Govinda Kamath

Can you give the output of these commands? ``` fasta2DB ecoli reads.fasta DBsplit -x500 -s100 ecoli HPC.daligner -t5 ecoli | csh -v ``` It looks like DAligner did not work...

Thank you Ali!

Could you run this command in the demo? ``` seqtk seq -a ecoli_p4_filtered.fastq > reads.fasta ``` Is there a `reads.fasta` in the current directory?

Have you run ``` source utils/setup.sh ``` That should set up the relevant paths.

It looks like the path set up did not work. I'm not completely sure why. @fxia22 any ideas?

I don't think so. HINGE is written primarily in C++ with some modules in python. As far as I know, that's not pypy compatible.

HINGE does not currently support multiple CPU cores yet. Most of the computational cost of HINGE is in DALIGNER, which does support multiple cores. However, we're under active development and...

The command would be ` HPC.daligner -T | bash -v ` More details are [here](https://dazzlerblog.wordpress.com/command-guides/daligner-command-reference-guide/)

Hi, Can you first split the `.las` using ``` LAsplit -v Stella.# 10 < Stella.las ``` And then run hinge with the `--mlas` option as ``` hinge filter --db Stella...

You should have used ``` /home/ag/HINGE/inst/bin/hinge filter --db Stella --las Stella --mlas -x Stella --config /home/ag/HINGE/utils/nominal.ini ``` instead of ``` /home/ag/HINGE/inst/bin/hinge filter --db Stella --las Stella.las --mlas -x Stella --config...