juicebox_tools.jar pre erro

[aidenlab]

juicebox_tools.jar pre erro

[nchernia]

The restriction site file is not a bed file. Please see: https://github.com/theaidenlab/juicer/wiki/Pre#restriction-site-file-format

On Thu, Sep 28, 2017 at 8:52 AM liufuyan2016 ***@***.***> wrote: Dear professor, when I use the command ,there also have an error. could you help me? java -jar /share/nas30/liufuyan/Project/AT/Interaction/06.TAD/Soft/juicebox-master/out/artifacts/Juicebox_tools_jar/juicebox_tools.jar pre -f ../QC/digest_AT.fa.bed -q 0 tmp/93500_allValidPairs.pre_juicebox_sorted test ../QC/AT.fa.len Skipping Chr1 30427671 Skipping Chr2 19698289 Skipping Chr3 23459830 Skipping Chr4 18585056 Skipping Chr5 26975502 Warning: Unable to process fragment file. Pre will continue without fragment file. 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$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1457) at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1228) at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:642) at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:373) at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:283) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:106) at juicebox.tools.HiCTools.main(HiCTools.java:83) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#38>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW2UJ3-XjTnYQvmpjoJxRJEM9vpTaks5sm5aNgaJpZM4PnN4d> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[nchernia]

Also please send the first few lines of your input - as the message says, you might have all intrafragment reads.

On Thu, Sep 28, 2017 at 9:17 AM Neva Durand ***@***.***> wrote: The restriction site file is not a bed file. Please see: https://github.com/theaidenlab/juicer/wiki/Pre#restriction-site-file-format On Thu, Sep 28, 2017 at 8:52 AM liufuyan2016 ***@***.***> wrote: > Dear professor, > when I use the command ,there also have an error. could you help me? > > java -jar > /share/nas30/liufuyan/Project/AT/Interaction/06.TAD/Soft/juicebox-master/out/artifacts/Juicebox_tools_jar/juicebox_tools.jar > pre -f ../QC/digest_AT.fa.bed -q 0 > tmp/93500_allValidPairs.pre_juicebox_sorted test ../QC/AT.fa.len > Skipping Chr1 30427671 > Skipping Chr2 19698289 > Skipping Chr3 23459830 > Skipping Chr4 18585056 > Skipping Chr5 26975502 > Warning: Unable to process fragment file. Pre will continue without > fragment file. > 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$MatrixZoomDataPP.mergeAndWriteBlocks(Preprocessor.java:1457) > at > juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.access$000(Preprocessor.java:1228) > at > juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:642) > at > juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:373) > at > juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:283) > at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:106) > at juicebox.tools.HiCTools.main(HiCTools.java:83) > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#38>, or mute the thread > <https://github.com/notifications/unsubscribe-auth/ABWiW2UJ3-XjTnYQvmpjoJxRJEM9vpTaks5sm5aNgaJpZM4PnN4d> > . > -- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[liufuyan2016]

Command:
/share/nas2/genome/biosoft/java/jdk/1.8.0_31/bin/java -jar　juicer_tools.1.7.6_jcuda.0.8.jar pre -f ./tmp/82156_resfrag.juicebox ./tmp/82156_allValidPairs.pre_juicebox_sorted XX/split_1_allValidPairs.hic extract.final.genome.fasta.chompspaceline.fa.corrected.len -q 0

The Content in ./tmp/82156_resfrag.juicebox file as belowed:
contig1 13929 14378 36971 39476 43322 61291 61836 76081 90801
contig2 752 2222 2877 3654 5137 6615 8094 9570 11053 12529 14170 15647 171

