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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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Always get java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment. #231

Closed Lattesnow closed 2 years ago

Lattesnow commented 3 years ago

[M::mem_pestat] low and high boundaries for proper pairs: (1, 19664) [M::mem_pestat] skip orientation RF [M::mem_process_seqs] Processed 3446404 reads in 2671.766 CPU sec, 42.518 real sec [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -SP5M -t 64 reference/hg38gatk.fastq /mnt/d/HiC/Test/package/juicer/CPU/splits/CRPC_S4_L001_R1_001.fastq /mnt/d/HiC/Test/package/juicer/CPU/splits/CRPC_S4_L001_R2_001.fastq [main] Real time: 187.903 sec; CPU: 9590.500 sec (-: Align of /mnt/d/HiC/Test/package/juicer/CPU/splits/CRPC_S4_L001_001.fastq.sam done successfully (-: Finished sorting all sorted files into a single merge. Picked up _JAVA_OPTIONS: -Xmx16384m Picked up _JAVA_OPTIONS: -Xmx16384m Not including fragment map Start preprocess Writing header Writing body java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment. at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1650) at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1419) at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:832) at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:582) at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:346) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:116) at juicebox.tools.HiCTools.main(HiCTools.java:96) Picked up _JAVA_OPTIONS: -Xmx16384m Not including fragment map Start preprocess Writing header Writing body java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment. at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1650) at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1419) at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:832) at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:582) at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:346) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:116) at juicebox.tools.HiCTools.main(HiCTools.java:96) /mnt/d/HiC/Test/package/juicer/scripts/common/juicer_tools is post-processing Hi-C for hg19 Data read from /mnt/d/HiC/Test/package/juicer/CPU/aligned/inter_30.hic. Motifs read from /mnt/d/HiC/Test/package/juicer/references/motif

ARROWHEAD:

Picked up _JAVA_OPTIONS: -Xmx16384m Reading file: /mnt/d/HiC/Test/package/juicer/CPU/aligned/inter_30.hic Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at juicebox.data.DatasetReaderV2.readFooter(DatasetReaderV2.java:468) at juicebox.data.DatasetReaderV2.read(DatasetReaderV2.java:235) at juicebox.data.HiCFileTools.extractDatasetForCLT(HiCFileTools.java:64) at juicebox.tools.clt.juicer.Arrowhead.run(Arrowhead.java:184) at juicebox.tools.HiCTools.main(HiCTools.java:96) ***! Problem while running Arrowhead (-: Pipeline successfully completed (-: Run cleanup.sh to remove the splits directory

Lattesnow commented 3 years ago

Got the .hic file but not the matrices in the folder

nchernia commented 3 years ago

What does the head of your merged nodups file look like?

Usually this is due to the error reported, either all mapq 0 or all aligning to same fragment

On Tue, Jul 13, 2021 at 4:09 PM Lattesnow @.***> wrote:

Got the .hic file but not the matrices in the folder

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Lattesnow commented 3 years ago

