Trinity not able to detect Java 1.8

[Hasnahana Chetia]

Hi All,

I have Java 1.8 installed in my system. Running java -version shows 1.8. However, Trinity 2.5.1 detects the older version 1.7.

I proceeded with the java override option, but Trinity run fails between the chrysalis step.

Please help.

--

Ms. Hasnahana Chetia

Research Scholar,

Bioengineering Research Laboratory,

Dept. of Biosciences and Bioengineering ,

Indian Institute of Technology Guwahati, Assam-39

[Brian Haas]

Hi,

Just make sure that java 1.8 version is found in your PATH setting before the 1.7 version.

which java

should point to the 1.8 version.

If that doesn't happen, update your PATH env var setting.

best,

~b

--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Hasnahana Chetia]

Hi Brian,

I am using a slurm script to submit Trinity assembly of my dataset. Can you please comment on what might be wrong? Is it still Java?

Here's my script-

#!/bin/sh

#SBATCH --job-name=Trinity_32    # Job name

#SBATCH -N 1                           # Maximum CPU cores for job

#SBATCH -n 12                   #all cores from same node

#SBATCH --mem=20gb                     # Memory limit

#SBATCH --time=2-00:00:00               # Time limit days-hrs:min:sec

#SBATCH -e errorlog_%j.err               # standard error

#SBATCH --output=loggeneraltrinity32   # Standard output and error log

for file in *R1.fq

do

. ~/.profile

withpath="${file}"

filename=${withpath##*/}

base="${filename%*_*.fq}"

echo "${base}"

time Trinity --seqType fq --bypass_java_version_check --max_memory 18G --left "${base}"_R1.fq  --right "${base}"_R2.fq --CPU 12 --no_normalize_reads --KMER_SIZE 32 --output general_trinity_"${base}"_32

done;

Here's what I get after run fail,

--------------------------------------------------------

-------------------- Chrysalis -------------------------

-- (Contig Clustering & de Bruijn Graph Construction) --

--------------------------------------------------------

inchworm_target: /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/both.fa

bowite_reads_fa: /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/both.fa

chrysalis_reads_fa: /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/both.fa

* Running CMD: /home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/inchworm.K32.L32.DS.fa 100 10 > /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/chrysalis/inchworm.K32.L32.DS.fa.min100

* Running CMD: bowtie2-build -o 3 /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/chrysalis/inchworm.K32.L32.DS.fa.min100 /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/chrysalis/inchworm.K32.L32.DS.fa.min100 1>/dev/null

* Running CMD: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 12 -f --score-min G,46,0 -x /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/chrysalis/inchworm.K32.L32.DS.fa.min100 /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/both.fa  | samtools view -@ 12 -F4 -Sb - | samtools sort -m 805306368 -@ 12 -no - - > /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/chrysalis/iworm.bowtie.nameSorted.bam"

139641624 reads; of these:

  139641624 (100.00%) were unpaired; of these:

    281744 (0.20%) aligned 0 times

    57569891 (41.23%) aligned exactly 1 time

    81789989 (58.57%) aligned >1 times

99.80% overall alignment rate

[bam_sort_core] merging from 96 files...

[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.

[E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes

[bam_merge_core] error: './samtools.63291.393.tmp.0054.bam' is truncated.

Error, cmd: bash -c " set -o pipefail;bowtie2 --local -k 2 --threads 12 -f --score-min G,46,0 -x /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/chrysalis/inchworm.K32.L32.DS.fa.min100 /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/both.fa  | samtools view -@ 12 -F4 -Sb - | samtools sort -m 805306368 -@ 12 -no - - > /scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/headcropped_assembly/som_assembly/general_trinity_15TRIM_SOM_32/chrysalis/iworm.bowtie.nameSorted.bam"  2>tmp.62365.stderr died with ret 256 at /home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/PerlLib/Pipeliner.pm line 166

        Pipeliner::run('Pipeliner=HASH(0xa5c030)') called at /home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/Trinity line 1750

        main::run_chrysalis('/scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/...', '/scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/...', 200, 500, undef, '/scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/...', '/scratch/hasnahana/transcriptome/som/combinedOldNew/assembly/...') called at /home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/Trinity line 1595

        main::run_Trinity() called at /home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/Trinity line 1262

        eval {...} called at /home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/Trinity line 1261

Trinity run failed. Must investigate error above.