The content in ./tmp/82156_allValidPairs.pre_juicebox_sorted is as belowed:
ST-E00494:308:HG32VCCXY:6:1101:10084:72825 0 contig1 364497 103 1 contig1 367765 106 29 29
ST-E00494:308:HG32VCCXY:6:1101:10115:24181 0 contig1 366697 104 1 contig1 368297 107 60 60
ST-E00494:308:HG32VCCXY:6:1101:10521:43202 1 contig1 307572 79 1 contig1 342120 91 37 37
ST-E00494:308:HG32VCCXY:6:1101:10683:29419 0 contig1 421285 133 1 contig1 430571 136 37 29
ST-E00494:308:HG32VCCXY:6:1101:10845:43730 0 contig1 288605 65 0 contig1 440687 139 37 37
ST-E00494:308:HG32VCCXY:6:1101:18385:23495 1 contig1 414811 129 0 contig10 84341 19 37 37
ST-E00494:308:HG32VCCXY:6:1101:26453:64755 0 contig1 444966 141 0 contig10 399286 100 37 37
ST-E00494:308:HG32VCCXY:6:1101:5122:41725 1 contig1 351322 94 1 contig10 369549 97 37 37
ST-E00494:308:HG32VCCXY:6:1101:7080:45365 0 contig1 157847 34 1 contig10 322279 68 37 37
ST-E00494:308:HG32VCCXY:6:1102:10653:63577 0 contig1 407776 124 0 contig10 327999 69 37 37

The content in extract.final.genome.fasta.chompspaceline.fa.corrected.len as belowed:
contig1 509147
contig2 287020
contig3 373598
contig4 55310

An Error Occurred:
Problem with creating fragment-delimited maps, NullPointerException.
This could be due to a null fragment map or to a mismatch in the chromosome name in the fragment map vis-a-vis the input file or chrom.sizes file.

Could you help me?

[nchernia]

Is the fragment file you posted just a fragment? Otherwise it looks cut off. Are all the chromosomes listed in your "valid pairs" file also in your " extract.final.genome.fasta.chompspaceline.fa" file? It shouldn't matter anymore, but try making sure the " extract.final.genome.fasta.chompspaceline.fa" file is tab delimited. Be sure you are using the latest jar.

…

On Fri, Dec 29, 2017 at 2:18 AM, liufuyan2016 ***@***.***> wrote: Command: /share/nas2/genome/biosoft/java/jdk/1.8.0_31/bin/java -jar juicer_tools.1.7.6_jcuda.0.8.jar pre -f ./tmp/82156_resfrag.juicebox ./tmp/82156_allValidPairs.pre_juicebox_sorted XX/split_1_allValidPairs.hic extract.final.genome.fasta. chompspaceline.fa.corrected.len -q 0 The Content in ./tmp/82156_resfrag.juicebox file as belowed: contig1 13929 14378 36971 39476 43322 61291 61836 76081 90801 contig2 752 2222 2877 3654 5137 6615 8094 9570 11053 12529 14170 15647 171 The content in ./tmp/82156_allValidPairs.pre_juicebox_sorted is as belowed: ST-E00494:308:HG32VCCXY:6:1101:10084:72825 0 contig1 364497 103 1 contig1 367765 106 29 29 ST-E00494:308:HG32VCCXY:6:1101:10115:24181 0 contig1 366697 104 1 contig1 368297 107 60 60 ST-E00494:308:HG32VCCXY:6:1101:10521:43202 1 contig1 307572 79 1 contig1 342120 91 37 37 ST-E00494:308:HG32VCCXY:6:1101:10683:29419 0 contig1 421285 133 1 contig1 430571 136 37 29 ST-E00494:308:HG32VCCXY:6:1101:10845:43730 0 contig1 288605 65 0 contig1 440687 139 37 37 ST-E00494:308:HG32VCCXY:6:1101:18385:23495 1 contig1 414811 129 0 contig10 84341 19 37 37 ST-E00494:308:HG32VCCXY:6:1101:26453:64755 0 contig1 444966 141 0 contig10 399286 100 37 37 ST-E00494:308:HG32VCCXY:6:1101:5122:41725 1 contig1 351322 94 1 contig10 369549 97 37 37 ST-E00494:308:HG32VCCXY:6:1101:7080:45365 0 contig1 157847 34 1 contig10 322279 68 37 37 ST-E00494:308:HG32VCCXY:6:1102:10653:63577 0 contig1 407776 124 0 contig10 327999 69 37 37 The content in extract.final.genome.fasta.chompspaceline.fa.corrected.len as belowed: contig1 509147 contig2 287020 contig3 373598 contig4 55310 An Error Occurred: Problem with creating fragment-delimited maps, NullPointerException. This could be due to a null fragment map or to a mismatch in the chromosome name in the fragment map vis-a-vis the input file or chrom.sizes file. Could you help me? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#38 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW40qJFcbXLAljhglRsaYpSDuhrWFks5tFJJEgaJpZM4PnN4d> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org