Open scholtzb opened 1 year ago
Hi Beata, thank you for using riboWaltz. As you correctly reported, the message about the stop_codon is just a warning and can be ignored. About the error, I cannot really answer you. It's not clear to me which function of riboWaltz is arising the issue. In any case I'm not even sure I knew about riboWaltz being available in the Galaxy environment, and I'm not able to find it. Maybe it's because I'm not registered. Just to be sure could you please send me a link or an indication about where/how to find the tool in Galaxy.eu? I can try and test it to see if it works fine or not.
Best Fabio
Hi Fabio,
Thanks for the quick response. If you look at the Galaxy tools (https://usegalaxy-eu.github.io/tools.html), in the RNA Analysis folder, at the very end are some riboseq tools, including riboWaltz. It is not available at usegalaxy.org, if that's the one you checked - I am using galaxy.eu.
Thank you for looking into it,
Cheers,
Beata
Feladó: fabiolauria @.> Elküldve: 2023. június 14., szerda 16:19 Címzett: LabTranslationalArchitectomics/riboWaltz @.> Másolatot kap: Scholtz Beáta @.>; Author @.> Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi Beata, thank you for using riboWaltz. As you correctly reported, the message about the stop_codon is just a warning and can be ignored. About the error, I cannot really answer you. It's not clear to me which function of riboWaltz is arising the issue. In any case I'm not even sure I knew about riboWaltz being available in the Galaxy environment, and I'm not able to find it. Maybe it's because I'm not registered. Just to be sure could you please send me a link or an indication about where/how to find the tool in Galaxy.eu? I can try and test it to see if it works fine or not.
Best Fabio
— Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1591313052, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPMHVWRPJUV7SPGYRRDXLHB7RANCNFSM6AAAAAAZGAQMXQ. You are receiving this because you authored the thread.Message ID: @.***>
This is the link to my Galaxy History, if that helps:
url: https://usegalaxy.eu/u/scholtz/h/ribowaltz-trial https://usegalaxy.eu/u/scholtz/h/ribowaltz-trial
Cheers,
Beata
Feladó: Scholtz Beáta @.> Elküldve: 2023. június 14., szerda 16:27 Címzett: LabTranslationalArchitectomics/riboWaltz @.> Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
Hi Fabio,
Thanks for the quick response. If you look at the Galaxy tools (https://usegalaxy-eu.github.io/tools.html), in the RNA Analysis folder, at the very end are some riboseq tools, including riboWaltz. It is not available at usegalaxy.org, if that's the one you checked - I am using galaxy.eu.
Thank you for looking into it,
Cheers,
Beata
Feladó: fabiolauria @.> Elküldve: 2023. június 14., szerda 16:19 Címzett: LabTranslationalArchitectomics/riboWaltz @.> Másolatot kap: Scholtz Beáta @.>; Author @.> Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi Beata, thank you for using riboWaltz. As you correctly reported, the message about the stop_codon is just a warning and can be ignored. About the error, I cannot really answer you. It's not clear to me which function of riboWaltz is arising the issue. In any case I'm not even sure I knew about riboWaltz being available in the Galaxy environment, and I'm not able to find it. Maybe it's because I'm not registered. Just to be sure could you please send me a link or an indication about where/how to find the tool in Galaxy.eu? I can try and test it to see if it works fine or not.
Best Fabio
— Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1591313052, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPMHVWRPJUV7SPGYRRDXLHB7RANCNFSM6AAAAAAZGAQMXQ. You are receiving this because you authored the thread.Message ID: @.***>
Hi there, thanks for the links (and sorry, I found the link to riboWaltz 30 sec after I sent my reply).
Your history is a bit strange because after the alignment step (44), it jumps directly at the inclusion P-site-related info to your data structure (step 45, based on step 44 and the GTF file from step 40). I cannot understand when (if) the P-site has been computed. Is it called internally? Where you trying to perform a specific step on the pipeline when you got the error?
BTW it seems the error occurred while reading the GTF, even if I cannot understand the aim of this step. I'll check with my own data to be sure everything is still working off-line. I hope your history won't be delated too soon so I will have a chance to take a better look after this.
