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PouletAxel / SIP

SIP: Significant Interaction Peak caller
GNU General Public License v3.0
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Error java.nio.file.NoSuchFileException with mcool #18

Open ianakim opened 2 years ago

ianakim commented 2 years ago

Hi, thanks a lot for the wonderful software! It works really well on small genomes with hic file. However, I was trying to run it with mcool file using the following command: java -Xmx10g -jar ${dir}/SIP_HiC_v1.6.1.jar cool ${mcool} ${CHROMSIZE_TEST} ${OUTDIR}/SIP_01 ${cooltoolsPath} ${coolerPath} -res 400 -t 2000 -fdr 0.1 -d 10 -mat 5000 -nbZero 6 -del true -cpu $CPU -g 3 -min 2 -max 2

And got the following error but no output files generated (only parameters.txt). Could you please help me to solve this issue? 

cooltools, version 0.5.0

cooler, version 0.8.11

cool mode: 
input: path to mcool
output: path to /SIP_01
cooltools: ~/miniconda3/envs/cooltools_env/bin/cooltools
cooler: ~/.local/bin/cooler
norm: KR
gauss: 3.0
min: 2.0
max: 2.0
matrix size: 5000
diag size: 10
resolution: 400
saturated pixel: 0.01
threshold: 2000
number of zero :6
factor 1
fdr 0.1
del true
cpu 8
-isDroso false

start /home/loops/SIP_01/400kb.expected
Start cooltools compute-expected
java.nio.file.NoSuchFileException: /home/loops/SIP_01/400kb.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 /home/loops/SIP_01/400kb.expected
java.nio.file.NoSuchFileException: /home/loops/SIP_01/400kb.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 multiProcesing.RunnableDumpDataCooler.run(RunnableDumpDataCooler.java:71)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
##### End dump chr_1 400kb
Start loop detction step
/home/loops/SIP_01/400kb/chr_1/
###########End loop detction step
Exception in thread "pool-2-thread-1" java.lang.NullPointerException
    at multiProcesing.RunnableDetectLoops.run(RunnableDetectLoops.java:74)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
End of SIP loops are available in /home/loops/SIP_01
PouletAxel commented 2 years ago

Hi, Thanks for using SIP, Can you tell me which cool file are you using in input? Are you sure that the resolution you want use is present in the mcool file? Best Axel

ianakim commented 2 years ago

Hi Axel,

I am using our in-home Micro-C dataset from a non-bilaterian animal (genome size ~200Mb). The file contains the following resolutions:

['/resolutions/200',
 '/resolutions/400',
 '/resolutions/800',
 '/resolutions/1600',
 '/resolutions/3200',
 '/resolutions/6400',
 '/resolutions/12800',
 '/resolutions/25600',
 '/resolutions/51200',
 '/resolutions/102400',
 '/resolutions/204800',
 '/resolutions/409600']

Can the problem be that SIP looks for KR normalization in cool file that was balanced with ICE?

cool mode: 
input: path to mcool
output: path to /SIP_01
cooltools: ~/miniconda3/envs/cooltools_env/bin/cooltools
cooler: ~/.local/bin/cooler
norm: KR

Best, Iana

PouletAxel commented 2 years ago

Yes it is possible, I will look at that I need to release a new version soon, so I will correct this problem in the same. thanks for your patience Best Axel

ianakim commented 2 years ago

Thanks Axel! Looking forward to the new version. Cool Stuff! :)

xl5525 commented 2 years ago

I had the same problem yesterday but SIP worked for me a few months ago. And I solved the problem by using cooler=0.8.6, cooltools=0.3.2. I think it is more likely a compiling problem, but not the norm problem.

ianakim commented 2 years ago

thanks, xl5525! using cooler=0.8.6, cooltools=0.3.2 solved it!!!

PouletAxel commented 2 years ago

I will change that for the next version.Sorry about that

On Thu, 28 Apr 2022 at 09:40, ianakim @.***> wrote:

thanks, xl5525! using cooler=0.8.6, cooltools=0.3.2 solved it!!!

— Reply to this email directly, view it on GitHub https://github.com/PouletAxel/SIP/issues/18#issuecomment-1112217898, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABS4UBLDIUONO3HY6VYEPITVHKINPANCNFSM5S4BICOQ . You are receiving this because you commented.Message ID: @.***>

MarcoDiS commented 2 years ago

using cooler=0.8.6, cooltools=0.3.2 worked for me too! Thanks!

h3loiz commented 1 year ago

Hi Axel, I would like to try your nice program, but I'm running into the very same problem using my mcool file as input. So I wanted to know if you got a chance to fix it or if you know when this is going to be fixed? Or any other way for me to get around the problem... Because I have cooltools, version 0.5.1 and cooler, version 0.8.11, and I'd rather not downgrade them because I'm using them for other purposes. Thanks for your help !

xl5525 commented 1 year ago

Hi Axel, I would like to try your nice program, but I'm running into the very same problem using my mcool file as input. So I wanted to know if you got a chance to fix it or if you know when this is going to be fixed? Or any other way for me to get around the problem... Because I have cooltools, version 0.5.1 and cooler, version 0.8.11, and I'd rather not downgrade them because I'm using them for other purposes. Thanks for your help !

Try to setup independent environments for different purposes.

conda create -n SIP cooler=0.8.6 cooltools=0.3.2
conda activate SIP
h3loiz commented 1 year ago

Thanks Axel, this seem to make it work indeed! :-)