holtjma/msbwt

A python toolkit for building and querying multi-string BWTs

msbwt's Issues

How long does it take to build msbwt?

Hi Matt,

I'm interested in FMLRC and want to use it to correct my PacBio reads. I have ~50 X Illumina data (~125 Gb in total) and I'm building msbwt for Illumina reads. However, it seems that it takes too long to do it. Here is some information in the log file:
[2016-10-31 16:12:16] INFO: Formatting sequences for merging...
[2016-11-04 22:27:21] INFO: Beginning MSBWT construction...
[2016-11-05 00:20:34] INFO: Processing groups of size 256...
[2016-11-06 18:33:50] INFO: Processing groups of size 512...
[2016-11-09 19:07:49] INFO: Processing groups of size 1024...
[2016-11-13 12:56:12] INFO: Processing groups of size 2048...
I wonder what does the "size" mean and when will it finish?

Thank you for your time.
Yuncong Geng

no ouput

gunzip -c reads.sorted.txt.gz | tr NT TN | ropebwt2 -LR | tr NT TN | msbwt convert /path/to/output/msbwt

This command does not produce any output file or folder when I try it. Is the tr NT TN command use twice correct?

TypeError: expected bytes, str found

I always get this error when trying to import a MSBWT using the Python API.

I have a small FASTQ file, 400 long sequencing reads. I've tried creating the BWT using both the msbwt package and by converting from the output of ropebwt2. Querying using the command-line also works so I'm wondering what if I'm missing anything. The package has been installed with Python 2.7.

I can provide the data needed to reproduce the above error if necessary.