Hi,
Two issues using SIPMeta 1.3.1, Java 1.8.0_102, CentOS7, command line like:
java -jar $SIPMeta hic simple $bedpe $hicfile $outdir $chrsizes $juicer_tools $bullseye 21 1000 -norm -res 10000
Issue 1: if juicer tools 1.13 as recommended on the wiki (specifically juicer_tools_1.13.02.jar), then "-norm " has no effect. It always dies with error "Norm not available at BP_X VC" where X is the -res argument, no matter what resolution. Basically it always tries to pull VC, and always fails, even though I can manually dump VC data at every resolution, from 1k to 1M.
Issue 2: I tried a different version of juicer tools (feature_tools_2.13.07.jar) and apparently this does dump data correctly, but then dies with a completely different issue:
java.nio.file.NoSuchFileException: /n/core/Bioinformatics/analysis/Rohner/tb2500/cbio.tb2500.100/data/juicer_new/analysis/loops/SIP/comp/sipmeta/cave_only/Pachon/25kb/AMEX_1.1_unplaced_55/AMEX_1.1_unplaced_55_0_53027_expected.txt
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
at java.nio.file.Files.newByteChannel(Files.java:361)
at java.nio.file.Files.newByteChannel(Files.java:407)
at java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:384)
at java.nio.file.Files.newInputStream(Files.java:152)
at java.nio.file.Files.newBufferedReader(Files.java:2784)
at utils.DumpData.getExpected(DumpData.java:142)
at multiProcessing.RunnableDumpData.run(RunnableDumpData.java:71)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Unknown chromosome: AMEX_1.1_unplaced_55
java.nio.file.NoSuchFileException: /n/core/Bioinformatics/analysis/Rohner/tb2500/cbio.tb2500.100/data/juicer_new/analysis/loops/SIP/comp/sipmeta/cave_only/Pachon/25kb/AMEX_1.1_unplaced_56/AMEX_1.1_unplaced_56_0_52918_expected.txt
The message itself seems confused as to whether the offending scaffold was AMEX_1.1_unplaced_55 or AMEX_1.1_unplaced_56, which are lines 80 and 81 in the $chrsizes file, respectively. I assume this is because these chromosomes have no signal in the hic file, which is possible. However, such a minor issue should never cause the script to die. Besides, the input bedpe file does not even have any loops on these scaffolds.
Thanks,
Ariel
Hi,
Two issues using SIPMeta 1.3.1, Java 1.8.0_102, CentOS7, command line like:
java -jar $SIPMeta hic simple $bedpe $hicfile $outdir $chrsizes $juicer_tools $bullseye 21 1000 -norm -res 10000
Issue 1: if juicer tools 1.13 as recommended on the wiki (specifically juicer_tools_1.13.02.jar), then "-norm " has no effect. It always dies with error "Norm not available at BP_X VC" where X is the -res argument, no matter what resolution. Basically it always tries to pull VC, and always fails, even though I can manually dump VC data at every resolution, from 1k to 1M.
Issue 2: I tried a different version of juicer tools (feature_tools_2.13.07.jar) and apparently this does dump data correctly, but then dies with a completely different issue:
java.nio.file.NoSuchFileException: /n/core/Bioinformatics/analysis/Rohner/tb2500/cbio.tb2500.100/data/juicer_new/analysis/loops/SIP/comp/sipmeta/cave_only/Pachon/25kb/AMEX_1.1_unplaced_55/AMEX_1.1_unplaced_55_0_53027_expected.txt
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
at java.nio.file.Files.newByteChannel(Files.java:361)
at java.nio.file.Files.newByteChannel(Files.java:407)
at java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:384)
at java.nio.file.Files.newInputStream(Files.java:152)
at java.nio.file.Files.newBufferedReader(Files.java:2784)
at utils.DumpData.getExpected(DumpData.java:142)
at multiProcessing.RunnableDumpData.run(RunnableDumpData.java:71)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Unknown chromosome: AMEX_1.1_unplaced_55
java.nio.file.NoSuchFileException: /n/core/Bioinformatics/analysis/Rohner/tb2500/cbio.tb2500.100/data/juicer_new/analysis/loops/SIP/comp/sipmeta/cave_only/Pachon/25kb/AMEX_1.1_unplaced_56/AMEX_1.1_unplaced_56_0_52918_expected.txt
The message itself seems confused as to whether the offending scaffold was AMEX_1.1_unplaced_55 or AMEX_1.1_unplaced_56, which are lines 80 and 81 in the $chrsizes file, respectively. I assume this is because these chromosomes have no signal in the hic file, which is possible. However, such a minor issue should never cause the script to die. Besides, the input bedpe file does not even have any loops on these scaffolds.
Thanks,
Ariel