Re: [macs-announscement] ValueError: cannot resize this array: it does not own its data

[Tao Liu]

Hi Alex,

I have never seen such error before. Sometimes, if the upgrades of the same software on the nodes of your cluster haven’t been synchronized, strange error may happen.

I am still using Numpy 1.8, and I will try to test MACS2 on Numpy 1.10...

Best,
Tao Liu


> On Feb 17, 2016, at 3:45 PM, Alexis Blanchet-Cohen <ablanch...@gmail.com> wrote:
>
> Hi,
>
> I get the error message "ValueError: cannot resize this array: it does not own its data" while running MACS 2.1.0.20151222 with Numpy 1.10.4.
>
> Command
>
> #!/bin/bash
> #PBS -o MACS2_FL115_CTBP1_mfold10,30_outputfile.txt
> #PBS -e MACS2_FL115_CTBP1_mfold10,30_errorfile.txt
> #PBS -V
> #PBS -N MACS2_FL115_CTBP1_mfold10,30.txt
>
> cd $PBS_O_WORKDIR
> macs2 callpeak -t FL115_CTBP1_sorted.bam -c FL115d_inputRS_sorted.bam --name MACS2_FL115_CTBP1_mfold10,30 --bw 250 -g mm --mfold 10 30 -p 1e-5
>
> Tail of log file
>
> [blancha@lg-1r17-n02 test]$ tail -n 25 MACS2_FL115_CTBP1_mfold10,30_errorfile.txt
> INFO @ Wed, 17 Feb 2016 15:17:05: #2 alternative fragment length(s) may be 110 bps
> INFO @ Wed, 17 Feb 2016 15:17:05: #2.2 Generate R script for model : MACS2_FL115_CTBP1_mfold10,30_model.r
> INFO @ Wed, 17 Feb 2016 15:17:05: #3 Call peaks...
> INFO @ Wed, 17 Feb 2016 15:17:05: #3 Call peaks with given -log10pvalue cutoff: 5.00000 ...
> INFO @ Wed, 17 Feb 2016 15:17:05: #3 Pre-compute pvalue-qvalue table...
> INFO @ Wed, 17 Feb 2016 15:25:09: #3 Call peaks for each chromosome...
> Traceback (most recent call last):
> File "/sb/software/areas/ircm/tools/Python-2.7.8/bin/macs2", line 4, in <module>
> __import__('pkg_resources').run_script('MACS2==2.1.0.20151222', 'macs2')
> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 517, in run_script
>
> File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1443, in run_script
> register_loader_type(zipimport.zipimporter, ZipProvider)
> File "/sb/software/areas/ircm/tools/Python-2.7.8/lib/python2.7/site-packages/MACS2-2.1.0.20151222-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>
>
> File "/sb/software/areas/ircm/tools/Python-2.7.8/lib/python2.7/site-packages/MACS2-2.1.0.20151222-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 56, in main
>
> File "build/bdist.linux-x86_64/egg/MACS2/callpeak_cmd.py", line 261, in run
> File "MACS2/PeakDetect.pyx", line 105, in MACS2.PeakDetect.PeakDetect.call_peaks (MACS2/PeakDetect.c:1632)
> File "MACS2/PeakDetect.pyx", line 251, in MACS2.PeakDetect.PeakDetect.__call_peaks_w_control (MACS2/PeakDetect.c:3172)
> File "MACS2/IO/CallPeakUnit.pyx", line 858, in MACS2.IO.CallPeakUnit.CallerFromAlignments.call_peaks (MACS2/IO/CallPeakUnit.c:12334)
> File "MACS2/IO/CallPeakUnit.pyx", line 912, in MACS2.IO.CallPeakUnit.CallerFromAlignments.call_peaks (MACS2/IO/CallPeakUnit.c:12086)
> File "MACS2/IO/CallPeakUnit.pyx", line 967, in MACS2.IO.CallPeakUnit.CallerFromAlignments.__chrom_call_peak_using_certain_criteria (MACS2/IO/CallPeakUnit.c:12492)
> File "MACS2/IO/CallPeakUnit.pyx", line 475, in MACS2.IO.CallPeakUnit.CallerFromAlignments.__pileup_treat_ctrl_a_chromosome (MACS2/IO/CallPeakUnit.c:6861)
> ValueError: cannot resize this array: it does not own its data
>
> Thank you for your help,
>
> Alexis
>
>
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