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 ?
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 ?
Comment