galaxy cuffdiff running too long
Hello, When we run cuffdiff from the command line we get this; [galaxy@q ~]$ /bin/cuffdiff /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available (required by /bin/cuffdiff) cuffdiff v2.0.2 (3522) It looks like we are using a more recent version of cuffdiff than is supported by the galaxy tool wrappers (0.0.5 and 0.0.6). Using the 0.0.5 tool gives empty outputs. Using the 0.0.6 tool results in runs that last for five days without terminating. Has this behavior been seen before? How can we get good outputs to feed into cummeRbund? -Rob
[galaxy@q ~]$ /bin/cuffdiff /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available (required by /bin/cuffdiff) cuffdiff v2.0.2 (3522)
This definitely indicates a problem with your cuffdiff install. Did you build cuffdiff on that system or install in some other way? (very odd to have it installed in /bin).
Hello, I have reinstalled cufflinks from source and now I get a new error. I am using the Cuffdiff wrapper (version 0.0.6) and cufflinks-2.1.1. The boxes come back green but there is no output and there is a message in the standard error box. Error running cuffdiff. [21:34:00] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [21:34:12] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::thread_resource_error>
' what(): boost::thread_resource_error: Resource temporarily unavailable
WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'wsf': 'module' object has no attribute 'wsf' WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no attribute 'BlastXml' Thankyou, -Rob On Tue, Jun 11, 2013 at 5:40 PM, James Taylor <james@jamestaylor.org> wrote:
[galaxy@q ~]$ /bin/cuffdiff /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available (required by /bin/cuffdiff) cuffdiff v2.0.2 (3522)
This definitely indicates a problem with your cuffdiff install. Did you build cuffdiff on that system or install in some other way? (very odd to have it installed in /bin).
Hello, I have installed "blast" on the server and updated datatypes.xml by copying datatypes.xml.sample. This removes the last three errors from stderror. Still working on: Error running cuffdiff. [12:48:21] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [12:48:33] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::thread_resource_error>>' what(): boost::thread_resource_error: Resource temporarily unavailable -Rob On Mon, Jun 24, 2013 at 11:36 AM, Robert Chase <rerpc@channing.harvard.edu>wrote:
Hello,
I have reinstalled cufflinks from source and now I get a new error. I am using the Cuffdiff wrapper (version 0.0.6) and cufflinks-2.1.1. The boxes come back green but there is no output and there is a message in the standard error box.
Error running cuffdiff. [21:34:00] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [21:34:12] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::thread_resource_error> >' what(): boost::thread_resource_error: Resource temporarily unavailable
WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'wsf': 'module' object has no attribute 'wsf' WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no attribute 'BlastXml'
Thankyou,
-Rob
On Tue, Jun 11, 2013 at 5:40 PM, James Taylor <james@jamestaylor.org>wrote:
[galaxy@q ~]$ /bin/cuffdiff /bin/cuffdiff: /usr/lib64/libz.so.1: no version information available (required by /bin/cuffdiff) cuffdiff v2.0.2 (3522)
This definitely indicates a problem with your cuffdiff install. Did you build cuffdiff on that system or install in some other way? (very odd to have it installed in /bin).
Error running cuffdiff. [12:48:21] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [12:48:33] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::thread_resource_error>
' what(): boost::thread_resource_error: Resource temporarily unavailable
This is a linkage error with the Boost library; you might need to modify the Boost path and then recompile Cufflinks. That said, I don't recommend compiling from source unless needed; the Cufflinks suite is provided precompiled for many platforms. Getting the Cufflinks suite working and getting it working with Galaxy are two different things. I recommend: (a) getting Cufflinks working from the command line first using the tutorial: http://cufflinks.cbcb.umd.edu/tutorial.html (b) doing the tutorial in Galaxy; (c) using your own data with Cufflinks in Galaxy. Cufflinks can run very slow, especially if using a limited number of threads, so long running time is not necessarily an indication of error. Good luck, J.
Hello, When I install from binary files the boost problem doesn't go away and I get one extra error message in the beginning. Error running cuffdiff. cuffdiff: /usr/lib64/libz.so.1: no version information available (required by cuffdiff) [14:51:54] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [14:52:05] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::thread_resource_error>
' what(): boost::thread_resource_error
When I inspect the file libz.so.1 I get a symbolic link to another file, libz.so.1.2.3 which appears in the same directory. [@]# file /usr/lib/libz.so.1 /usr/lib/libz.so.1: symbolic link to `libz.so.1.2.3' [@]# file /usr/lib/libz.so.1.2.3 /usr/lib/libz.so.1.2.3: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), stripped -Rob On Mon, Jun 24, 2013 at 8:15 PM, Jeremy Goecks <jeremy.goecks@emory.edu>wrote:
Error running cuffdiff. [12:48:21] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [12:48:33] Inspecting maps and determining fragment length distributions. terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::thread_resource_error>>' what(): boost::thread_resource_error: Resource temporarily unavailable
This is a linkage error with the Boost library; you might need to modify the Boost path and then recompile Cufflinks. That said, I don't recommend compiling from source unless needed; the Cufflinks suite is provided precompiled for many platforms.
Getting the Cufflinks suite working and getting it working with Galaxy are two different things. I recommend:
(a) getting Cufflinks working from the command line first using the tutorial:
http://cufflinks.cbcb.umd.edu/tutorial.html
(b) doing the tutorial in Galaxy;
(c) using your own data with Cufflinks in Galaxy.
Cufflinks can run very slow, especially if using a limited number of threads, so long running time is not necessarily an indication of error.
Good luck, J.
participants (3)
-
James Taylor -
Jeremy Goecks -
Robert Chase