PouletAxel
commented
2 years ago Hi,
the same question was asked in the in the issue #18 can you try if using cooler=0.8.6, cooltools=0.3.2 solved your problem? I will close your issue you can answer then in the issue #18
Thanks Axel
Can you help me to solve the following problem?
INPUT: I am trying to call loops on a .mcool file from micro-C in dm6 with observed and balanced entries at resolutions 100, 400 and 800 base-pairs, which I checked using cooltools: ['/resolutions/100', '/resolutions/400', '/resolutions/800'].
_chromsizes.txt: chr3L 28110227 chr3R 32079331 chr2L 23513712 chr2R 25286936 chrX 23542271 chrY 3667352 chrM 19524 chr4 1348131
COMMAND: java -jar SIP_HiC_v1.6.1.jar cool my_data.mcool chrom_sizes.txt SIP_output /usr/bin/cooltools /usr/bin/cooler -isDroso false -res 400 -factor 2 -t 2000 -fdr 0.1 -d 15 -mat 5000 -nbZero 6 -del true -cpu 8 -g 3 -min 2 -max 2
OUTPUT (first part): cooltools, version 0.5.1
cooler, version 0.8.11
cool mode: input: my_data.mcool output: SIP_output cooltools: /usr/bin/cooltools cooler: /usr/bin/cooler norm: KR gauss: 3.0 min: 2.0 max: 2.0 matrix size: 5000 diag size: 15 resolution: 400 saturated pixel: 0.01 threshold: 2000 number of zero :6 factor 2 fdr 0.1 del true cpu 8 -isDroso false
start SIP_output/400kb.expected Start cooltools compute-expected java.nio.file.NoSuchFileException: SIP_output/400kb.expected at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86) at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102) at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107) at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214) at java.nio.file.Files.newByteChannel(Files.java:361) at java.nio.file.Files.newByteChannel(Files.java:407) at java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:384) at java.nio.file.Files.newInputStream(Files.java:152) at java.nio.file.Files.newBufferedReader(Files.java:2784) at utils.CoolerExpected.parseExpectedFile(CoolerExpected.java:90) at utils.CoolerExpected.dumpExpected(CoolerExpected.java:79) at multiProcesing.ProcessCoolerDumpData.go(ProcessCoolerDumpData.java:61) at sipMain.Hic_main.main(Hic_main.java:280) !!!!!!! End SIP_output/400kb.expected ...
COMMENT: It seems it is looking for a resolution of 400kb, which I never asked for, and (of course) it is not present in the input. It does the same for 800kb since my factor parameter is 2. Additionally, it is looking for 'KR' normalization, which I think is what a .hic file may have, but not a .mcool.