problem in juicer tools run

[Ritz]

Hello,

I am using Juicer tools for Hi-C analysis and run test data using the following command:

/home/juicer-master/CPU/juicer.sh -d /home/Juicer_test_run -s MboI -p /home/Juicer_test_run/references -y /home/Juicer_test_run/restriction_sites -z /home/Juicer_test_run/references/chr19.fa -D /home/Programs/juicer-master -t 35

After running the programme following error got:

(-: Looking for fastq files...fastq files exist
(-: Aligning files matching /home/Juicer_test_run/fastq/*_R*.fastq*
 to genome hg19 with site file /home/Juicer_test_run/restriction_sites
(-: Created /home/Juicer_test_run/splits and /home/Juicer_test_run/aligned.
Running command bwa mem -t 35 /home/Juicer_test_run/references/chr19.fa /home/Juicer_test_run/splits/chr19_R1.fastq.gz > /home/Juicer_test_run/splits/chr19_R1.fastq.gz.sam

:

:

:

:

[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 35 /home/Juicer_test_run/references/chr19.fa /home/Juicer_test_run/splits/chr19_R2.fastq.gz
[main] Real time: 774.304 sec; CPU: 27144.391 sec
(-: Mem align of /home/Juicer_test_run/splits/chr19_R2.fastq.gz.sam done successfully
(-: Sort read 1 aligned file by readname completed.
(-: Sort read 2 aligned file by readname completed.
(-: /home/samir/Juicer_test_run/splits/chr19.fastq.gz.sam created successfully.
(-: Finished sorting all sorted files into a single merge.
Picked up _JAVA_OPTIONS: -Xmx16384m
Picked up _JAVA_OPTIONS: -Xmx16384m
java.io.FileNotFoundException: /home/Juicer_test_run/references (Is a directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at juicebox.data.HiCFileTools.loadChromosomes(HiCFileTools.java:140)
    at juicebox.tools.clt.old.PreProcessing.readArguments(PreProcessing.java:80)
    at juicebox.tools.HiCTools.main(HiCTools.java:97)
Exception in thread "main" java.lang.NullPointerException
    at java.io.Reader.<init>(Reader.java:78)
    at java.io.InputStreamReader.<init>(InputStreamReader.java:72)
    at juicebox.data.HiCFileTools.loadChromosomes(HiCFileTools.java:154)
    at juicebox.tools.clt.old.PreProcessing.readArguments(PreProcessing.java:80)
    at juicebox.tools.HiCTools.main(HiCTools.java:97)
Picked up _JAVA_OPTIONS: -Xmx16384m
Picked up _JAVA_OPTIONS: -Xmx16384m
java.io.FileNotFoundException: /home/Juicer_test_run/references (Is a directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at juicebox.data.HiCFileTools.loadChromosomes(HiCFileTools.java:140)
    at juicebox.tools.clt.old.PreProcessing.readArguments(PreProcessing.java:80)
    at juicebox.tools.HiCTools.main(HiCTools.java:97)
Exception in thread "main" java.lang.NullPointerException
    at java.io.Reader.<init>(Reader.java:78)
    at java.io.InputStreamReader.<init>(InputStreamReader.java:72)
    at juicebox.data.HiCFileTools.loadChromosomes(HiCFileTools.java:154)
    at juicebox.tools.clt.old.PreProcessing.readArguments(PreProcessing.java:80)
    at juicebox.tools.HiCTools.main(HiCTools.java:97)
***! Can't find inter.hic in /home/Juicer_test_run/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 /home/Juicer_test_run/aligned for results

Please give me suggestion what doing wrong.

Thank you

[Neva Durand]

The -p should refer to your chrom.sizes file. You have it pointing to a directory, not to a file. You may have a similar problem with the restriction site file. 

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Ritz]

Thank you for the quick reply. It is working.

[Ritz]

Hello Neva,

After alignment of HiC data, following error got related to HiCCUPs:

GPUs are not installed so HiCCUPs cannot be run

(-: Postprocessing successfully completed, maps too sparse to annotate or GPUs unavailable (-:
(-: Pipeline successfully completed (-:
Run cleanup.sh to remove the splits directory
Check /home/juicer_test_run/aligned for results.

Kindly give me suggestions what doing wrong.

Thank you in advance

[Ritz]

[Neva Durand]

You don’t have GPUs installed so HiCCUPS will not run. Otherwise the pipeline worked and you can look at statistics and visualize the hic file with Juicebox. 

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/f2948f87-12e3-4f63-a3b4-88d7fd2b1f1f%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.