Odd error: ValueError: invalid literal for int() with base 10: 'all'

[apelin20]

Hello, trying the tool for the first time.

@OHRI-bell-virt ~/programs/nanocorrect $ make -f nanocorrect-overlap.make INPUT=/scratch/apelin/MinION_sequencing/Kevin_plasmid/MinION/Pass_2D_seqtk.fasta NAME=nc
nanocorrect-preprocess.pl /scratch/apelin/MinION_sequencing/Kevin_plasmid/MinION/Pass_2D_seqtk.fasta > nc.pp.fasta
fasta2DB nc nc.pp.fasta
DBsplit -s50 nc
DBdust nc
HPCdaligner -t5 -mdust nc > HPCcommands.txt
/bin/bash HPCcommands.txt
LAcat nc > nc.las
rm nc.*.las

So far so good.
Then got pip to install pysam and biopython.

Second step:
@OHRI-bell-virt ~/programs/nanocorrect $ python nanocorrect.py nc all > corrected.fasta
[fai_load] build FASTA index.
Traceback (most recent call last):
File "nanocorrect.py", line 183, in
(start, end) = [ int(x) for x in read_range.split(':') ]
ValueError: invalid literal for int() with base 10: 'all'

Not sure what is causing this.

@OHRI-bell-virt ~/programs/nanocorrect $ python -V
Python 2.7.9

Adrian

[jts]

Hi Adrian,

Can you double-check to make sure you are using the latest version of
nanocorrect?

Thanks,
Jared

On Sun, Dec 13, 2015 at 1:00 PM, apelin20 notifications@github.com wrote:

Hello, trying the tool for the first time

@OHRI-bell-virt ~/programs/nanocorrect $ make -f nanocorrect-overlapmake
INPUT=/scratch/apelin/MinION_sequencing/Kevin_plasmid/MinION/Pass_2D_seqtkfasta
NAME=nc
nanocorrect-preprocesspl
/scratch/apelin/MinION_sequencing/Kevin_plasmid/MinION/Pass_2D_seqtkfasta >
ncppfasta
fasta2DB nc ncppfasta
DBsplit -s50 nc
DBdust nc
HPCdaligner -t5 -mdust nc > HPCcommandstxt
/bin/bash HPCcommandstxt
LAcat nc > nclas
rm nc*las

So far so good
Then got pip to install pysam and biopython

Second step:
@OHRI-bell-virt ~/programs/nanocorrect $ python nanocorrectpy nc all >
correctedfasta
[fai_load] build FASTA index
Traceback (most recent call last):
File "nanocorrectpy", line 183, in
(start, end) = [ int(x) for x in read_rangesplit(':') ]
ValueError: invalid literal for int() with base 10: 'all'

Not sure what is causing this

@OHRI-bell-virt ~/programs/nanocorrect $ python -V
Python 279

Adrian

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