[Brian Haas]

not sure...  

the key error is:  [bam_merge_core] error: './samtools.63291.393.tmp.0054.bam' is truncated.

If samtools or bowtie are giving you trouble, you can try adding the --no_bowtie parameter and see if that compensates.

[Hasnahana Chetia]

Hi Brian and All,

The /usr/bin/java has version 1.8.

Yet, Trinity throws the foll. error-

Error, Trinity requires access to Java version 1.8 or higher.  Currently installed version is: java version "1.7.0_65"

OpenJDK Runtime Environment (rhel-2.5.1.2.el6_5-x86_64 u65-b17)

OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode)

Anyone else facing this problem? 

On Mon, Oct 23, 2017 at 10:42 PM, Brian Haas <bh...@broadinstitute.org> wrote:

[Brian Haas]

assembling w/o bowtie should make a minor difference, likely won't matter much in most cases, but we prefer to include it when possible.

Wrt the java issue, you might need to update your job runner script to update the PATH setting so that /usr/bin  is the first thing in your PATH. 

putting

  export PATH=/usr/bin:${PATH}

right before the Trinity command.

~b

[Hasnahana Chetia]

Hi Brian,

I think I am able to figure out most of the things now.

FInal question, Trinity requires JDK or JRE?

On Tue, Oct 24, 2017 at 2:21 AM, Brian Haas <bh...@broadinstitute.org> wrote:

It looks like it’s finding the right version of Java here.

You might try just having it run Java with the -version parameter to report it just to be sure 

-Brian

(by iPhone)

On Oct 23, 2017, at 4:30 PM, Hasnahana Chetia <hasc...@gmail.com> wrote:

Here you go.

