Christopher Dunn
Christopher Dunn
Run `FALCON-examples/run/synth0`. The input is available via git-sym, but also internally at `/pbi/dept/secondary/siv/testdata/hgap/synth5k/subreads.fasta`.
I am unable to reproduce this anymore. **LAshow** reports perfect alignements, and **LA4Falcon -mo** reports `100.00` instead of `99.45`. Maybe the other fix also fixed this, or maybe there was...
> 'length_cutoff': 1891, 'genome_length': 5000 You might need to clean the work-directory before running a different example.
The restriction is in Gene Myers' **fasta2DB**. However, that was made more flexible recently. We'll have to do some testing to see how it works today. If you have a...
Maybe the default changed. ``` job_type = sge ```
> By the way, pypeflow has always reported time about 7 hours in the future. Is pypeflow tied to GMT or something? (grin) Yes, that's a requirement for PB. Finding...
Well, it's a DEBUG in this case, but it says we are missing outputs from task_build_rdb. You should see something in stderr for task_build_rdb.
@tangerzhang, `job_type=slurm` is already supported, thanks to a contribution by a user.
``` $ samtools --version samtools 1.6 Using htslib 1.6 Copyright (C) 2017 Genome Research Ltd. ``` * https://github.com/PacificBiosciences/pypeFLOW/blob/cb894bb12a19eba6cdda2a2485bf8a5cbeadda9d/pypeflow/io.py Line 29 looks fine there. We're simply call `os.system("which samtools")`. Hmmm. ```...
Let's see... 1. One idea is to generate an empty `.las` file. That can be done with restrictive daligner settings. Maybe you can try that in a pinch. 2. Another...