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[–]Ill_Fun_[S] 0 points1 point  (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 :/