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Pair_Frags...read error with HiSIF command #2
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Hi yaojiayingJenny, If you just only run one chromosome with HISIF, please also make the empty file for other chromosomes. You can run the shell like the following: ###Linux Shell to make all empty files Thanks. |
Thanks for your reply. Actually my input contain 25 files which were generated by "proc" command(HiSIF_V1.00/bin/proc split/ test/ -t) from a validPairs file. I also tried your suggestion with 23 files(chr1.tmp to chr23.tmp) and 24 files (chr1.tmp to chr24.tmp), while neither of them succeeded. Please let me know if there are any other rules need to follow, or could you upload the test data with the running command If it's convenient for you ? Thanks a lot. Here're other information about my command: -c hg19.MboI.bed(from HiSIF_V1.00/resources/ after "cat" command) |
Hi yaojiayingJenny, I have uploaded the example data, please find them on: https://github.com/yufanzhouonline/HiSIF/tree/master/HiSIF_V1.00/example Please try to run HiSIF with these example data. Please let me know if it works. Thanks. |
Hi yufanzhouonline, your command: my command: (-m parameter is forced) Program: HiSIF - HiC Significant Interaction Fragments
Experimental: |
Hi yaojiayingJenny, Please download the latest version and install HiSIF as mentioned (Just input "make" on the folder of HiSIF) Then follow my command, not your command. Thanks. |
I got an error with HiSIF step. It seems my input files aren't in correct format. But I followed the pipeline tutorial instructions strictly. Could anyone know the reason? Thanks.
$head test/chr1.tmp
1 10000001 1 1 10001638 1
1 10000018 1 1 9996231 1
1 10000020 1 1 9383708 1
1 10000021 1 1 9564208 1
1 100000267 0 1 103050925 0
command:
HiSIF -g hg19_bowtie2_index -c hg19.MboI.bed -p 1 29 -w 50 500 5000 -T 1 -s 0.1 -i 2 -m 1 -x 5 -o test/result test/
out.log:
(=:...........Start processing files...........:=)
cuttingSiteTotal == 7127585
<-----Parsed enzyme cutting site map----->
<-----Extended cutting site region----->
<-----Combining Data from Child Processes----->
<-----Reading Vector Sizes for Bootstrapping----->
<-----Found 25 files----->
<-----Reading sum pipe----->
<-----Performing filtration----->
<-----Writing to test__PoisMix.txt----->
<-----Main Process 1 finished writing distrubitions----->
<-----Finished Vector Sizes for Bootstrapping----->
<-----Child Processes Finished----->
<-----Beginning Bootstrapping----->
<-----Using samplesize of 13555475 elements----->
<-----Random Dataset 1----->
Iteration: 1--> LLH: -3.26381
Iteration: 2--> LLH: -2.88868
Iteration: 3--> LLH: -2.69257
Iteration: 4--> LLH: -2.58041
Iteration: 5--> LLH: -2.51447
<-----Random Dataset 2----->
Iteration: 1--> LLH: -3.47266
Iteration: 2--> LLH: -3.7416
Iteration: 3--> LLH: -3.9588
<-----Proximate ligation events extracted from mixture model----->
<-----Starting Frequency Generation----->
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