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Trinity freezes on clustering

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  • Trinity freezes on clustering

    Recently we tried to replicate our previous result of de novo assembly using Trinity 2.0.6.
    and
    Bowtie 1.2.0

    First it seems working but Just after
    "Trinity Phase 1: Clustering of RNA-Seq Reads",
    on the command

    cmd: bash -c " set -o pipefail; bowtie -a -m 20 --best --strata --threads 32 --chunkmbs 512 -q -S -f \
    ./chrysalis/inchworm.K25.L25.fa.min100 both.fa | samtools view [email protected] 32 -F4 -Sb - | samtools sort [email protected] 32 -no - - > /project/hikaku_db/nono/sync/opium_poppy2/trinity.3s1/trinity.POL2/chrysalis/iworm.bowtie.nameSorted.bam" 2>/dev/null
    1
    it seems to freeze for hours and days without any output.

    Also, I run the corresponding command directly, instead of use pipeline, save the output for a temporary file, but the process froze again before finishing to write the temporal output file.

    Does anyone has some comment or suggestion to solve the problem ?

  • #2
    I have edited the cmd to use bowtie version 1.0.0, and it worked.

    Can someone guess what was the problem?

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    • #3
      The same trouble occurred using
      Trinity 2.4.0
      Bowtie 2.3.1
      Samtools 1.4

      It goes to the line

      * Running CMD: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 16 -f --score-min G,46,0 \
      -x chrysalis/inchworm.K25.L25.fa.min100 both.fa | samtools view - @ 16 -F4 -Sb - | samtools \
      sort -m 4294967296 [email protected] 16 -no - - > chrysalis/iworm.bowtie.nameSorted.bam"

      and stalled without creating output file.
      Last edited by naono; 05-12-2017, 04:29 PM.

      Comment


      • #4
        I updated samtools to 1.4.1 and it worked!!

        Trinity 2.4.0
        Bowtie 2.3.2
        Samtools 1.4.1

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