Question: Error running Trinity
0
gravatar for Vijay Lakhujani
2.5 years ago by
Vijay Lakhujani3.1k
India
Vijay Lakhujani3.1k wrote:

I am running Trinity with following commands:

Trinity --seqType fq --JM 1G --SS_lib_type FR --left my_R1.fq --right my_R2.fq --output /out

and I am encountering below issue,any help?

Current settings:
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 1105984
max locked memory       (kbytes, -l) unlimited
max memory size         (kbytes, -m) unlimited
open files                      (-n) 4096
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) unlimited
cpu time               (seconds, -t) unlimited
max user processes              (-u) 1105984
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited


Paired mode requires bowtie. Found bowtie at: /usr/local/bin/bowtie

 and bowtie-build at /home/corona/bin/bowtie-build


Found samtools at: /share/apps/bioscope-1.3.1/bioscope/bin/samtools

-since butterfly will eventually be run, lets test for proper execution of java
#######################################
Running Java Tests
Tuesday, May 17, 2016: 12:13:10 CMD: java -Xmx64m -jar /export/apps/trinityrnaseq_r20140717/util/support_scripts/ExitTester.jar 0
CMD finished (1 seconds)
Tuesday, May 17, 2016: 12:13:11 CMD: java -Xmx64m -jar /export/apps/trinityrnaseq_r20140717/util/support_scripts/ExitTester.jar 1
-we properly captured the java failure status, as needed.  Looking good.
Java tests succeeded.
###################################

Converting input files. (in parallel)Use of uninitialized value in array dereference at /export/apps/trinityrnaseq_r20140717/Trinity line 1171.
Use of uninitialized value in array dereference at /export/apps/trinityrnaseq_r20140717/Trinity line 1172.
Can't locate auto/threads/error.al in @INC (@INC contains: /export/apps/trinityrnaseq_r20140717/PerlLib /share/apps/bioscope-1.3.1/bioscope/lib/perl/x86_64-linux-thread-multi /share/apps/bioscope-1.3.1/bioscope/lib/perl /home/corona/Desktop/toral_rice_small_rna/mirdeep2/lib/ /share/apps/MOCAT/src /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /export/apps/trinityrnaseq_r20140717/Trinity line 1174
error trinity • 1.2k views
ADD COMMENTlink modified 5 months ago • written 2.5 years ago by Vijay Lakhujani3.1k
0
gravatar for Alvin
2.4 years ago by
Alvin0
Alvin0 wrote:

I also met this problem. My error message is shown below:

Can't locate auto/threads/error.al in @INC (@INC contains: /home/yb47525/software/trinityrnaseq-2.2.0/util/../PerlLib /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /home/yb47525/software/trinityrnaseq-2.2.0/util/insilico_read_normalization.pl line 336
Error, cmd: /home/yb47525/software/trinityrnaseq-2.2.0/util/insilico_read_normalization.pl --seqType fq --JM 2G  --max_cov 50 --CPU 4 --output /home/yb47525/work_items/test_software/trinity_test/trinity_out_dir/insilico_read_normalization --SS_lib_type RF  --no_cleanup  --left /home/yb47525/software/trinityrnaseq-2.2.0/sample_data/test_Trinity_Assembly/reads.left.fq.gz,/home/yb47525/software/trinityrnaseq-2.2.0/sample_data/test_Trinity_Assembly/reads2.left.fq.gz --right /home/yb47525/software/trinityrnaseq-2.2.0/sample_data/test_Trinity_Assembly/reads.right.fq.gz,/home/yb47525/software/trinityrnaseq-2.2.0/sample_data/test_Trinity_Assembly/reads2.right.fq.gz --pairs_together --PARALLEL_STATS   died with ret 512 at /home/yb47525/software/trinityrnaseq-2.2.0/Trinity line 2206.

Then I installed threads.pm and set PERL5LIB to my environment variation. The problem has been solved.

ADD COMMENTlink modified 5 months ago by Vijay Lakhujani3.1k • written 2.4 years ago by Alvin0
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