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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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***! Error! Either inter.hic or inter_30.hic were not created #330

Open yuntan1992 opened 1 year ago

yuntan1992 commented 1 year ago

Hi, I get this error. Error while reading graphs file: java.io.FileNotFoundException: /share/home/qiuyuntan/juicer/work/noz/aligned/inter_hists.m (No such file or directory) And ***! Error! Either inter.hic or inter_30.hic were not created Either inter.hic or inter_30.hic were not created. Check for results Actually, the inter.hic or inter_30.hic does exist. image

here is the running log juicer.log Is this running result normal? I have a sense that something is a little off.

chenzhao12 commented 11 months ago

I encountered the same problem, have you solved it?

yuntan1992 commented 11 months ago

I couldn't find a solution, so I ended up switching to Juicer version 1.6.

允郯

@. | ---- Replied Message ---- | From | @.> | | Date | 12/15/2023 09:43 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [aidenlab/juicer] ! Error! Either inter.hic or inter_30.hic were not created (Issue #330) |

I encountered the same problem, have you solved it?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

jlchen5 commented 11 months ago

I met the same problem with jucier 2.0:

bash scripts/juicer.sh -d ~/Yasmine/HiCData/juicer -D ~/Yasmine/HiCData/juicer -y ~/Yasmine/HiCData/juicer/hg19_MseI.txt -z ~/Yasmine/HiCData/juicer/reference/BWAIndex/hg19.fa -p ~/Yasmine/HiCData/juicer/hg19.chrom.sizes -s MseI -S "final"
Using /home/msbb/Yasmine/HiCData/juicer/hg19_MseI.txt as site file
Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics
    at juicebox.tools.HiCTools.main(HiCTools.java:96)
Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics
    at juicebox.tools.HiCTools.main(HiCTools.java:96)
Picked up _JAVA_OPTIONS: -Xmx16000m -Xms16000m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Using 1 CPU thread(s)
Not including fragment map
Error while reading graphs file: java.io.FileNotFoundException: /home/msbb/Yasmine/HiCData/juicer/aligned/inter_hists.m (No such file or directory)
Start preprocess
Writing header
Writing body
......................
Writing footer

Finished preprocess
Done creating .hic file. Normalization not calculated due to -n flag.
To run normalization, run: juicebox addNorm <hicfile>

real    0m3.653s
user    0m11.543s
sys 0m0.922s
Picked up _JAVA_OPTIONS: -Xmx16000m -Xms16000m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Using 1 CPU thread(s)

Calculating norms for zoom BP_2500000java.lang.ArrayIndexOutOfBoundsException: Index 22 out of bounds for length 22
    at juicebox.tools.utils.norm.NormalizationCalculations.computeVC(NormalizationCalculations.java:355)
    at juicebox.tools.utils.norm.NormalizationVectorUpdater.buildVCOrVCSQRT(NormalizationVectorUpdater.java:186)
    at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:139)
    at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:128)
    at juicebox.tools.HiCTools.main(HiCTools.java:94)

real    0m0.545s
user    0m1.676s
sys 0m0.579s
Fri Dec 15 13:09:57 CET 2023
Picked up _JAVA_OPTIONS: -Xmx16000m -Xms16000m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Using 1 CPU thread(s)
Not including fragment map
Error while reading graphs file: java.io.FileNotFoundException: /home/msbb/Yasmine/HiCData/juicer/aligned/inter_30_hists.m (No such file or directory)
Start preprocess
Writing header
Writing body
......................
Writing footer

Finished preprocess
Done creating .hic file. Normalization not calculated due to -n flag.
To run normalization, run: juicebox addNorm <hicfile>

real    0m3.551s
user    0m11.683s
sys 0m0.946s
Picked up _JAVA_OPTIONS: -Xmx16000m -Xms16000m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Using 1 CPU thread(s)

Calculating norms for zoom BP_2500000java.lang.ArrayIndexOutOfBoundsException: Index 22 out of bounds for length 22
    at juicebox.tools.utils.norm.NormalizationCalculations.computeVC(NormalizationCalculations.java:355)
    at juicebox.tools.utils.norm.NormalizationVectorUpdater.buildVCOrVCSQRT(NormalizationVectorUpdater.java:186)
    at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:139)
    at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:128)
    at juicebox.tools.HiCTools.main(HiCTools.java:94)

real    0m0.520s
user    0m1.762s
sys 0m0.502s
/home/msbb/Yasmine/HiCData/juicer/scripts/common/juicer_postprocessing.sh: option requires an argument -- g
Usage: /home/msbb/Yasmine/HiCData/juicer/scripts/common/juicer_postprocessing.sh [-h] -j <juicer_tools_file_path> -i <hic_file_path> -m <bed_file_dir> -g <genome ID>
***! Error! Either inter.hic or inter_30.hic were not created
Either inter.hic or inter_30.hic were not created.  Check  for results
z4668640 commented 10 months ago

me too. Have you found any solutions? I also noticed that there was this error at the same time /home/juicer-main/CPU/common/juicer_postprocessing.sh: option requires an argument -- g I forgot to specify the-g parameter when I started juicer.sh. This problem is solved when I use the parameter -g hg19.

