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  • lupid
    replied
    Yes I do the test and was successful

    Leave a comment:


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

    Leave a comment:


  • lupid
    replied
    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

    Leave a comment:


  • lupid
    replied
    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:
    tomas@HP-Pavilion:~/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.

    Leave a comment:


  • GenoMax
    replied
    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/

    Leave a comment:


  • lupid
    started a topic Trinity fail to start

    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.

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