Unable to access juicer_tools.jar

[aakashsur]

I get this error -

Error: Unable to access jarfile /opt/scripts/common/juicer_tools.jar

When trying to run the docker image through singularity, here's the full error -

[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -SP5M -t 40 /juicedir/yeast_100x.contigs.fasta /data/splits/yeast_R1.fastq.gz /data/splits/yeast_R2.fastq.gz
[main] Real time: 11.350 sec; CPU: 141.117 sec
(-:  Align of /data/splits/yeast.fastq.gz.sam done successfully
(-: Finished sorting all sorted files into a single merge.
Picked up _JAVA_OPTIONS: -Xmx16384m
Error: Unable to access jarfile /opt/scripts/common/juicer_tools.jar
Picked up _JAVA_OPTIONS: -Xmx16384m
Error: Unable to access jarfile /opt/scripts/common/juicer_tools.jar
***! Can't find inter.hic in /data/aligned/inter_30.hic
***! Error! Either inter.hic or inter_30.hic were not created
Either inter.hic or inter_30.hic were not created.  Check /data/aligned for results

[charlotte-west]

I'm also having a similar issue. When run using Singularity:

singularity shell docker://aidenlab/juicer:latest

I'm able to access juicer.sh, but I want to use arrowhead and hiccups from juicer tools which I believe is accessed through the /opt/scripts/common/juicer_tools.jar file which points to /opt/scripts/common/juicer_tools.1.7.6_jcuda.0.8.jar. However juicer_tools.1.7.6_jcuda.0.8.jar has read only rights (-rw------- 1 root root 31M Oct 27 2017 juicer_tools.1.7.6_jcuda.0.8.jar) :

Singularity> /opt/scripts/common/juicer_tools.1.7.6_jcuda.0.8.jar
bash: /opt/scripts/common/juicer_tools.1.7.6_jcuda.0.8.jar: Permission denied

[charlotte-west]

I've made a work-around that seems to be working for me. I believe it's to do with Singularity's permissions. In the docker image the juicer_tools.jar does not have general read/write/execute permissions. I built my own docker container, the Dockerfile is very simple:

FROM aidenlab/juicer:1.0.13

# Add executability to juicer tools file
RUN chmod 777 /opt/juicer-1.6.2/CPU/common/juicer_tools.1.7.6_jcuda.0.8.jar

# Remove entrypoint
ENTRYPOINT []

I add all permissions to the file that juicer_tools.jar points to. I removed the entrypoint for debugging purposes. I built the docker file:

docker build -f ./Dockerfile -t my/container:latest .

And run it up using singularity. Once the container is spun up:

Singularity> java -Xms512m -Xmx2048m -jar juicer_tools.1.7.6_jcuda.0.8.jar
Juicer Tools Version 1.7.6
Usage:
	dump <observed/oe> <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize> [outfile]
	dump <norm/expected> <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr> <BP/FRAG> <binsize> [outfile]
	dump <loops/domains> <hicFile URL> [outfile]
	pre [options] <infile> <outfile> <genomeID>
	addNorm <input_HiC_file>
	pearsons [-p] <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr> <BP/FRAG> <binsize> [outfile]
	eigenvector -p <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr> <BP/FRAG> <binsize> [outfile]
	apa <hicFile(s)> <PeaksFile> <SaveFolder>
	arrowhead <hicFile(s)> <output_file>
	hiccups <hicFile> <outputDirectory>
	hiccupsdiff <firstHicFile> <secondHicFile> <firstLoopList> <secondLoopList> <outputDirectory>
	validate <hicFile>
	-h, --help print help
	-v, --verbose verbose mode
	-V, --version print version
Type juicer_tools <commandName> for more detailed usage instructions

works as expected.

[nchernia]

Thank you, this is great info to share. Meanwhile, we are working on updating the Juicer Docker and will share it once it's finished.