0 CM000663.2 13420 0 0 CM000663.2 184247 1 0 151M GATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCCGCTGGAGACGGTGTTTGTCATGGGCCTGGTCTGCAGGGATCG 0 151M CCAATCTGTCTTCCATCCTGCGTGGCCGAGGGCCAGGCTTCTCACTGGGCCTCTGCAGGAGGCTGCCATTTGTCCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTAAAGTTAGCTGCC M05563:69:000000000-JL6C6:1:2116:10759:13652 M05563:69:000000000-JL6C6:1:2116:10759:13652 0 CM000663.2 13420 0 0 CM000663.2 186275 1 0 151M GATCACATTTCTCACTGCCTTTTGTCTGCCCAGTTTCACCAGAAGTAGGCCTCTTCCTGACAGGCAGCTGCACCACTGCCTGGCGCTGTGCCCTTCCTTTGCTCTGCCCGCTGGAGACGATGTTTGTCATGGGCCTGGTCTGCAGGGATCC 3 138M13S TTGCCCAAGGCCCTCCGACTGCAAGCTCCAGGGCCCGCTCACCTTGCTCCTGCTCCTTCTGCTTCTTCTTCTCCAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTGATCTCACGGATG M05563:69:000000000-JL6C6:1:2112:26248:12738 M05563:69:000000000-JL6C6:1:2112:26248:12738 0 CM000663.2 27525 0 0 CM000663.2 191354 1 0 75M76S CACATATGCGACTTAAATATTTCTTTTCTTTTTCTTTCCTCTCACTCAGCGTCCTGTGATTCCAAAGAAATGAGTACTCTCTCCCCACCACGCAGCTCAGGCCCCAGTACAGCCCGGCCTCTGGCCTCACTGGCGTCTGTGCCCAGTGACG 22 150M CCACAGAAAACAGAGCCACCACAGAAAACAGAGGGGTGACTGTCATCCCCTCCAGTCTCTGCACACTCCCAGCTGCAGCAGAGCCGGAGGAGAGAGCACAGCCTGCAATGCTAATTTGCCAGGAGCTCACATGCCTGCGTCACTGGGCAC M05563:69:000000000-JL6C6:1:2116:10832:20102 M05563:69:000000000-JL6C6:1:2116:10832:20102 0 CM000663.2 34848 0 0 CM000663.2 464028 1 0 150M CTGGCTCCGATGGCCACATCTCACTGCAGGGGCAGCTGGGAAATACAGTCTGGCTGTCTACCCAGGAGGAAGAGCAGCCAGTTTCTACTGCTGATGATCAGGAGGTGGAGAAAATGTTCAGTCAGGCAGGGAGTGGGAATAGACAAGACC 0 125M26S AGTACAGGCATTGGGTAAATGCAGCAATTTCAAATGGTAAAATTTACCCAAAACAAAGGGACTAAAGGCTCCAAGTAAGTCCGAAATCCAGTGGGACAGTCAAATCTTAAAGCTCCAAAATGATCAATCCAGTATTGCTACCCACCTCTCT M05563:69:000000000-JL6C6:1:2118:22506:6557 M05563:69:000000000-JL6C6:1:2118:22506:6557 0 CM000663.2 70393 0 0 CM000663.2 84033 1 0 151M AAAGAACTGTCACATCTTAATTTAAAAAATATATGCTTAGTGNTAAGGAGATATATGCCAACTTTTAAGAGGTTGAAAAACAAACGCCTCCCATTATAAGTTTATACTTCACCTCCCACCACTATAACAACCCAGAATCCATGAGGGCATT 1 77M73S AGAAAGAAAAGCAAGCAAGCTTTAAAAGTTCATGTTTGGTAGGCTGTACTTCAAGATACACTTTTAAAAAAAAGACTGATCCCTCTAAATTCTTTCTACTGCTTATGAGCAGTTATACCACAGACGTCTAGGACCTAGAAGGCACATTTC M05563:69:000000000-JL6C6:1:1105:16352:6992 M05563:69:000000000-JL6C6:1:1105:16352:6992 0 CM000663.2 76919 0 0 CM000663.2 117552123 1 0 36M115S GATCCCAGCATTTTGGGAGGCTGAGGCGGGCAGATCGATCTTGGTGCTTTGGTATTGGGTGCATATATATTTGGGATAGTTATATCTTCTTGTTAAATTGAACCATTTGTCATTATATAATAACTTTTGTCCTTTTTTACAGTTATTGATT 60 150M ATTACCACATTTTTTATCCAGTCATCTGTAGATGGACACTTAGGTTGATTCCATGACTTTGCTATTGTGAATAGTGCTGCAATAAACATATGAAAAACTATACCATGCAAACAGAAAACAAAAATGAGCAGGAGTAGCTATATTTATGTC M05563:69:000000000-JL6C6:1:1117:10603:11949 M05563:69:000000000-JL6C6:1:1117:10603:11949 0 CM000663.2 76998 0 0 CM000663.2 197974288 1 0 93M58S AACCCCATCTCTACCAAAAATACAAAAATTAGCTGGGCGTGGTGGTGCACACTTGTAATTCCAGCTACTTGAGAGGCTGAGGTGGGAGGATCGATCCTCTTCAAGGCAGTTCCTGTGTCCTTTCAACATATAGCCATCATTCTTTGTATAC 60 124M26S GATCCTGAGGGCAGGGAAAGTAGAAGGTAAAACTGGAACATTTTGTTGTATCAGAAAGCAAAAAAGTATACAAAGAATGATGGCTATATGTTGAAAGGACACAGGAACTGCCTTGAAGAGGATCGATCCTCCCACCTCAGCCTCTCAAGT