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Old 10-14-2010, 10:09 AM   #1
Sherry
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Default Cufflinks error message on test data

Hi,

I compiled cufflinks after installing samtools and the boost libraries. Everything went fine. However, when I tested using cufflinks test_data.sam, the following error message appears.

cufflinks: error while loading shared libraries: libboost_thread.so.1.44.0: cann
ot open shared object file: No such file or directory

It seems that cufflinks is not seeing the shared object file. However, when I ran the configure, it said as the following:
checking whether the Boost::Thread library is available... yes

Any help will be appreciated.

Sherry
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Old 10-14-2010, 10:18 AM   #2
adarob
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Are you sure you followed all of the directions at http://cufflinks.cbcb.umd.edu/tutorial.html ?

What system are you compiling on?
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Old 10-14-2010, 10:27 AM   #3
Sherry
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It's a quad 4x4 processors, 64 bit machine running Red Hat Enterprise Linux Server release 5.3
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Old 10-14-2010, 10:52 AM   #4
kalidaemon
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Hi Sherry
I had a similar problem which I solved by downloaded the pre-compiled executable software (cufflinks-0.9.1.Linux_x86_64) and following the (much simpler) install directions in the manual. Hope this helps.
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Old 10-14-2010, 10:55 AM   #5
Sherry
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thanks! I will give it a try!
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Old 10-14-2010, 11:51 AM   #6
Sherry
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Thumbs up

Thanks! It worked!

It gave a minor error message:
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)

but this doesn't seem to affect the running.

Thanks again,

Sherry
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Old 01-31-2011, 11:36 AM   #7
e-kim
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Hi ,
I got the same message
"cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)"
Is it really minor error message for running cufflinks?
Is there any way to fix it?
Thanks,

e-kim
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Old 03-14-2011, 03:32 PM   #8
frankyue50
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got the same error msg. wonder if it matters ............

Quote:
Originally Posted by Sherry View Post
Thanks! It worked!

It gave a minor error message:
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)

but this doesn't seem to affect the running.

Thanks again,

Sherry
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Old 05-18-2011, 03:33 PM   #9
waseem
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We started with Bowtie and made indexes from Soybean transcript indexes then ran our dataset with commond
nice -10 ./bowtie --best --sam Gmax /Users/waseem/Desktop/inputdata/s_5_sequence_S53A.txt /Users/waseem/Desktop/Outputs/s_5_sequence_S53Aoutput.sam

And Got the Output in Sam Format.
Then it was converted to Bam as
/share/apps/samtools/samtools samtools import Gmax_109_transcript.fa.fai Outputs/s_4_sequence_S24Aoutput.sam Outputs/s_4_sequence_S24Aoutput.bam

Then The Bam file was sorted as;
/share/apps/samtools/samtools sort Outputs/s_4_sequence_S24Aoutput.bam Outputs/s_4_sequence_S24Aoutputsorted

and this sorted Bam file was run in cufflinks to find the counts of reads hitting in each transcript region as;
./cufflinks -o output s_4_sequence_S24Asorted.bam

It runs till 80% of data is processed and hangs;

erml90-68:cufflinks-1.0.0.OSX_x86_64 waseem$ ./cufflinks -o output s_4_sequence_S24Asorted.bam
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v1.0.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
open: No such file or directory
File s_4_sequence_S24Asorted.bam doesn't appear to be a valid BAM file, trying SAM...
Error: cannot open alignment file s_4_sequence_S24Asorted.bam for reading
erml90-68:cufflinks-1.0.0.OSX_x86_64 waseem$ ./cufflinks -o output s_4_sequence_S24Aoutputsorted.bam
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v1.0.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
[18:21:30] Inspecting reads and determining fragment length distribution.
> Processing Locus Glyma0169s00210.1|PACid:162 [******************** ] 80%

I don't know whats going on, and where lies the error.
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Old 09-21-2011, 06:43 AM   #10
sd3
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Hi,

I also had the same problem (on 32-bit ubuntu)
"cufflinks: error while loading shared libraries: libboost_thread.so.1.42.0: cannot open shared object file: No such file or directory"

Setting the LD_LIBRARY_PATH fixed it for me:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/

/usr/local/lib is the default installation directory, but you should use the path to your directory containing libboost_thread.so.1.42.0

Hope that helps

Last edited by sd3; 09-21-2011 at 07:09 AM. Reason: clarification of path
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Old 09-21-2011, 06:58 AM   #11
Sherry
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Will try. Thanks!
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Old 10-24-2011, 12:01 AM   #12
qqtwee
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the same error,need help! thanks!
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Old 07-23-2012, 05:02 AM   #13
Jluis
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I read this post searching for a solution to an issue I'm suffering while using Cufflinks. I try to run it on a series of tophat bam files obtained from an alignment to the Rattus norvegicus reference genome (rn4).
Cufflinks hangs at 80% of the analysis while trying to match a result against the ChrUn reference. I tried to create a "ChrUn free" reference in order to avoid this bug, but it still gets stuck at the same reads group:

"Inspecting bundle chrUn:427619-427681 with 20 reads"

It stays there for hours as if the program were running, but don't do anything...

Can somebody please help me on how to avoid this error or to solve it?

Thanks in advance

JL

Last edited by Jluis; 07-23-2012 at 07:03 AM. Reason: Grammar
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