Best Fabio
Hi Fabio,
Steps 45-49 are supposed to be the output files from riboWaltz, not sequential steps in the pipeline. When calling up riboWaltz from the Tools section, all I had to provide for the program were the bam file and the gtf file (screenshot attached). I will leave the history available for you.
Cheers,
Beata
Feladó: fabiolauria @.> Elküldve: 2023. június 14., szerda 16:48 Címzett: LabTranslationalArchitectomics/riboWaltz @.> Másolatot kap: Scholtz Beáta @.>; Author @.> Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi there, thanks for the links (and sorry, I found the link to riboWaltz 30 sec after I sent my reply).
Your history is a bit strange because after the alignment step (44), it jumps directly at the inclusion P-site-related info to your data structure (step 45, based on step 44 and the GTF file from step 40). I cannot understand when (if) the P-site has been computed. Is it called internally? Where you trying to perform a specific step on the pipeline when you got the error?
BTW it seems the error occurred while reading the GTF, even if I cannot understand the aim of this step. I'll check with my own data to be sure everything is still working off-line. I hope your history won't be delated too soon so I will have a chance to take a better look after this.
Best Fabio
— Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1591377777, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPOTYA7ONWK7HMQM43LXLHFKPANCNFSM6AAAAAAZGAQMXQ. You are receiving this because you authored the thread.Message ID: @.***>
Hi Beata, I tried most of my functions and I was not able to replicate the error you mentioned and everything works with data from our lab. There are two options: either something is going on with your data or the Galaxy implementation somehow introduced some bugs. Either way, it would be nice to understand which function throws the error, but if you just list the inputs at the beginning of the process and everything is run automatically, debugging is a bit hard. Could you try to find out at which step you get the error? It would be useful for investigating this issue with some indications and criteria.
Best, Fabio
Hi Fabio,
Thank you very much for testing. I will try and contact the Galaxy Support team about the issue, maybe something went wrong with the wrapper. Unfortunately I cannot test the analysis steps in Galaxy, everything runs kinda hidden in the wrapper, but maybe they can see where it gets stuck. The data is really nothing fancy, human cell line, it worked with ribotaper on galaxy.eu (although I used the HISAT2-aligned files for that), and the P-site graphs for some selected genes looked as expected, good triplet periodicity.
I will get back to you with the answer (hopefully some really simple issue).
Thanks again,
Beata
Feladó: fabiolauria @.> Elküldve: 2023. június 19., hétfő 18:17 Címzett: LabTranslationalArchitectomics/riboWaltz @.> Másolatot kap: Scholtz Beáta @.>; Author @.> Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi Beata, I tried most of my functions and I was not able to replicate the error you mentioned and everything works with data from our lab. There are two options: either something is going on with your data or the Galaxy implementation somehow introduced some bugs. Either way, it would be nice to understand which function throws the error, but if you just list the inputs at the beginning of the process and everything is run automatically, debugging is a bit hard. Could you try to find out at which step you get the error? It would be useful for investigating this issue with some indications and criteria.
Best, Fabio
— Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1597451956, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPOZXR5JEPLMBC5QLNDXMB3Q7ANCNFSM6AAAAAAZGAQMXQ. You are receiving this because you authored the thread.Message ID: @.***>
Thank you Beata. Let me know how it is going.
I'll keep this issue open for a while to have your feedbacks.
Best Fabio
Will do so, thank you!
Beata
Feladó: fabiolauria @.> Elküldve: 2023. június 20., kedd 8:23 Címzett: LabTranslationalArchitectomics/riboWaltz @.> Másolatot kap: Scholtz Beáta @.>; Author @.> Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Thank you Beata. Let me know how it is going.
I'll keep this issue open for a while to have your feedbacks.
Best Fabio
— Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1598183532, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPJVJETQVEGQZPGBERTXME6XVANCNFSM6AAAAAAZGAQMXQ. You are receiving this because you authored the thread.Message ID: @.***>
@scholtzb , have you managed to solve the issue? I'm trying to run RiboWaltz on Galaxy.eu as well, and hit the same error as you. Thanks!
