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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Python int too large to convert to C long #142

Open junxiW opened 8 years ago

junxiW commented 8 years ago

Hi, all,

Just ran MACS2 (2.1.1.20160309) using -f BAM and got this error:

WARNING @ Thu, 18 Aug 2016 17:07:57: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 18 Aug 2016 17:07:57: #2 You may need to consider one of the other alternative d(s): 85,488,546 WARNING @ Thu, 18 Aug 2016 17:07:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 18 Aug 2016 17:07:57: #3 Call peaks... Traceback (most recent call last): File "/home/junxi/.local/bin/macs2", line 617, in main() File "/home/junxi/.local/bin/macs2", line 57, in main run( args ) File "/home/junxi/.local/lib/python2.7/site-packages/MACS2/callpeak_cmd.py", line 264, in run peakdetect.call_peaks() File "MACS2/PeakDetect.pyx", line 105, in MACS2.PeakDetect.PeakDetect.call_peaks (MACS2/PeakDetect.c:1632) File "MACS2/PeakDetect.pyx", line 157, in MACS2.PeakDetect.PeakDetect.__call_peaks_w_control (MACS2/PeakDetect.c:1942) OverflowError: Python int too large to convert to C long

Have you any thoughts? Thanks!

PS: the version of python is 2.7.12.

taoliu commented 8 years ago

Hi Junxi,

I saw such errors reported several times, such as #67, #102, and #106. It seems it is related to C and the operating system. Could you share me the information about the version of your C library and OS?

Best, Tao

junxiW commented 8 years ago

Hi Tao,

my OS is ubuntu 16.04.1 LTS.

But I'm not sure the version of my C library. I've tried to run the commend: ldd --version and get the following message:

ldd (Ubuntu GLIBC 2.23-0ubuntu3) 2.23

Otherwise I've also tried the commend: apt-cache show libc6, then the message is :

Package: libc6 Priority: required Section: libs Installed-Size: 9584 Maintainer: Ubuntu Developers ubuntu-devel-discuss@lists.ubuntu.com Original-Maintainer: GNU Libc Maintainers debian-glibc@lists.debian.org Architecture: i386 Source: glibc Version: 2.23-0ubuntu3 Replaces: libc6-i386, libc6-xen Provides: libc6-i686, libc6-xen Depends: libgcc1 Suggests: glibc-doc, debconf | debconf-2.0, locales Conflicts: libc6-xen Breaks: hurd (<< 1:0.5.git20140203-1), libtirpc1 (<< 0.2.3), locales (<< 2.23), locales-all (<< 2.23), nscd (<< 2.23) Filename: pool/main/g/glibc/libc6_2.23-0ubuntu3_i386.deb Size: 2269702 MD5sum: a45c39d770bc63cdffcc137151ef6cc7 SHA1: c93a132c90c044bfa57c9dc02fdc4acd9ce7055f SHA256: 38200f93d7ed961421eada598e8e96a6428cc1a22c4b7a7a2242a9b240c7c1a0 Description-en: GNU C Library: Shared libraries Contains the standard libraries that are used by nearly all programs on the system. This package includes shared versions of the standard C library and the standard math library, as well as many others. Description-md5: fc3001b0b90a1c8e6690b283a619d57f Multi-Arch: same Homepage: http://www.gnu.org/software/libc/libc.html Bugs: https://bugs.launchpad.net/ubuntu/+filebug Origin: Ubuntu Supported: 5y Task: minimal

I hope it'll be useful to you.

Kind regards. Junxi

2016-08-18 22:10 GMT+02:00 Tao Liu (τν) notifications@github.com:

Hi Junxi,

I saw such errors reported several times, such as #67 https://github.com/taoliu/MACS/issues/67, #102 https://github.com/taoliu/MACS/issues/102, and #106 https://github.com/taoliu/MACS/issues/106. It seems it is related to C and the operating system. Could you share me the information about the version of your C library and OS?

Best, Tao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/taoliu/MACS/issues/142#issuecomment-240841398, or mute the thread https://github.com/notifications/unsubscribe-auth/AUIPV02Fli14WKvp5kekpvjDGybEbpXIks5qhLwtgaJpZM4JnnK7 .

taoliu commented 8 years ago

Hi Junxi,

I noticed that the 'architecture' is i386 which means the library is for 32bit system. This might be the main reason why it said 'Python int too large'. I recommend you re-install MACS2 in a 64bit system and try again. As for Ubuntu, it means the 'amd64' version.

Best, Tao

junxiW commented 8 years ago

Hi Tao,

You're right. I've reinstalled MACS2 in the 64bit system. Now everything is in order.

If it's possible, please tell the other Ubuntu-users that MACS2 is just for 64 bit system. Thank you very much.

Kind regards, Junxi

2016-08-19 18:14 GMT+02:00 Tao Liu (τν) notifications@github.com:

Hi Junxi,

I noticed that the 'architecture' is i386 which means the library is for 32bit system. This might be the main reason why it said 'Python int too large'. I recommend you re-install MACS2 in a 64bit system and try again. As for Ubuntu, it means the 'amd64' version.

Best, Tao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/taoliu/MACS/issues/142#issuecomment-241062348, or mute the thread https://github.com/notifications/unsubscribe-auth/AUIPV2MhfVxLHbFXR1_U4so1tPrHM6jfks5qhdZPgaJpZM4JnnK7 .