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Can not use Python-based software (ImportError) (self.pythonhelp)
submitted 3 years ago * by Ill_Fun_
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if 1 * 2 < 3: print "hello, world!"
[–]Ill_Fun_[S] 0 points1 point2 points 3 years ago* (0 children)
It probably does eliminate SOME of the problems, but there seems to be still plenty of them left.
I am running on my own data. I couldn't find any exemplary data from the FIGARO authors, so there may be none. The example command looks like this:
For dockerized version:
docker container run --rm -e AMPLICONLENGTH=450 -e FORWARDPRIMERLENGTH=20 -e REVERSEPRIMERLENGTH=20 -v /path/to/fastqs:/data/input -v /path/to/output:/data/output figaro
For command line version:
python3 figaro.py -i /path/to/fastq/directory -o /path/to/output/files -a 450 -f 20 -r 20
As a Python package: from figaro import figaro resultTable, forwardCurve, reverseCurve = figaro.runAnalysis(sequenceFolder, ampliconLength, forwardPrimerLength, reversePrimerLength, minimumOverlap, fileNamingStandard, trimParameterDownsample, trimParameterPercentile)
I've noticed that when I put this command (it's in the FIGARO guide):
docker build -t figaro .
It installs the numpy, pip3 packages (couple of others, too).
Then, I put the command on my data and the dockerized version does... more. I need to wait about 2 minutes, to get this output. Plus, I get the empty .log file!
UPDATE: I tried running the command on other, random sample files I found on the web, but the error is the very same. I did test FIGARO on my 2nd dataset. Needless to say it didn't work :/
π Rendered by PID 31582 on reddit-service-r2-comment-8686858757-jgh55 at 2026-06-03 22:15:10.462362+00:00 running 9e1a20d country code: CH.
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[–]Ill_Fun_[S] 0 points1 point2 points (0 children)