Entering edit mode
7.9 years ago
lakhujanivijay
5.8k
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
