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20 hours ago •
aidenlab
aidenlab
***! Error! Either inter.hic or inter_30.hic were not created
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.
here is the running log juicer.log Is this running result normal? I have a sense that something is a little off.
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: @.***>
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
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
