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  • Trinity fail to start

    Hi I'm new with Trinity, I just trimmed my sequences, but an error appeared and I can not see what's wrong, help!!!
    here my console thanks
    Code:
    perl Trinity --seqType fq --left /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq --right /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq --CPU 6 --max_memory 20G --verbose
    Trinity version: v2.0.6
    -currently using the latest production release of Trinity.
    
    Paired mode requires bowtie. Found bowtie at: /usr/bin/bowtie
    
     and bowtie-build at /usr/bin/bowtie-build
    
    
    Found samtools at: /usr/bin/samtools
    
    -since butterfly will eventually be run, lets test for proper execution of java
    #######################################
    Running Java Tests
    Thursday, March 26, 2015: 15:21:14	CMD: java -Xmx64m -jar /home/tomas/Documentos/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
    CMD finished (1 seconds)
    Thursday, March 26, 2015: 15:21:15	CMD: java -Xmx64m -jar /home/tomas/Documentos/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1
    -we properly captured the java failure status, as needed.  Looking good.
    Java tests succeeded.
    ###################################
    
    
    
    ----------------------------------------------------------------------------------
    -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
    ----------------------------------------------------------------------------------
    
    Converting input files. (in parallel)Thursday, March 26, 2015: 15:21:15	CMD: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq >> left.fa 2> /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq.readcount 
    Thread 1 terminated abnormally: Error, cmd: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq >> left.fa 2> /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1_001_-N_q20.fastq.readcount  died with ret 32512 at Trinity line 2116.
    Use of uninitialized value in array dereference at Trinity line 1211.
    Thursday, March 26, 2015: 15:21:15	CMD: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq >> right.fa 2> /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq.readcount 
    Thread 2 terminated abnormally: Error, cmd: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq >> right.fa 2> /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R2_001_-N_q20.fastq.readcount  died with ret 32512 at Trinity line 2116.
    Use of uninitialized value in array dereference at Trinity line 1212.
    Error prepping sequences. at Trinity line 1215.
    
    Trinity run failed. Must investigate error above.

  • #2
    Have you tried to run the sample data included with Trinity to make sure everything is installed correctly?

    How much memory does your server have? 64G may not be enough.

    See this thread for information similar to your error: http://sourceforge.net/p/trinityrnas...sage/32702412/

    Comment


    • #3
      As you say are an problem with my instalation
      I probe:
      cd $TRINITY_HOME/sample_data/test_Trinity_Assembly/

      ./runMe.sh
      and I have this answer

      Code:
      [email protected]:~/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly$ ./runMe.sh 
      #!/bin/bash -ve
      
      
      if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
          gunzip -c reads.right.fq.gz > reads.right.fq
      fi
      
      if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
          gunzip -c reads.left.fq.gz > reads.left.fq
      fi
      
      if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
          gunzip -c reads2.right.fq.gz > reads2.right.fq
      fi
      
      if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
          gunzip -c reads2.left.fq.gz > reads2.left.fq
      fi
      
      
      
      #######################################################
      ##  Run Trinity to Generate Transcriptome Assemblies ##
      #######################################################
      
      ../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4
      Trinity version: v2.0.6
      -currently using the latest production release of Trinity.
      
      Thursday, March 26, 2015: 16:02:00	CMD: java -Xmx64m -jar /home/tomas/Documentos/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
      Thursday, March 26, 2015: 16:02:01	CMD: java -Xmx64m -jar /home/tomas/Documentos/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1
      Thursday, March 26, 2015: 16:02:01	CMD: mkdir -p /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir
      Thursday, March 26, 2015: 16:02:01	CMD: mkdir -p /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis
      
      
      ----------------------------------------------------------------------------------
      -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
      ----------------------------------------------------------------------------------
      
      Converting input files. (in parallel)Thursday, March 26, 2015: 16:02:01	CMD: gunzip -c /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq.gz > /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq
      Thursday, March 26, 2015: 16:02:01	CMD: gunzip -c /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq.gz > /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq
      Thursday, March 26, 2015: 16:02:01	CMD: gunzip -c /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads2.left.fq.gz > /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads2.left.fq
      Thursday, March 26, 2015: 16:02:01	CMD: gunzip -c /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads2.right.fq.gz > /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads2.right.fq
      Thursday, March 26, 2015: 16:02:01	CMD: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --rev  --illumina-trinity --to-fasta /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa 2> /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq.readcount 
      Thread 1 terminated abnormally: Error, cmd: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --rev  --illumina-trinity --to-fasta /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq >> left.fa 2> /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.left.fq.readcount  died with ret 32512 at ../../Trinity line 2116.
      Use of uninitialized value in array dereference at ../../Trinity line 1211.
      Thursday, March 26, 2015: 16:02:01	CMD: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa 2> /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq.readcount 
      Thread 2 terminated abnormally: Error, cmd: /home/tomas/Documentos/trinityrnaseq-2.0.6/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq >> right.fa 2> /home/tomas/Documentos/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly/reads.right.fq.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.

      Comment


      • #4
        When I use trinity fail to continue, just stay paralised in inchworm, I remember some part of the code that now I can not found it, something like --vermisomethig
        here is what I'm trying
        Code:
        perl Trinity --seqType fq --left /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R1_001_-N_-a_-q20.fastq --right /home/tomas/bin/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R2_001_-N_-a_-q20.fastq --CPU 4 --max_memory 8G

        Comment


        • #5
          Did you successfully run the test data?
          Last edited by GenoMax; 03-31-2015, 06:19 AM.

          Comment


          • #6
            Yes I do the test and was successful

            Comment


            • #7
              How big are you data files (# of reads)?

              This is a quote from Trinity site (and may have changed some but use this as a guide).

              Ideally, you will have access to a large-memory server, roughly having ~1G of RAM per 1M reads to be assembled.
              Your command line option (--max_memory 8G) may be limiting here.

              Comment


              • #8
                I read the same message
                My data are in average 8M reads

                Comment


                • #9
                  One question about trinity too, if I have two differents states of my samples, is better do trinity in both at the same time or I could do it in separate?

                  Comment


                  • #10
                    Since you have 64G use a higher number (e.g. 16G) to see if you can get past the problem.

                    Log the std out/err messages to a file (if you are not using a job scheduler) to see if you can catch additional details.

                    Comment


                    • #11
                      And about my another question, what do you think?

                      Comment


                      • #12
                        --verbose was the part of the command that I was looking for
                        without this trinity don't start in my pc

                        Comment


                        • #13
                          I had to format my laptop, so I was reinstalling trinity, and get this error when run runMe.sh

                          Code:
                          [email protected]:~/Documentos/rna-seq/trinityrnaseq-2.0.6/sample_data/test_Trinity_Assembly$ ./runMe.sh 
                          #!/bin/bash -ve
                          
                          
                          if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
                              gunzip -c reads.right.fq.gz > reads.right.fq
                          fi
                          
                          if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
                              gunzip -c reads.left.fq.gz > reads.left.fq
                          fi
                          
                          if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
                              gunzip -c reads2.right.fq.gz > reads2.right.fq
                          fi
                          
                          if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
                              gunzip -c reads2.left.fq.gz > reads2.left.fq
                          fi
                          
                          
                          
                          #######################################################
                          ##  Run Trinity to Generate Transcriptome Assemblies ##
                          #######################################################
                          
                          ../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4
                          ./runMe.sh: lĂ­nea 26: ../../Trinity: Permiso denegado

                          Comment


                          • #14
                            Looks like you need to add execute permissions for trinity.

                            Comment


                            • #15
                              and how do I do that?

                              Comment

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