M05563:69:000000000-JL6C6:1:1107:17649:13789 M05563:69:000000000-JL6C6:1:1107:17649:13789 0 CM000663.2 79989 0 0 CM000663.2 15352251 1 0 151M AAAGAGCCCACATAGCCAAAGCAAGACTAAGCAAAAAGAATAAATCTAGAGGCATCACATTACTCGACTTCAAACTATACTATAAGGCCATAGTCACCAAAACAGCATGGTACTGGTATAAAAATAGGCATATAGACCAATGGAATAGAAT 60 67M83S ACAGCTGCAGATAGAGTTTTTCAAACCCTCCCTAGCTGTTTACCTCCCAGGGCGTGTACAGGTGAGTGATCAGTTGGCTGAAAGTATTTGGCTTTATTTCTGGGTTCTTTATTCTATTCCATTGGTCTATATGCCTATTTTTATACCAGT M05563:69:000000000-JL6C6:1:1112:6330:11796 M05563:69:000000000-JL6C6:1:1112:6330:11796 0 CM000663.2 120847 0 0 CM000663.2 90792181 1 0 84M67S NTGAATGATTAACAAGGTGATAGTCAGTTCTTCATTGAATCCTGGATGCTTTATTTTTCTTAATAAGAGGAATTCATATGGATCGATCATGAGTATTTCTCTTAGGAATTTCCCGACTTTAGCTCTGCCTCTTCCCTCCCTGATTGCAGTG 60 136M15S AGAGGCAAGGGGCAGAACTAAGCTTACGGAAGGAGAAATAACCCCGAAGTGCAGTGCATAGGGATAAGGCACTGCAATCAGGGAGGGAAGAGGCAGAGCTAAAGTCGGGAAATTCCTAAGAGAAATACTCATGATCGATCCATATGAATTC M05563:69:000000000-JL6C6:1:1114:8111:24177 M05563:69:000000000-JL6C6:1:1114:8111:24177 0 CM000663.2 122358 0 0 CM000663.2 771042 1 0 150M CATGTTAGTTGATACCAGAGAACTATATTTAAAGGGACAGCAATAAGCAAATTGATTACTCTGGTGATTATTGGAGTGACATTGCCTTTTAGTTGTACTTTCACAAAAATTCACAATATTTGCCAAAGTCAAGTTATCCATTACACTATT 0 151M GATCGCCTCCAGGTGAGCCTGCCCACTTTGTGCCCAGGGGCCTGTAGAAAACCACAGCTCCCCATGGTTATGGCCCCAGGAGTGGGGCAGAGCAGGGAGGAGTCCTGGACAGAGGAGAGGCAGGGGCAGGAGGGAGTGGGCCTGAAACTCC M05563:69:000000000-JL6C6:1:2113:5267:16074 M05563:69:000000000-JL6C6:1:2113:5267:16074 0 CM000663.2 125038 0 0 CM000663.2 715564 1 0 126M25S AATACTAAAGAAATTTCTGAGTTAAATGGTATAATGTTAGCTTATGCCAGAGCTGACCTTGAAAGATTGTTCAAATATGGCTCAGTGTGATTGAAAGTTCTGTGTGAATATGTTTTTGGAAAGATCACTCAAGCTATTCTTCCACCTCAGC 0 150M TGTGGCTTATGTCTGTAATATCAGCATGTTGGGAGGCCAAGGCAGGATTACTTGAGCCCAGAAATTCCAGACCAGCCTGAGAATTTGGCAAAACTCTGTCTCTACAAAAAGTACAAAAATTAGCCAAGTTTGGTGGCATGTGCCTGTAGT M05563:69:000000000-JL6C6:1:1112:19261:9188 M05563:69:000000000-JL6C6:1:1112:19261:9188 0 CM000663.2 169243 0 0 CM000663.2 175496 1 0 151M TGTAGAATTCTGGCCTTCAGACCTGTAAGGGAATACATTTTGGTTGTTTTAAGTCACTAAGTGTGTGGTAATTTGTTGCAGCAGCCACAGGAAACTAGTATTGTAGTGAAGCCTCAAAACCCCCCTGAAGGGGCTGGGCTCAGTGGCTCAT 0 151M GATCAAATCAGCTGCCAGTCTCGCAAAGTGTCGGGTAACATCCTATTAAGCTTGCTGCTTACACATCATCTATAAAATACTGAAAATATCATTTTAAGAAATCTTTTTTTTATTTTGAGACAGAGTTTTGCTCGTTGCCCAGGCTGGAGTG M05563:69:000000000-JL6C6:1:1111:8938:8971 M05563:69:000000000-JL6C6:1:1111:8938:8971 0 CM000663.2 197183 0 0 CM000663.2 223923115 1 0 151M AGTCTCAAAAACAACTAAACTCAAATTAAATTCATTCTACTCCAGTCATGAGTACAAAGCTAAGGAGTGACAAATCCCTTTTGGAGTTAGGGGAGTCAGGAAAAAGCTCTTAGCAGAATGTGTGCCTCTCGGCCAGGCGCAGCGGCTCACG 0 151M CCTTCATTCTAACAATTTACTGGAGTACACAATTGTGACTATTTTTAGCCATAGGAACTCATAGAAAGACCAACTTCATTAGACCTACAAAATCGAATTGTGTAACAGTATATGCAGTATGTGTAGGAATAAAAAGCATTTCTCAAATATG M05563:69:000000000-JL6C6:1:2101:8362:20452 M05563:69:000000000-JL6C6:1:2101:8362:20452 0 CM000663.2 200998 0 0 CM000663.2 529248 1 0 125M24S ATTCAGAATTAAGCACTTTATATTTTATTTGCTGCCTCTGGCCACCCTACTCTCTTCCTAACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCCTGCCTCCTCTTCTGGGGGAGTTAGATCGATCAGCCCAGGGGTAAGGAAGGAGA 