Dear Nathalie,
Thank you for getting back to me - no, I haven't received any help so far, I'm stuck...
Do you have any suggestions what I could try?
Cheers,
Beata
Feladó: Nathalie Lailler @.> Elküldve: 2023. szeptember 3., vasárnap 14:45 Címzett: LabTranslationalArchitectomics/riboWaltz @.> Másolatot kap: Scholtz Beáta @.>; Mention @.> Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
@scholtzbhttps://github.com/scholtzb , have you managed to solve the issue? I'm trying to run RiboWlatz on Galaxy.eu as well, and hit the same error as you. Thanks!
— Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1704296766, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPI33BEKSPFXPB7XJWTXYR3UZANCNFSM6AAAAAAZGAQMXQ. You are receiving this because you were mentioned.Message ID: @.***>
Hi Beata, I haven't managed to make it work with Galaxy so I ran it as command line. @scholtzb
Hi Nathalie,
So, if I understand correctly, it is not possible to know at this point which step causes the problem with ribowaltz with Galaxy.eu, right?
Feladó: Nathalie Lailler @.> Elküldve: 2023. szeptember 17., vasárnap 11:14 Címzett: LabTranslationalArchitectomics/riboWaltz @.> Másolatot kap: Scholtz Beáta @.>; Mention @.> Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi Beata, I haven't managed to make it work with Galaxy so I ran it as command line. @scholtzbhttps://github.com/scholtzb
— Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1722432582, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPMECKYKLLIW75526T3X225Q7ANCNFSM6AAAAAAZGAQMXQ. You are receiving this because you were mentioned.Message ID: @.***>
Hi Fabio,
I am trying to run riboWaltz on galaxy.eu. The transcriptome-mapped.bam file was generated by RNA STAR, using the built-in index and hg38 on the Galaxy server, and gencode.v43.basic.annotation.gtf.gz, which I uploaded into Galaxy directly from the database. I used the same gtf for riboWaltz. RiboWaltz failed to run, with the following error message:
Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Warning message: In .get_cds_IDX(mcols0$type, mcols0$phase) : The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored. Error in (function (x) : attempt to apply non-function
If I understand correctly from your feedback on previous issues, the "The "phase" metadata column contains non-NA values for features of type stop_codon." is just a warning, and should not cause the failure. But I cannot figure out what the last line, "Error in (function (x) : attempt to apply non-function" may refer to, although I suppose it indicates the error causing the failure.
Your help would be greatly appreciated,
Thank you very much,
Beata
I am copying here the command line from Galaxy:
ln -s /data/dnb08/galaxy_db/files/2/9/8/dataset_2989d96b-5e2d-4547-8700-b4e45121c568.dat ls180_1'.bam' && Rscript '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/ribowaltz_process/6d4c94373bba/ribowaltz_process/ribowaltz.R' -b . -g '/data/dnb08/galaxy_db/files/e/1/0/dataset_e10dfbb5-19e4-49cf-a8eb-29ea41fa2295.dat' --refseq_sep '' --params_duplicate_filterting '[{"extremity": "both", "keep": "shortest"}]' --params_peridiocity_filterting '[{"periodicity_threshold": 50}]' --params_psite_additional '[{"flanking": 6, "use_start": true, "psite_extrimity": "auto", "cl": 99}]' --params_coverage_additional '[{"psites_per_region": true, "min_overlap": 1, "start_nts": 0, "stop_nts": 0}]' --psite_info_rdata '/data/jwd02f/main/060/770/60770492/outputs/galaxy_dataset_e1178f2c-57e6-4162-b986-bea0a3ca3aaa.dat' --codon_coverage_info '/data/jwd02f/main/060/770/60770492/outputs/galaxy_dataset_32b21edf-1c05-4f7e-82e1-a1b5e8f81f6d.dat' --cds_coverage_info '/data/jwd02f/main/060/770/60770492/outputs/galaxy_dataset_a6016f82-a5e0-45d6-be7d-587c497ef070.dat' && cd plots && for i in /.pdf; do mv $i ${i/\//-}; done;