cufflinks libz error/warning
Hi all - I'm running Galaxy on my Redhat linux cluster. When I run cufflinks from the shell I get the error/warning: cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks) but it still seems to run ok. It looks like Galaxy is choking on this. I tried compling cufflinks manually but that was more troublesome. Is there a way I can get Galaxy to ignore this error and continue? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.
Hi all - I'm running Galaxy on my Redhat linux cluster. When I run cufflinks from the shell I get the error/warning:
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)
but it still seems to run ok. It looks like Galaxy is choking on this. I tried compling cufflinks manually but that was more troublesome. Is there a way I can get Galaxy to ignore this error and continue?
Ryan, There's currently no way to tell Galaxy to ignore some error messages and not others; we're working on this functionality but it's far from being done*. Unfortunately, your best bet is to compile Cufflinks on your system. FYI, here's a technical description of this problem: http://seqanswers.com/forums/showthread.php?t=8042 *To detect particular errors, we envision XML elements in a tool's output definition that use regular expressions to identify errors amongst a program's output. We think this is the right approach, but we haven't started implementing it yet. You are welcome to do so; we welcome code contributions from the community. Thanks, J.
On 3/17/11 3:40 PM, Jeremy Goecks wrote:
Hi all - I'm running Galaxy on my Redhat linux cluster. When I run cufflinks from the shell I get the error/warning:
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)
but it still seems to run ok. It looks like Galaxy is choking on this. I tried compling cufflinks manually but that was more troublesome. Is there a way I can get Galaxy to ignore this error and continue?
Ryan,
There's currently no way to tell Galaxy to ignore some error messages and not others; we're working on this functionality but it's far from being done*. Unfortunately, your best bet is to compile Cufflinks on your system. FYI, here's a technical description of this problem: http://seqanswers.com/forums/showthread.php?t=8042
*To detect particular errors, we envision XML elements in a tool's output definition that use regular expressions to identify errors amongst a program's output. We think this is the right approach, but we haven't started implementing it yet. You are welcome to do so; we welcome code contributions from the community.
Thanks, J.
ok - I managed to compile cufflinks myself. When I run it I get a line of output that reads "linked against Boost version 104601". When I run cufflinks in Galaxy, Galaxy complains about this line being an error. Hmmm. How is cufflinks running in the public version of galaxy?
ok - I managed to compile cufflinks myself. When I run it I get a line of output that reads "linked against Boost version 104601". When I run cufflinks in Galaxy, Galaxy complains about this line being an error.
Hmmm. How is cufflinks running in the public version of galaxy?
Ryan, We compile Cufflinks ourselves as well for main, but for some reason we don't see the message that you're seeing when Cufflinks is run. We have Cufflinks v0.9.3, but I wonder whether we might be using a slightly older version of the code. In any case, looking at the Cufflinks code, I see: -- cufflinks.cpp:85: fprintf(stderr, "linked against Boost version %d\n", BOOST_VERSION); gtf_to_sam.cpp:46: fprintf(stderr, "linked against Boost version %d\n", BOOST_VERSION); -- Try removing these lines and recompiling cufflinks; this should solve your problem. Thanks, J.
Jeremy, I believe Galaxy need to update not only Cufflink 0.9.3 but also TopHat 1.2.0. Thanks --- On Thu, 3/17/11, Jeremy Goecks <jeremy.goecks@emory.edu> wrote: From: Jeremy Goecks <jeremy.goecks@emory.edu> Subject: Re: [galaxy-dev] cufflinks libz error/warning To: golharam@umdnj.edu Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Date: Thursday, March 17, 2011, 9:01 PM
ok - I managed to compile cufflinks myself. When I run it I get a line of output that reads "linked against Boost version 104601". When I run cufflinks in Galaxy, Galaxy complains about this line being an error.
Hmmm. How is cufflinks running in the public version of galaxy?
Ryan, We compile Cufflinks ourselves as well for main, but for some reason we don't see the message that you're seeing when Cufflinks is run. We have Cufflinks v0.9.3, but I wonder whether we might be using a slightly older version of the code. In any case, looking at the Cufflinks code, I see: -- cufflinks.cpp:85: fprintf(stderr, "linked against Boost version %d\n", BOOST_VERSION); gtf_to_sam.cpp:46: fprintf(stderr, "linked against Boost version %d\n", BOOST_VERSION); -- Try removing these lines and recompiling cufflinks; this should solve your problem. Thanks, J. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
On 3/17/11 10:01 PM, Jeremy Goecks wrote:
ok - I managed to compile cufflinks myself. When I run it I get a line of output that reads "linked against Boost version 104601". When I run cufflinks in Galaxy, Galaxy complains about this line being an error.
Hmmm. How is cufflinks running in the public version of galaxy?
Ryan,
We compile Cufflinks ourselves as well for main, but for some reason we don't see the message that you're seeing when Cufflinks is run. We have Cufflinks v0.9.3, but I wonder whether we might be using a slightly older version of the code. In any case, looking at the Cufflinks code, I see:
-- cufflinks.cpp:85: fprintf(stderr, "linked against Boost version %d\n", BOOST_VERSION); gtf_to_sam.cpp:46: fprintf(stderr, "linked against Boost version %d\n", BOOST_VERSION); --
Try removing these lines and recompiling cufflinks; this should solve your problem.
Thanks, J.
It looks like the output only occurs when cufflinks can't run on the provided dataset. I checked my inputs, and I think that is the problem...its a sam file from bowtie, not from tophat, hence not a sorted sam file. Perhaps this stderr message doesn't matter after all, its just misleading...
It looks like the output only occurs when cufflinks can't run on the provided dataset. I checked my inputs, and I think that is the problem...its a sam file from bowtie, not from tophat, hence not a sorted sam file. Perhaps this stderr message doesn't matter after all, its just misleading...
Yes, I think you are correct. Let us know if you have more questions. Best, J.
participants (3)
-
Jeremy Goecks -
Ryan Golhar -
vasu punj