fasta and gtf files. Can you try changing the gene_id and transcript_id to be separated with _ instead of . in your fasta, gtf, and eventalign.txt files as a . is possibly recognized as transcript_version by xpore dataprep.

Thanks!

Best wishes,
Yuk Kei

[cent0134]

Hello, I have encountered the same problem as you. Have you solved it?

[cent0134]

Sorry, I didn't quite understand what you meant. Could you please show me your modified fasta and gft files? Thank you.

[villegmb]

Sorry. That project is closed and I no longer have access to those files. But the problem was that I was calling my transcripts like "STRG.446.1", but you should replace the dots with underscores "STRG_446_1"

…

On Mon, Jul 15, 2024 at 10:46 AM cent0134 ***@***.***> wrote: Sorry, I didn't quite understand what you meant. Could you please show me your modified fasta and gft files? Thank you. — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/GoekeLab/xpore/issues/214*issuecomment-2227884398__;Iw!!Nmw4Hv0!xAc1otmyoqrXodKR5WruFo7gIPuCfEKxcuIsKGTo6B3w5NUFIfRLzrQ0CgAMKrQ_pGmIhJTX7Z3APFmrQrBCnQGu8EdmFvZbZg$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/BDB2FFLBTHVPCYC6YNP4JXLZMN45PAVCNFSM6AAAAABK3XBYNWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRXHA4DIMZZHA__;!!Nmw4Hv0!xAc1otmyoqrXodKR5WruFo7gIPuCfEKxcuIsKGTo6B3w5NUFIfRLzrQ0CgAMKrQ_pGmIhJTX7Z3APFmrQrBCnQGu8EeIcU3AyQ$> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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