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This queue is for tickets about the Bio-SamTools CPAN distribution.

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The Basics
Id: 59584
Status: resolved
Priority: 0/
Queue: Bio-SamTools
People
Owner: Nobody in particular
Requestors: kr2 [...] sanger.ac.uk
Cc:
AdminCc:
Bug Information
Severity: Important
Broken in: 1.20
Fixed in: (no value)

History Show all quoted text
  Wed Jul 21 00:10:20 2010 kr2 [...] sanger.ac.uk - Ticket created
Subject: BigWig generation - 'Line too long' error
Hi, bamToGBrowse.pl bins out mid way through generating the BW file. ---- Calculating coverage for interval 7:62000001..63000000 Calculating coverage for interval 7:63000001..64000000 Writing bigwig file Line too long (more than 536870912 chars) line 359723889 of /lustre/scratch101/sanger/cgppipe/nst_pipe/data/gb/537375_89727/wigfileJsyrA.wig WARNING: bedGraphToBigWig exited with an error. /lustre/scratch101/sanger/cgppipe/nst_pipe/data/gb/537375_89727/x.bw will be removed. ---- This appears to be a message internal to the bedGraphToBigWig binary. The input file is 49GB, however we have successfully generated BW files from files in excess of 100GB in the past. Regards, Keiran
  Wed Jul 21 08:39:27 2010 kr2 [...] sanger.ac.uk - Correspondence added
From: kr2 [...] sanger.ac.uk
This ticket can be closed, upgrading to the latest release of the kent source tree resolves this issue (also reduces memory usage). bedGraphToBigWig reports v4 on the working version
  Wed Jul 21 10:21:59 2010 LDS [...] cpan.org - Correspondence added
User reports that upgrading to latest Kent source tree fixes the line too long error.
  Wed Jul 21 10:22:00 2010 The RT System itself - Status changed from 'new' to 'open'
  Wed Jul 21 10:22:00 2010 LDS [...] cpan.org - Status changed from 'open' to 'resolved'