…

On Wed, Apr 7, 2021 at 8:55 AM charlotte-west ***@***.***> wrote: I've made a work-around that seems to be working for me. I believe it's to do with Singularity's permissions. In the docker image the juicer_tools.jar does not have general read/write/execute permissions. I built my own docker image, the Dockerfile is very simple: FROM aidenlab/juicer:1.0.13 # Add executability to juicer tools file RUN chmod 777 /opt/juicer-1.6.2/CPU/common/juicer_tools.1.7.6_jcuda.0.8.jar # Remove entrypoint ENTRYPOINT [] I add all permissions to the file that juicer_tools.jar points to. I removed the entrypoint for debugging purposes. I built the docker file: docker build -f ./Dockerfile -t my/container:latest . And run it up using singularity. Once the container is spun up: java -Xms512m -Xmx2048m -jar juicer_tools.1.7.6_jcuda.0.8.jar works as expected. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAK2EW3SPSFOXMH2CEPP46DTHRI3ZANCNFSM4WDK5ZMA> .

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

[trum994]

I'm also running into the exact same issue while running with Singularity:

[main] Real time: 609.011 sec; CPU: 1911.661 sec
(-: Align of /data/splits/HIC003_S2_L001_001.fastq.gz.sam done successfully
(-: Finished sorting all sorted files into a single merge.
Picked up _JAVA_OPTIONS: -Xmx16384m
> Error: Unable to access jarfile /opt/scripts/common/juicer_tools.jar
Picked up _JAVA_OPTIONS: -Xmx16384m
> Error: Unable to access jarfile /opt/scripts/common/juicer_tools.jar
***! Can't find inter.hic in /data/aligned/inter_30.hic
***! Error! Either inter.hic or inter_30.hic were not created
Either inter.hic or inter_30.hic were not created. Check /data/aligned for results

I'll have to try workaround from @charlotte-west

[apredeus]

Yep, same issue still.

[adthrasher]

+1 for this issue.

[icmeyer]

This is still an issue. Went ahead with the same fix as @charlotte-west. I built the container locally using Docker and then pushed to docker hub. I ran into another issue with the scripts path (similar to aidenlab/juicer#352 (comment)). Was able to fix that using the -D flag. That lets me call the singularity image like so

#!/bin/bash
# Run juicer using the Docker container using singularity
singularity exec -B ./testdir/:/data \
                 -B ./testdir/:/juicerdir \
                 docker://icmeyer/juicer_tools /opt/scripts/juicer.sh \
                 -d /data \
                 -D  /opt/ \
                 ...

Works well for me, because sometimes I want to use juicer tools instead and they can be accessed in the same image.

[SomePersonSomeWhereInTheWorld]

This is still an issue. Went ahead with the same fix as @charlotte-west. I built the container locally using Docker and then pushed to docker hub. I ran into another issue with the scripts path (similar to aidenlab/juicer#352 (comment)). Was able to fix that using the -D flag. That lets me call the singularity image like so

#!/bin/bash
# Run juicer using the Docker container using singularity
singularity exec -B ./testdir/:/data \
                 -B ./testdir/:/juicerdir \
                 docker://icmeyer/juicer_tools /opt/scripts/juicer.sh \
                 -d /data \
                 -D  /opt/ \
                 ...

Works well for me, because sometimes I want to use juicer tools instead and they can be accessed in the same image.

Thanks I got further with your container, albeit I get this error:

ARROWHEAD:

Picked up _JAVA_OPTIONS: -Xmx16384m
Reading file: /data/aligned/inter_30.hic
Warning: Hi-C map is too sparse to find many domains via Arrowhead.
Exiting. To disable sparsity check, use the --ignore_sparsity flag.

HiCCUPS:

GPUs are not installed so HiCCUPs cannot be run

(-: Postprocessing successfully completed, maps too sparse to annotate or GPUs unavailable (-:
/opt/scripts/common/check.sh: line 47: [: users: integer expression expected
(-: Pipeline successfully completed (-:
Run cleanup.sh to remove the splits directory
Check /data/aligned for results

Edit: it appears this is a bug in 1.x versions of Juicer for CPU. No fix mentioned anywhere.