Errors running Trinity

[p3280...@gmail.com]

Hi,

I am having some difficulty running trinity.

Here is my command

Trinity --seqType fq --max_memory 50G --bypass_java_version_check --no_version_check --no_bowtie --min_kmer_cov 3 --left /HOME/gdim_sl_xielw/WORKSPACE/User/Pan/huangsangyu/Wei_NGS/C1/reads_1.fq  --right /HOME/gdim_sl_xielw/WORKSPACE/User/Pan/huangsangyu/Wei_NGS/C1/reads2_2.fq --CPU 10

There are a lot of the following errors like this:

##############

perl: warning: Setting locale failed.

perl: warning: Please check that your locale settings:

LANGUAGE = (unset),

LC_ALL = (unset),

LANG = "zh_CN.UTF-8"

    are supported and installed on your system.

perl: warning: Falling back to the standard locale ("C").

Tuesday, October 24, 2017: 11:01:31 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /WORK/app/Trinity/v2.3.2/util/support_scripts/ExitTester.jar 0

Error encountered in testing for running of a simple java application. Please check your java configuration.

Error, cmd: java -Xmx64m -XX:ParallelGCThreads=2 -jar /WORK/app/Trinity/v2.3.2/util/support_scripts/ExitTester.jar 0 died with ret 11 at /WORK/app/Trinity/v2.3.2/Trinity line 2427.

#################

There are also errors with java_version and Trinity version and bowtie, but I skipped them.

My Trinity version is 2.3.2

My Java version is 1.8.0_141

Thanks.

Xiaohan

[Brian Haas]

bypassing the java version check can be ok, but it still needs to be able to run java.

If you run

  java -Xmx64m -XX:ParallelGCThreads=2 -jar /WORK/app/Trinity/v2.3.2/util/support_scripts/ExitTester.jar 0 

do you get an error message?

--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.
To post to this group, send email to trinityrnaseq-users@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[maria Rodriguez]

Hi, I am working with trinity, I have been this error, but I dont understant which is the error?

could you help me please?

inchworm_target: /home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/both.fa

bowite_reads_fa: /home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/both.fa

chrysalis_reads_fa: /home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/both.fa

* Running CMD: /home/jhernandez/data/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/inchworm.K25.L25.fa 100 10 > /home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/chrysalis/inchworm.K25.L25.fa.min100

* Running CMD: bowtie2-build -o 3 /home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/chrysalis/inchworm.K25.L25.fa.min100 /home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/chrysalis/inchworm.K25.L25.fa.min100 1>/dev/null

bowtie2-build: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

Error, cmd: bowtie2-build -o 3 /home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/chrysalis/inchworm.K25.L25.fa.min100 /home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/chrysalis/inchworm.K25.L25.fa.min100 1>/dev/null 2>tmp.135821.stderr died with ret 32512 at /home/jhernandez/data/trinityrnaseq-Trinity-v2.4.0/PerlLib/Pipeliner.pm line 166.

        Pipeliner::run('Pipeliner=HASH(0x2286980)') called at /home/jhernandez/data/trinityrnaseq-Trinity-v2.4.0/Trinity line 1750

        main::run_chrysalis('/home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/inc...', '/home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/bot...', 200, 500, 'FR', '/home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/bot...', '/home/jhernandez/data/librerias/Cc/outputJNCA/Trinity_8Cc/bot...') called at /home/jhernandez/data/trinityrnaseq-Trinity-v2.4.0/Trinity line 1595

        main::run_Trinity() called at /home/jhernandez/data/trinityrnaseq-Trinity-v2.4.0/Trinity line 1262

        eval {...} called at /home/jhernandez/data/trinityrnaseq-Trinity-v2.4.0/Trinity line 1261

Trinity run failed. Must investigate error above.

On Tuesday, October 24, 2017 at 5:23:51 AM UTC-5, Brian Haas wrote:

bypassing the java version check can be ok, but it still needs to be able to run java.

If you run

  java -Xmx64m -XX:ParallelGCThreads=2 -jar /WORK/app/Trinity/v2.3.2/util/support_scripts/ExitTester.jar 0 

do you get an error message?

thanks for your help

To post to this group, send email to trinityrn...@googlegroups.com.

Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.