java.nio.file.NoSuchFileException in .mcool

[MarcoDiS]

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'].

chrom_sizes.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.

[PouletAxel]

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