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After last Qualimap module update #2020 behavior changed, and we lost "percentage_aligned" sections in our reports.
Looks like the reason behind it is moving percentage_aligned into additional try:
Our report doesn't have Globals inside section (due to full genome analysis) and looks like try causing missing entire block - not only percentage_aligned_on_target section.
I'm not using last version (due to Python 3.8 requirement), but according to blame and changelogs - nothing is changed in this part.
Thanks so much for reporting the issue, and providing a test example!
Should be fixed in #2207 😌
I added you example in the test data repo: MultiQC/test-data#308
@vladsavelyev Hello, we rechecked results after 1.19 release - looks like there is one major difference in report_saved_raw_data section:
general_error_rate changed from 0.0068 to 0.6799999999999999 (100 time more) likely due to 100 multiplier in code. It this intended? In original file (attached in issue) we have:
>>>>>>> Mismatches and indels
general error rate = 0.0068
number of mismatches = 48,036
number of insertions = 648
mapped reads with insertion percentage = 0.78%
number of deletions = 734
mapped reads with deletion percentage = 0.89%
homopolymer indels = 57.96%
Description of bug
After last Qualimap module update #2020 behavior changed, and we lost "percentage_aligned" sections in our reports.
Looks like the reason behind it is moving
percentage_aligned
into additionaltry
:Our report doesn't have
Globals inside
section (due to full genome analysis) and looks liketry
causing missing entire block - not onlypercentage_aligned_on_target
section.I'm not using last version (due to Python 3.8 requirement), but according to blame and changelogs - nothing is changed in this part.
File that triggers the error
genome_results.txt
MultiQC Error log
Before submitting
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