ORQAS fails at Ribomap step #1
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Just repeated with a fresh install of everything and using sample data. Same error. Sorry it's a lot to read through: |
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UPDATE: Tried with a fresh ubuntu VM instead of using my university cluster. Same error. Getting closer... Definitely an issue with the riboprof step of ribomap: I believe I am failing on line 147 of ribomap in read_mapper.cpp
Specifically, I think one of the function arguments for rprofile is being provided as a string, when a double is expected, leading to the following error: I think that would be one of these arguments when running riboprof, although they are all numeric....: I think the next step is to |
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I wrote a hack to get it working for the most part. The issue seems to be that the line headers of the quant.sf are read into riboprof and cause it to crash. deleting the header of quant.sf allows riboprof to complete successfully. I replaced step 2 or run_ORQAS.sh starting at line 99 with the following code. while this is not elegant, I ran into other issues when I tried to delete the first line of quant.sf before running run_ribomap.sh once. I hope this information helps you implement a proper solution, but maybe helps others in the meantime. |
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Hi Alex-Nesta, I'm also trying to use ORQAS and what you have reported is really useful for me. Really appreciate! May I ask if you or any other has ever meet another issue which reported like this: Please let me know if you know how to deal with it. Thank you!
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I cc Marina in case she can indicate what could be the cause of this
ribomap issue
E.
…On Wed, 30 Mar 2022 at 21:39, Noah Yu Zhang ***@***.***> wrote:
Hi Alex-Nesta,
I'm also trying to use ORQAS and what you have reported is really useful
for me. Really appreciate!
May I ask if you or any other has ever meet another issue which reported
like this:
run_ribomap.sh: line 331: 45925 Segmentation fault (core dumped) /riboprof
${options}
Please let me know if you know how to deal with it. Thank you!
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I believe the issue is the output file column names. Not sure if it was a software version mismatch? Hopefully that narrows things down. A docker/singularity container might help eliminate such issues in the future.
On Oct 11, 2022, at 4:09 AM, Eduardo Eyras ***@***.***> wrote:
I cc Marina in case she can indicate what could be the cause of this
ribomap issue
E.
…On Wed, 30 Mar 2022 at 21:39, Noah Yu Zhang ***@***.***> wrote:
Hi Alex-Nesta,
I'm also trying to use ORQAS and what you have reported is really useful
for me. Really appreciate!
May I ask if you or any other has ever meet another issue which reported
like this:
run_ribomap.sh: line 331: 45925 Segmentation fault (core dumped) /riboprof
${options}
Please let me know if you know how to deal with it. Thank you!
—
Reply to this email directly, view it on GitHub
<#1 (comment)>, or
unsubscribe
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.
You are receiving this because you are subscribed to this thread.Message
ID: ***@***.***>
--
Prof. E Eyras
EMBL Australia Group Leader
The John Curtin School of Medical Research - Australian National University
https://github.com/comprna
http://scholar.google.com/citations?user=LiojlGoAAAAJ
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Hi, Alex, lots of thanks, this helps me a lot! |
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I have tried running both the run_ORQAS.sh script and running the pipeline step by step. I have tried using my ownrnaseq and riboseq data and the sample data. I keep getting the same error.
terminate called after throwing an instance of 'std::invalid_argument'
what(): stod
ORQAS/ribomap/scripts/run_ribomap.sh: line 329: 180610 Aborted
Do you have any experience with this error. I have been digging through this for a whole day now. I appreciate any insight!
I verified I am using salmon 0.7.2 for index and alignment as well as STAR 0.4.2j for the riboprof step.
If you suspect it is a software version incompatibility, would you consider making a docker or singularity container?
Thanks for your help!
Alex
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