Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • trinity run error

    Hi,everyone

    I am using trinity for assembly.I installed trinity according to this website https://github.com/trinityrnaseq/trinityrnaseq/wiki ,but when I use this commands to test it,it running failure.The commands is:

    cd sample_data/test_Trinity_Assembly/

    ./runMe.sh

    After I use that commands to test trinity,it feedback the following error.



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



    #######################################################################
    Inchworm file: /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.K25.L25.fa detected.
    Skipping Inchworm Step, Using Previous Inchworm Assembly
    #######################################################################

    -- Skipping CMD: /home/hanxuan/trinityrnaseq-2.1.1/util/misc/fasta_filter_by_min_length.pl /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/inchworm.K25.L25.fa 100 > /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100, checkpoint exists.
    -- Skipping CMD: bowtie-build -q /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100, checkpoint exists.
    * Running CMD: bash -c " set -o pipefail; bowtie -a -m 20 --best --strata --threads 4 --chunkmbs 512 -q -S -f /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa | samtools view -@ 4 -F4 -Sb - | samtools sort -m 536870912 -@ 4 -no - - > /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"
    [bam_header_read] EOF marker is absent. The input is probably truncated.
    [samopen] SAM header is present: 342 sequences.
    # reads processed: 122300
    # reads with at least one reported alignment: 106930 (87.43%)
    # reads that failed to align: 15370 (12.57%)
    Reported 127560 alignments to 1 output stream(s)
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    bash: 行 1: 8337 已完成 bowtie -a -m 20 --best --strata --threads 4 --chunkmbs 512 -q -S -f /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa
    8338 段错误 (核心已转储) | samtools view -@ 4 -F4 -Sb -
    8339 段错误 (核心已转储) | samtools sort -m 536870912 -@ 4 -no - - > /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam
    Trinity run failed. Must investigate error above.





    Would you please give me some advice to solve this problem? I cant't solve it.Pleasre help me!

    thanks
    TomBoy;

  • #2
    I would take the failing command:

    Code:
    set -o pipefail; bowtie -a -m 20 --best --strata --threads 4 --chunkmbs 512 -q -S -f /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/inchworm.K25.L25.fa.min100 both.fa | samtools view -@ 4 -F4 -Sb - | samtools sort -m 536870912 -@ 4 -no - - > /home/hanxuan/trinityrnaseq-2.1.1/sample_data/test_Trinity_Assembly/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam"
    And run each of the sub-programs (i.e., those within a pipe) one at a time to see if the individual programs throws up an error.

    It is very hard to debug a large command with lots of pipes. Better to break down the large command.

    Comment


    • #3
      Dear westernman

      To tell the truth,I'm a college student major in software engineering.I had not used it before.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X