RaverJay

Alright. I was thinking that an experimental rescue mode might still be useful. Straight up discarding them all bears the risk of losing long reads that are potentially vital for...

Having the same error on my conda installation (v2.2.1) ``` $> which bwa-mem2 /home/username/miniconda3/envs/bwa-mem2/bin/bwa-mem2 $> bwa-mem2 ERROR: prefix is too long! $> /home/username/miniconda3/envs/bwa-mem2/bin/bwa-mem2 Looking to launch executable "/home/ya86gul/miniconda3/envs/bwa-mem2/bin/bwa-mem2.avx2", simd =...

This looks to be docker specific, did not run into this with `-profile singularity`

I second that it should be the default Also, the timeout seems unnecessary - why produce an error when things could still finish correctly?

Thanks, that clears it up a lot! Does that mean that Taiyaki's prepare_mapped_reads.py is not really best suited as a resquiggler, e.g. to extract signal means for individual bases for...

Had the same/a similar problem, fixed it by installing the 0.2.4-beta from development branch: e.g. run: pip install git+https://github.com/rrwick/Porechop.git@development See here: https://github.com/rrwick/Porechop/issues/44#issuecomment-362465575

Just ran into this bug, still exists today with mpl v3.7.2

Just ran into the same problem. Running v 0.4.7 from bioconda. ``` Determining low score threshold (2018-10-11 17:25:20) Before conducting semi-global alignment of the long reads to the assembly graph,...

Running the same setup still, for a very similar sample (different barcode from the same nanopore run - and matching illumina data) the problem did **not** occur and unicycler is...

Reran the failed sample, "Aligning reads" went though without problems. Guess the fix is: Try until it works ¯\\\_(ツ)_/¯