/usr/bin/:/usr/bin/:/usr/bin/:/usr/bin/:/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java:/usr/bin:/home/hasnahana/softwares/FastQC/:/usr/bin/:/home/hasnahana/bin:/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java:/usr/bin:/home/hasnahana/softwares/FastQC/:/usr/bin:/home/hasnahana/softwares/FastQC/:/home/hasnahana/bin:/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java:/home/hasnahana/bin:/home/hasnahana/bin:/usr/bin:/home/hasnahana/softwares/FastQC/:/home/apps/cdac/Python-2.7.10/bin:/cm/shared/apps/slurm/15.08.13/sbin:/cm/shared/apps/slurm/15.08.13/bin:/cm/local/apps/gcc/5.2.0/bin:/cm/local/apps/cuda/libs/current/bin:/cm/shared/apps/cuda75/sdk/7.5.18/bin/x86_64/linux/release:/cm/shared/apps/cuda75/toolkit/7.5.18/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/bin:/home/hasnahana/bin:/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java:/home/hasnahana/softwares/:/home/hasnahana/softwares/standard-RAxML-master/:/home/hasnahana/softwares/SOAPdenovo-Trans-bin-v1.03/:/home/hasnahana/softwares/bbmap/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish-2.2.6/bin/:/home/hasnahana/softwares/Rcorrector-master/:/home/hasnahana/softwares/cutadapt-master/cutadapt/:/home/hasnahana/softwares/cutadapt-master/cutadapt/scripts:/home/hasnahana/softwares/FastQC/:/home/hasnahana/softwares/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/BIN/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/parafly-code/bin/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/Trimmomatic-0.36/:/home/hasnahana/softwares/bowtie2-2.3.3/:/home/hasnahana/softwares/velvet-master/:/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java:/home/hasnahana/softwares/:/home/hasnahana/softwares/standard-RAxML-master/:/home/hasnahana/softwares/SOAPdenovo-Trans-bin-v1.03/:/home/hasnahana/softwares/bbmap/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish-2.2.6/bin/:/home/hasnahana/softwares/Rcorrector-master/:/home/hasnahana/softwares/cutadapt-master/cutadapt/:/home/hasnahana/softwares/cutadapt-master/cutadapt/scripts:/home/hasnahana/softwares/FastQC/:/home/hasnahana/softwares/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/BIN/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/parafly-code/bin/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/Trimmomatic-0.36/:/home/hasnahana/softwares/bowtie2-2.3.3/:/home/hasnahana/softwares/velvet-master/:/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/:/usrn/:/home/hasnahana/softwares/:/home/hasnahana/softwares/standard-RAxML-master/:/home/hasnahana/softwares/SOAPdenovo-Trans-bin-v1.03/:/home/hasnahana/softwares/bbmap/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish-2.2.6/bin/:/home/hasnahana/softwares/Rcorrector-master/:/home/hasnahana/softwares/cutadapt-master/cutadapt/:/home/hasnahana/softwares/cutadapt-master/cutadapt/scripts:/home/hasnahana/softwares/FastQC/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/BIN/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/parafly-code/bin/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/Trimmomatic-0.36/:/home/hasnahana/softwares/bowtie2-2.3.3/:/home/hasnahana/softwares/velvet-master/:/home/abc123/custom_bin_directory/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/java:/usr/lib/jvm/jre-1.8.0-openjdk.x86_64/bin/:/usr/bin/:/usrn/:/home/hasnahana/softwares/:/home/hasnahana/softwares/standard-RAxML-master/:/home/hasnahana/softwares/SOAPdenovo-Trans-bin-v1.03/:/home/hasnahana/softwares/bbmap/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/jellyfish-2.2.6/bin/:/home/hasnahana/softwares/Rcorrector-master/:/home/hasnahana/softwares/cutadapt-master/cutadapt/:/home/hasnahana/softwares/cutadapt-master/cutadapt/scripts:/home/hasnahana/softwares/FastQC/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/BIN/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/parafly-code/bin/:/home/hasnahana/softwares/trinityrnaseq-Trinity-v2.4.0/trinity-plugins/Trimmomatic-0.36/:/home/hasnahana/softwares/bowtie2-2.3.3/:/home/hasnahana/softwares/velvet-master/:/home/hasnahana/bin:/home/hasnahana/bin

/usr/bin/java

On Tue, Oct 24, 2017 at 1:54 AM, Brian Haas <bh...@broadinstitute.org> wrote:

To debug it, try adding 

  echo $PATH;   which java

to your script, and let's see what it outputs.  You can comment out the Trinity command so that doesn't run.

~b

On Mon, Oct 23, 2017 at 4:20 PM, Hasnahana Chetia <hasc...@gmail.com> wrote:

Hi Brian,

I am sorry to say that I am still getting the same error.

I also tried setting PATH and ~/.profile

Not working. 🙁

On Tue, Oct 24, 2017 at 1:35 AM, Brian Haas <bh...@broadinstitute.org> wrote:

no worries.

You'd want to include that line exactly as I specified it.  It just puts the /usr/bin path at the front of whatever the current PATH setting is set to.

best,

~b

On Mon, Oct 23, 2017 at 3:50 PM, Hasnahana Chetia <hasc...@gmail.com> wrote:

Thank you Brian for your prompt replies so late.

Last query- should I use the export command as you perovided it or specify the path of java 1.8 in the red part--- export PATH=/usr/bin:${PATH}

[Brian Haas]

Great!

You should just need the JRE.

best,

~b

[Hasnahana Chetia]

Thanks for all the help Brian.

For HPC users facing problem wirh java.

Download the java version of your choice from officiial website (.tar.gz file).

Unzip it in HPC account and add the path to your ~/.profile.

Then add . ~/.profile to your script before your command.

Sail smoothly.