Trinity version 2.0.6 error

[Odeta Czeranková]

To who it may concern

could you please help us with these kind of errors

./Trinity --seqType fq --SS_lib_type FR --max_memory 32G --left /media/sotino/disk/h_tomentosum/left.fastq --right /media/sotino/disk/h_tomentosum/right.fastq --CPU 12 --no_bowtie --output /media/sotino/disk/h_tomentosum/trinity_results
Trinity version: v2.0.6
sh: 1: curl: not found
sh: 1: curl: not found
-ERROR: couldn't run the network check to confirm latest Trinity software version.

Thursday, September 10, 2015: 13:59:03    CMD: java -Xmx64m -jar /home/sotino/Programy/Trinity/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
Thursday, September 10, 2015: 13:59:03    CMD: java -Xmx64m -jar /home/sotino/Programy/Trinity/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1


----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
----------------------------------------------------------------------------------

Converting input files. (in parallel)Thursday, September 10, 2015: 13:59:04    CMD: /home/sotino/Programy/Trinity/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /media/sotino/disk/h_tomentosum/left.fastq >> left.fa 2> /media/sotino/disk/h_tomentosum/left.fastq.readcount
Thread 1 terminated abnormally: Error, cmd: /home/sotino/Programy/Trinity/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /media/sotino/disk/h_tomentosum/left.fastq >> left.fa 2> /media/sotino/disk/h_tomentosum/left.fastq.readcount  died with ret 32512 at ./Trinity line 2116.
Use of uninitialized value in array dereference at ./Trinity line 1211.
Thursday, September 10, 2015: 13:59:04    CMD: /home/sotino/Programy/Trinity/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --rev  --illumina-trinity --to-fasta /media/sotino/disk/h_tomentosum/right.fastq >> right.fa 2> /media/sotino/disk/h_tomentosum/right.fastq.readcount
Thread 2 terminated abnormally: Error, cmd: /home/sotino/Programy/Trinity/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --rev  --illumina-trinity --to-fasta /media/sotino/disk/h_tomentosum/right.fastq >> right.fa 2> /media/sotino/disk/h_tomentosum/right.fastq.readcount  died with ret 32512 at ./Trinity line 2116.
Use of uninitialized value in array dereference at ./Trinity line 1212.
Trinity run failed. Must investigate error above.

Thanks in advance

[Fulton, Ben]

Hi,

 

I believe error 32512 indicates that fastool was not found. From your Trinity directory, run

 

make

make plugins

 

and then try restarting Trinity.

 

--

Ben Fulton

Research Technologies

Scientific Applications and Performance Tuning

Indiana University

E-Mail: befu...@iu.edu

--
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-u...@googlegroups.com.
To post to this group, send email to trinityrn...@googlegroups.com.
Visit this group at http://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

[sunil...@gmail.com]

Dear Trinity User,

I am new to ubuntu and Trintiy, I am trying to run sample on Trintiyt v 2.0.6 and I got this message, please suggest, Thanks in Advance:

my@server:~$ perl $TRINITY_HOME/Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 4 --max_memory 10G

Trinity version: v2.0.6
sh: 1: curl: not found
sh: 1: curl: not found
-ERROR: couldn't run the network check to confirm latest Trinity software version.

Thursday, September 24, 2015: 13:49:48    CMD: java -Xmx64m -jar /home/ibsd/ngstools/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar
Thursday, September 24, 2015: 13:49:48    CMD: java -Xmx64m -jar /home/ibsd/ngstools/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar
Error, cannot locate file: reads_1.fq at /home/ibsd/ngstools/trinityrnaseq-2.0.6/Trinity line 2084.
    main::create_full_path(ARRAY(0x14e3288), 1) called at /home/ibsd/ngstools/trinityrnaseq-2.0.6/Trinity line 998

Regards,

Sunil

[Mark Chapman]

Dear Sunil,

The error 'Error, cannot locate file: reads_1.fq' suggests your reads aren't in the place you're saying they are, or are called something else. Are they in the folder you are running the command from?

Thanks, Mark

--
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-u...@googlegroups.com.
To post to this group, send email to trinityrn...@googlegroups.com.
Visit this group at http://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.

--

Dr. Mark A. Chapman

M.Ch...@soton.ac.uk

+44 (0)2380 594396

------------------------------------

Centre for Biological Sciences
University of Southampton

Life Sciences Building 85
Highfield Campus
Southampton
SO17 1BJ