0 151M TGCCCAGGGGCCTGTAGAAAACCACAGCTCCCCATGGTTATGGCCCCAGGAGTGGGGCAGAGCAGGGAGGAGTCCTGGACAGAGGAGAGGCAGGGGCAGGAGGGAGTGGGCCTCAAACTCCAGGAGGGGGCCCTTCTCATGGGTCCTGCTT M05563:69:000000000-JL6C6:1:2107:18357:15879 M05563:69:000000000-JL6C6:1:2107:18357:15879 0 CM000663.2 274158 0 0 CM000663.2 223828238 1 0 40M110S CTTCAGTTCTCAAGATTTTATCTGATGGAAGAGATGGAGTGATCCAGGGAAGGCACAATGTATATGAATAAGAATGGTATGTGGTTATTTTCATCATTGATTGCTTAAAAAATCAATTTTATTGTGCACGTGGTACATTCTAGAAAATTT 60 151M GTTTTGTTATAAAACAGTGCTCACTGTATCCTATTATGCATACACATCTACAGGCACAGAAAAAAGCCTGAAACTATATTCACCAAATTAACAGTAGTTATGCCCTGGTGGTGGGATGACTAAGTGAATTTTTAGGAACTTATCTACGTTT M05563:69:000000000-JL6C6:1:2112:20857:14401 M05563:69:000000000-JL6C6:1:2112:20857:14401 0 CM000663.2 284801 0 0 CM000663.2 223919569 1 0 151M NNNTTTNNATGGNTNCTATAACAACCAAATATATTCTCAATTGATTAACTGTTTTGCTGACTACTGCCTTCCATAAGAATGGAAAGAAAACNTGGCCAGGTGCANTGGCTCACACCTGTAATCCCACCACATCAGGAGGCTGAGGCAACAT 0 119M32S AGTGTGGACCTCTCACGAATGTCTTGGTGCCATCCAAGTGAGTTCTTGCTCGCTCTTTTTTTTCTTTTTGAGATGTAGTTGCACTCTTGCTGCCCAGGTTGGGATGTAGTGGTGCGATCGATCCTCTTGCCTCCACAACATCAAGCTCACT M05563:69:000000000-JL6C6:1:1116:24366:3799 M05563:69:000000000-JL6C6:1:1116:24366:3799 0 CM000663.2 294295 0 0 CM000663.2 474410 1 0 149M GGAGAGATCTTCCTGGGTTACCCAGATGGGCCCAGTCTAATCACATGAGTTCTTAAAAATGGAGAACCTTTCTTAGCTGAGTCCAGAGAGAGATGTGACAATGAAAGAATGGTCAGAGAAATGTGACATTGCCAGCTTTAAAAAGAGAG 0 79M72S CCCAAAAATCAACAGGAAAAATAAGACATAGAACAAGCAAAATGCATAAACAAAAGAAGGCAAAACAAAAATAATGACTAATCCATATCCTGGCCTTTTCTATCTTCTAGAGAACATCAGCATTCCTTTTCTCATTGCCTCTCCTCTCTCT M05563:69:000000000-JL6C6:1:2107:10625:11218 M05563:69:000000000-JL6C6:1:2107:10625:11218 0 CM000663.2 354141 0 0 CM000663.2 501873 1 0 64M86S CTCTGGTTCTAATCCTAACCCTAACCCTGTCCCAAGACTTTGACACTGAACCTAAATCCTGATCGATCTCAAACTCCTGGCCTCAAGTAATATACCTCTCTCAGCCTCCCAAAGTGCTGAGATTACAGGCATAAGCCACCACCCTCAACC 0 128M23S CAAGTAATCTCACTTAATTTTTATTTGGTTTAAGAAAGTCTTGGTTGAGGGTGGTGGCTTATGCCTGTAATCTCAGCACTTTGGGAGGCTGAGAGAGGTATATTACTTGAGGCCAGGAGTTTGAGATCGATCAGGATTTAGGTTCAGTGTC M05563:69:000000000-JL6C6:1:2109:16447:13706 M05563:69:000000000-JL6C6:1:2109:16447:13706 0 CM000663.2 357318 0 0 CM000663.2 738807 1 0 150M TGACCCACAGATGTGAAGCTGAGGCTGAAGGAGACTGATGTGGTTTCTCCTCAGTTTCTCTGTGCGGCACCAGGTGGCAGCAGAGGTCAGCAAGGCAAACCCGAGCCCAGGGATGCGGGGTGGGGGCAGCTACGTCCTCTCTTGAGCTAC 3 140M11S CATATACCAAAATCCATGCTTACTCACGTTTTGCTGTCACCCCTCTGGAATCCACGTATACGAAAATTCCAAATATTAGTTGGGCATAGTGGCAAGCACCTGTAGTCTCAGCCACGTGGGAGGTTGAGGTGGGAGGATCGATCCAAAGCTT M05563:69:000000000-JL6C6:1:1115:7877:10295 M05563:69:000000000-JL6C6:1:1115:7877:10295 0 CM000663.2 404500 0 0 CM000663.2 436259 1 0 121M30S CGCCATCAGCCTTGTGACCTTCAAGTTCATTCTCCACATGGATGTCAGAGTAACTTTCTAAAATGAAAATCTGACCACGTTACTCTCTTGCCTAAATCCGCCTATGGCCGCTGTTAGGATCGATCTTTTTTTCTTTTTTGATTTAGGCTTT 0 146M5S GTACACCATGCTTTGATATATATTCTAAAATCAGGTAGCATGAAAATGTAAACATAACATACTAAAACATATGGGATGCAACAAAAGCAGTTATAAGAGGGACACTTATAGCAATAAATGCCTACATCAAAAAAGAAAAAAAGATCGATCC M05563:69:000000000-JL6C6:1:2111:7640:22127 M05563:69:000000000-JL6C6:1:2111:7640:22127

