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Old 04-23-2017, 08:22 PM   #1
naono
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Location: Japan

Join Date: Dec 2012
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Default 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 ?
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Old 04-30-2017, 06:05 PM   #2
naono
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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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Old 05-12-2017, 04:27 PM   #3
naono
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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 at 04:29 PM.
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Old 05-12-2017, 11:49 PM   #4
naono
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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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bowtie 1.2, trinity 2.0.6

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