Bug: v0.2.0 Deepbinner bin - "readclass not found"
Opened this issue · 3 comments
I am running deepbinner bin on already basecalled minion data.
The tool throws a KeyError("not found"), if an unclassified read id is encountered.
Data:
Flow-Cells: FLO-MIN106
Kit: SQK-RBK004
Classification was generated per run with:
deepbinner classify --rapid p_root/fast5/pass/{R_num} 1> {output} 2> {log}
Binning with:
deepbinner bin --classes {input.classi} --reads {input.pass_fastq} --out_dir {outdir}
For some runs the classification omits one read and this prompts the bin.py to switch into a previously untested or disabled section of code.
Maybe I just have an old version of the code.
Any chance this pull request will be merged anytime soon?
I have a large run (380GB of fast5) where I'm not done calling bases, but I want to take the (120GB) of fastq files I have base called already and debarcode them. It's throwing the KeyError("not found")
for those fastq files not base called from the fast5 files yet.
jrherr i dont know if this is a suitable solution for you, but:
If you have acquired deepbinner using git, you can merge the hotfix into your local repository using:
git pull origin pull/30/head
In case you need a docker container, i have just added the above line to mine. Its on Docker Hub: https://hub.docker.com/r/ttubb/deepbinner/dockerfile (currently waiting on Docker Hub to build the updated version, should be done in a few hours).