Lattesnow commented 3 years ago

I copied the first 20 lines of the header here. Thanks for the help!

nchernia commented 3 years ago

It’s all the same fragment. This shouldn’t cause a problem with the most recent version of juicer tools (so make sure you’ve downloaded a recent version). Alternatively change field 4 to always be 0 and field 8 to be 1.

On Tue, Jul 13, 2021 at 5:45 PM Lattesnow @.***> wrote:

I copied the first 20 lines of the header here. Thanks for the help!

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

Lattesnow commented 3 years ago

Thanks for the quick answer. I will download the most recent version. for the Same fragment issue, does this mean I have too many duplicates? I used the Arima kit for processing the sample.

wuxingbo1986 commented 3 years ago

Hi, did you solve this issue? I have the same problem running Juicer v1.6.2? Thanks.

Lattesnow commented 3 years ago

Hi, did you solve this issue? I have the same problem running Juicer v1.6.2? Thanks.

I solved it by reinstalling Juicer

wuxingbo1986 commented 3 years ago

Did you reinstall by docker? what version should it be? Thanks.

wuxingbo1986 commented 3 years ago

I rerun the Juicer(v1.6.2) but still getting the issue. Can you help? @Lattesnow @nchernia

peterdfields commented 3 years ago

I'm getting this same error as well.

nchernia commented 3 years ago

Please search the forum, this question has come up many times.

https://groups.google.com/g/3d-genomics

On Wed, Aug 4, 2021 at 6:29 PM peterdfields @.***> wrote:

I'm getting this same error as well.

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