I met the same problem with jucier 2.0:

bash scripts/juicer.sh -d ~/Yasmine/HiCData/juicer -D ~/Yasmine/HiCData/juicer -y ~/Yasmine/HiCData/juicer/hg19_MseI.txt -z ~/Yasmine/HiCData/juicer/reference/BWAIndex/hg19.fa -p ~/Yasmine/HiCData/juicer/hg19.chrom.sizes -s MseI -S "final"
Using /home/msbb/Yasmine/HiCData/juicer/hg19_MseI.txt as site file
Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics
  at juicebox.tools.HiCTools.main(HiCTools.java:96)
Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Exception in thread "main" java.lang.RuntimeException: Unknown command: statistics
  at juicebox.tools.HiCTools.main(HiCTools.java:96)
Picked up _JAVA_OPTIONS: -Xmx16000m -Xms16000m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Using 1 CPU thread(s)
Not including fragment map
Error while reading graphs file: java.io.FileNotFoundException: /home/msbb/Yasmine/HiCData/juicer/aligned/inter_hists.m (No such file or directory)
Start preprocess
Writing header
Writing body
......................
Writing footer

Finished preprocess
Done creating .hic file. Normalization not calculated due to -n flag.
To run normalization, run: juicebox addNorm <hicfile>

real  0m3.653s
user  0m11.543s
sys   0m0.922s
Picked up _JAVA_OPTIONS: -Xmx16000m -Xms16000m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Using 1 CPU thread(s)

Calculating norms for zoom BP_2500000java.lang.ArrayIndexOutOfBoundsException: Index 22 out of bounds for length 22
  at juicebox.tools.utils.norm.NormalizationCalculations.computeVC(NormalizationCalculations.java:355)
  at juicebox.tools.utils.norm.NormalizationVectorUpdater.buildVCOrVCSQRT(NormalizationVectorUpdater.java:186)
  at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:139)
  at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:128)
  at juicebox.tools.HiCTools.main(HiCTools.java:94)

real  0m0.545s
user  0m1.676s
sys   0m0.579s
Fri Dec 15 13:09:57 CET 2023
Picked up _JAVA_OPTIONS: -Xmx16000m -Xms16000m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Using 1 CPU thread(s)
Not including fragment map
Error while reading graphs file: java.io.FileNotFoundException: /home/msbb/Yasmine/HiCData/juicer/aligned/inter_30_hists.m (No such file or directory)
Start preprocess
Writing header
Writing body
......................
Writing footer

Finished preprocess
Done creating .hic file. Normalization not calculated due to -n flag.
To run normalization, run: juicebox addNorm <hicfile>

real  0m3.551s
user  0m11.683s
sys   0m0.946s
Picked up _JAVA_OPTIONS: -Xmx16000m -Xms16000m
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Using 1 CPU thread(s)

Calculating norms for zoom BP_2500000java.lang.ArrayIndexOutOfBoundsException: Index 22 out of bounds for length 22
  at juicebox.tools.utils.norm.NormalizationCalculations.computeVC(NormalizationCalculations.java:355)
  at juicebox.tools.utils.norm.NormalizationVectorUpdater.buildVCOrVCSQRT(NormalizationVectorUpdater.java:186)
  at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:139)
  at juicebox.tools.clt.old.AddNorm.run(AddNorm.java:128)
  at juicebox.tools.HiCTools.main(HiCTools.java:94)

real  0m0.520s
user  0m1.762s
sys   0m0.502s
/home/msbb/Yasmine/HiCData/juicer/scripts/common/juicer_postprocessing.sh: option requires an argument -- g
Usage: /home/msbb/Yasmine/HiCData/juicer/scripts/common/juicer_postprocessing.sh [-h] -j <juicer_tools_file_path> -i <hic_file_path> -m <bed_file_dir> -g <genome ID>
***! Error! Either inter.hic or inter_30.hic were not created
Either inter.hic or inter_30.hic were not created.  Check  for results
xusheng-code commented 6 months ago

I also encountered the same problem with the newest version, and the result file "aligned" has "inter.hic" and "inter_30.hic" files, but no "merged_nodups.txt".

when I switched to Juicer version 1.6, the running information is: (-: Looking for fastq files...fastq files exist (-: Aligning files matching /home/user/juicer/work/fastq/_R.fastq* to genome hg19 with site file /home/user/juicer/restriction_sites/genome_DpnII.txt (-: Created /home/user/juicer/work/splits and /home/user/juicer/work/aligned.

But, why aligning my hic files to genome hg19???

OceanLyu commented 3 weeks ago

By looking into juicer.sh, I found that if you do not specify the flag -g, $genomeID in this script would not be assigned any value, which possibly lead to the error.

I think if you are working with your own genome, arbitrary setting of -g would be fine? $genomeID will just further be used for nominations for feature annotations in juicer_postprocessing.sh?