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rsa-tools / rsat-code

This repo contains the code required to run a local version of the software suite Regulatory Sequence Analysis Tools (RSAT).
http://rsat.eu
GNU Affero General Public License v3.0
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can't call get_attribute #4

Closed Ajeet1699 closed 4 weeks ago

Ajeet1699 commented 3 years ago

hi

When i am running peak-motifs, it gives me the following error:

./rsat peak-motifs -i myreg.fna -ctrl gn.rm.fna -motif_db footDB transfac ~/packages/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -prefix peaks -outdir outs -disco oligos,dyads -nmotifs 5 -minol 6 -maxol 8 -scan_markov 1 -noov -img_format png -task purge,seqlen,composition,disco,merge_motifs,split_motifs,timelog,motifs_vs_db,synthesis,small_summary,clean_seq

"# sequence length: 29383, number of masked symbols: 2157 (7.34 percent of the sequences)" "# sequence length: 138906, number of masked symbols: 9319 (6.71 percent of the sequences)" ; WARNING Number of patterns = 118. Exceeds top number = 100. Only the top 100 patterns will be assembled. Can't call method "get_attribute" on an undefined value at /home/mohini/packages/rsat/perl-scripts/lib/RSAT/MatrixAlignment.pm line 273. Can't call method "get_attribute" on an undefined value at /home/mohini/packages/rsat/perl-scripts/lib/RSAT/MatrixAlignment.pm line 273. Can't call method "get_attribute" on an undefined value at /home/mohini/packages/rsat/perl-scripts/lib/RSAT/MatrixAlignment.pm line 273.

santanaw commented 3 years ago

Hi Ajeet,

Many thanks for reporting this.

1) Could you manually double-check that the file ~/packages/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf contains relevant information?

2) In order to obtain a better insight of the problem, could you share the log file of this peak-motif run? This would be inside your output directory: "outs/reports/*_log.txt"

Best,

Walter

Ajeet1699 commented 3 years ago

Thanks for the response. "contains relevant information" means availability of plant species? That is (Prunus persica) available in footprintDB.plants.motif.tf.

Please find attached both files peaks_log.txt footprintDB.plants.motif.tf.txt

santanaw commented 3 years ago

Hi Ajeet,

Thanks for this information.

1) Regarding the footprintDB.plants.motif.tf file, I wanted to make sure that it indeed contained information of motifs as the current issue so far seems to be linked to the comparison step between the discovered motifs ("outs/results/discovered_motifs/dyads_test_vs_ctrl_m4/peaks_dyads_test_vs_ctrl_m4.tf") and the motif database footprintDB.plants.motif.tf .

2) If convenient for you, can I have both input files "myreg.fna" and "gn.rm.fna" to reproduce the error? This can also be sent to the rsat-contact mail if needed to be shared privately.

Best,

Walter

Ajeet1699 commented 3 years ago

Dear Walter, Thanks for your kind reply. Please find attached "myreg.fna" and "gn.rm.fna" files. Also I want to ask you if I can use peak-motifs for Chlamydomonas reinhardtii? Can you suggest any gn.rm.fna https://drive.google.com/file/d/1cOjF63VGIsaAhbx2tzhy5xLTHP-JSHBr/view?usp=drive_web motif database for Chlamydomonas reinhardtii?

Thanks and regards

On Mon, May 3, 2021 at 7:19 PM Walter Santana @.***> wrote:

Hi Ajeet,

Thanks for this information.

1.

Regarding the footprintDB.plants.motif.tf file, I wanted to make sure that it indeed contained information of motifs as the current issue so far seems to be linked to the comparison step between the discovered motifs ("outs/results/discovered_motifs/dyads_test_vs_ctrl_m4/ peaks_dyads_test_vs_ctrl_m4.tf") and the motif database footprintDB.plants.motif.tf . 2.

If convenient for you, can I have both input files "myreg.fna" and "gn.rm.fna" to reproduce the error? This can also be sent to the rsat-contact mail if needed to be shared privately.

Best,

Walter

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santanaw commented 3 years ago

Hi Ajeet,

Looking into this file file link, I noticed that it is only the "myreg.fna" file but the "gn.rm.fna" wasn't shared.

It is indeed possible to use the installed genome of Chlamydomonas reinhardtii in the RSAT Plants server for your peak-motifs analysis. In particular you can: (i) retrieve all the fasta interval sequences of interest from the Chlamydomonas reinhardtii genome using retrieve-seq-bed and (ii) input these sequences to peak-motifs to discover relevant motifs .

More information of available installed plants genomes can be found at http://rsat.eead.csic.es/plants/supported-organisms.cgi .

Regarding a motif database to use, the JASPAR plants collections could also be useful.

Kind regards

brunocontrerasmoreira commented 3 years ago

Hi, just adding that http://rsat.eead.csic.es/plants/motif_databases/footprintDB/footprintDB.plants.motif.tf is a non-redundant collection of plant motifs. It includes many from JASPAR, but also from other sources (see http://floresta.eead.csic.es/footprintdb/index.php), Bruno

Ajeet1699 commented 3 years ago

Hi Walter

Please find the attached gn.rm.fna https://drive.google.com/file/d/1IPVHswfNj7SV3DKD9nyhWiqFCocrRVGa/view?usp=drive_web "gn.rm.fna" file.

On Thu, May 6, 2021 at 11:09 PM brunocontrerasmoreira < @.***> wrote:

Hi, just adding that http://rsat.eead.csic.es/plants/motif_databases/footprintDB/footprintDB.plants.motif.tf is a non-redundant collection of plant motifs. It includes many from JASPAR, but also from other sources (see http://floresta.eead.csic.es/footprintdb/index.php), Bruno

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santanaw commented 3 years ago

Hi Ajeet,

Apologies, it was the opposite way. Could you please upload the "myreg.fna" file?

Thanks

Ajeet1699 commented 3 years ago

Hi Walter.

Please find the attached file. Thanks myreg.fna.txt On Fri, May 7, 2021 at 2:02 PM Walter Santana @.***> wrote:

Hi Ajeet,

Apologies, it was the opposite way. Could you please upload the "myreg.fna" file?

Thanks

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