Trinity freezes on clustering

[naono]

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 -@ 32 -F4 -Sb - | samtools sort -@ 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 ?

[naono]

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

Can someone guess what was the problem?

[naono]

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 -@ 16 -no - - > chrysalis/iworm.bowtie.nameSorted.bam"

and stalled without creating output file.

[naono]

I updated samtools to 1.4.1 and it worked!!

Trinity 2.4.0
Bowtie 2.3.2
Samtools 1.4.1