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 [email protected] 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

— Reply to this email directly or view it on GitHub https://github.com/jts/nanocorrect/issues/18.