Streme and MEME not working
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Samuel Ogunsola
May 17, 2022, 4:41:20 PM5/17/22
to MEME Suite Q&A
Hello,
I want to analyze some data but here is the response I'm getting form STREME and MEME. Please, what could be wrong?
Failed to write HTML output due to errors processing the XML:
motif@site_distr has invalid value "" at /data/apache-tomcat/instance/meme/work/meme-5.4.1/libexec/meme-5.4.1/streme_xml_to_html line 540, <$fh> line 80.
# Warning: streme_xml_to_html exited abnormally and may have failed to create HTML output.
Thank you,
Samuel
cegrant
May 17, 2022, 11:22:38 PM5/17/22
to MEME Suite Q&A
Hi Samuel,
Could you forward us a copy of your data and the exact command lines you used? Alternatively, if you were using the public web site just forward us a copy of the link to your results.
Having these will make it easier for us to troubleshoot the problem.
Charles
Samuel Ogunsola
May 18, 2022, 8:38:08 AM5/18/22
to MEME Suite Q&A
Hi Charles,
I used the public website and here is the link to my result.
Thank you
Samuel
Charles E Grant
May 20, 2022, 5:59:20 PM5/20/22
to samuelog...@gmail.com, MEME Suite Q&A
Hi Samuel,
There were a few issues with your job. First you used the default values for the widths of motifs to look for: running from 8 to 15. However, all of your sequences are of length 9, so you are asking STREME to find motifs that are wider than the sequences you provide. This triggers a bug in STREME. We should provide some sort of descriptive message letting you know what the problem is. Instead the job just fails.
I tried rerunning your job using a motif width of 9 (set in the advanced options section of the web form), and it turns out this triggers another bug in STREME. STREME fails if the sequences are exactly the same size as the requested motif width. I re-ran you job again, but searching motif from width 3 to width 8. That works, but no statistically significant motifs were found. You can see the results here:
https://meme-suite.org/meme/info/status?service=STREME&id=appSTREME_5.4.11653083722827-871217308
Our apologies for the inconvenience caused by the bugs and thank you for letting us know about the issues. We’ll get it fixed for the next release.
Charles
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There were a few issues with your job. First you used the default values for the widths of motifs to look for: running from 8 to 15. However, all of your sequences are of length 9, so you are asking STREME to find motifs that are wider than the sequences you provide. This triggers a bug in STREME. We should provide some sort of descriptive message letting you know what the problem is. Instead the job just fails.
I tried rerunning your job using a motif width of 9 (set in the advanced options section of the web form), and it turns out this triggers another bug in STREME. STREME fails if the sequences are exactly the same size as the requested motif width. I re-ran you job again, but searching motif from width 3 to width 8. That works, but no statistically significant motifs were found. You can see the results here:
https://meme-suite.org/meme/info/status?service=STREME&id=appSTREME_5.4.11653083722827-871217308
Our apologies for the inconvenience caused by the bugs and thank you for letting us know about the issues. We’ll get it fixed for the next release.
Charles
> You received this message because you are subscribed to the Google Groups "MEME Suite Q&A" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to meme-suite+...@googlegroups.com.
> To view this discussion on the web, visit https://groups.google.com/d/msgid/meme-suite/273fadb7-1fa1-4b31-8f80-cb6c65c0bf31n%40googlegroups.com.
cegrant
May 20, 2022, 6:00:05 PM5/20/22
to MEME Suite Q&A
There were a few issues with your job. First you used the default values for the widths of motifs to look for: running from 8 to 15. However, all of your sequences are of length 9, so you are asking STREME to find motifs that are wider than the sequences you provide. This triggers a bug in STREME. We should provide some sort of descriptive message letting you know what the problem is. Instead the job just fails.
I tried rerunning your job using a motif width of 9 (set in the advanced options section of the web form), and it turns out this triggers another bug in STREME. STREME fails if all the sequences are exactly the same size as the requested motif width. I re-ran you job again, but searching motif from width 3 to width 8. That works, but no statistically significant motifs were found. You can see the results here:
Our apologies for the inconvenience caused by the bugs and thank you for letting us know about the issues. We’ll get it fixed for the next release.
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