Can not extract data from .hic files by "dump" command

[jiluzh...@gmail.com]

Hello,

  When I want to get interaction data by "dump" command, I get wrong information as following:

  ERROR [2017-03-23 10:06:50,433]  [DatasetReaderV2.java:236] [main]  Error reading dataset

  java.net.SocketTimeoutException: Read timed out

        at java.net.SocketInputStream.socketRead0(Native Method)

        at java.net.SocketInputStream.read(SocketInputStream.java:150)

        at java.net.SocketInputStream.read(SocketInputStream.java:121)

        at sun.security.ssl.InputRecord.readFully(InputRecord.java:312)

        at sun.security.ssl.InputRecord.readV3Record(InputRecord.java:424)

        at sun.security.ssl.InputRecord.read(InputRecord.java:379)

        at sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:927)

        at sun.security.ssl.SSLSocketImpl.readDataRecord(SSLSocketImpl.java:884)

        at sun.security.ssl.AppInputStream.read(AppInputStream.java:102)

        at java.io.BufferedInputStream.read1(BufferedInputStream.java:273)

        at java.io.BufferedInputStream.read(BufferedInputStream.java:334)

        at sun.net.www.MeteredStream.read(MeteredStream.java:134)

        at java.io.FilterInputStream.read(FilterInputStream.java:133)

        at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:3035)

        at org.broad.igv.util.stream.IGVSeekableHTTPStream._read(IGVSeekableHTTPStream.java:128)

        at org.broad.igv.util.stream.IGVSeekableHTTPStream.read(IGVSeekableHTTPStream.java:84)

        at java.io.InputStream.read(InputStream.java:101)

        at juicebox.data.DatasetReaderV2.readFooter(DatasetReaderV2.java:437)

        at juicebox.data.DatasetReaderV2.read(DatasetReaderV2.java:232)

        at juicebox.data.HiCFileTools.extractDatasetForCLT(HiCFileTools.java:64)

        at juicebox.tools.clt.old.Dump.readArguments(Dump.java:345)

        at juicebox.tools.HiCTools.main(HiCTools.java:85)

Could not read hic file: Read timed out

  My command is " java -jar juicer_tools_linux_0.8.jar dump observed VC https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic 2:60081000:62081000 2:60081000:62081000 BP 1000 rs702873/rs702873_2M_observed_VC.txt". 

  This problem did not appear in previous time, I am so confused and wonder help!

  Thanks!

Best,

JiLuzhang

[Neva Durand]

It looks like your internet connection is having problems.

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www.aidenlab.org

[jiluzh...@gmail.com]

  So what should I do to solve this problem? Isn't it distal server problem?

在 2017年3月23日星期四 UTC+8下午1:56:48，Neva Durand写道：

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[Muhammad Saad Shamim]

Can you retry?

- Muhammad Saad Shamim

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[jiluzh...@gmail.com]

  I have tried so many times, but the problem is still existing.

在 2017年3月23日星期四 UTC+8下午2:16:39，Muhammad Shamim写道：

Can you retry?

- Muhammad Saad Shamim

[Muhammad Saad Shamim]

You mentioned this has worked in the past.

Has your institution implemented any changes to their firewall relating to AWS data?

There doesn't seem to be any other explanation... (the command you used works fine)

- Muhammad Saad Shamim

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[Neva Durand]

Actually it is on your end; I have just run this command on my machine with no problem.

I wonder if Amazon S3 might be blocked where you are?  Try opening a web browser and going to http://hicfiles.tc4ga.com.s3.amazonaws.com/public/juicebox.properties

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