Problem with Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region (Galaxy Version 1.1.1)

Question: Problem with Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region (Galaxy Version 1.1.1)

2.9 years ago by

jirin • 30

United States

jirin • 30 wrote:

First i don't know if this is the correct place to report tool problem. I did not get any bug dataset icon to click on it and report the problem. Please, advice me where to send this question if this is not appropriate place.

I have Sam Tool: Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region (Galaxy Version 1.1.1) in the middle of my workflow and until a few days ago it was working correctly. Now if I run the workflow I will get the message:

Internal Server Error

Galaxy was unable to successfully complete your request

An error occurred.

This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
The error has been logged to our team. If you want to contact us about this error, please reference the following

GURU MEDITATION: #a

However, the workflow runs anyway, but stops just before this Sam Tool. I can go to the history, use this tool manually and then proceeds with other workflows on top of that.

So problem is not that tool is not working but that can't be used as a part of workflow.

Thanks for help.

Jiri

software error • 986 views

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modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by jirin • 30

2.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Jiri,

This sounds like inputs do not have the required metadata assignments or there is some buggy behavior with workflows. This might be a known but I need to review that.

Would you please generate a share link to both the workflow and a history with the inputs/workflow executed (partial or completed manually). The goal is to run an independent but reproducible test to discover what is going on.

How to share: https://wiki.galaxyproject.org/Learn/Share

Please email those share links plus a link to this post to: galaxy-bugs@lists.galaxyproject.org

Sorry you had problems. We can troubleshoot! Jen, Galaxy team

ADD COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jennifer,

I just sent the links to shared workflow and histories to galaxy-bugs.

Thank you for your help.

Jiri

ADD REPLY • link written 2.9 years ago by jirin • 30

Hello, I sent you an email with details, but the short answer is that all of the inputs/jobs are not based off of the same reference genome build. Some are hg19, others hg38. A match is important for content (valid results) and may be a factor in the workflow stopping (certain tools use metadata assignments such as "database" as a critical input). There is still more testing to do before closing this out entirely and I will follow up by email when that is completed.

Thanks, Jen

ADD REPLY • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

Hi, I sent you yesterday e-mail reply but Google mail delivery subsystem indicates me today delay in delivery due to rejection by biostars.io server.

To remove hg19-hg38 compatibility issue from consideration, I prepared yesterday simplified workflow that does not include custom fasta reference retrieved from hg19. This workflow uses only hg38 genome provided by galaxy and bed file that is hg38 based and it still stops before Filter Sam ... step is reached and gives me Internal Server Error warning. I will send the links to new workflow and history produced by this workflow to galaxy-bugs@lists.galaxyproject.org.

Thank you, Jiri

ADD REPLY • link written 2.9 years ago by jirin • 30

Hello - avoid sending to biostars emails addresses. Just send the info to galaxy-bugs@lists.galaxyproject.org. Thanks! Jen

ADD REPLY • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

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