nchernia
commented
3 years ago The more recent jars have LibraryComplexity even though it's not in the usage statement
On Fri, Aug 20, 2021 at 4:13 PM edfajardo @.***> wrote:
Line 453 of the juicer.sh script (version 1.6 in CPU directory) results in the following error:
Exception in thread "main" java.lang.RuntimeException: Unknown command: LibraryComplexity
at juicebox.tools.HiCTools.main(HiCTools.java:99)
The offending line in juicer.sh is:
${juiceDir}/scripts/common/juicer_tools LibraryComplexity $outputdir inter.txt >> $outputdir/inter.txt
This error is not dependent on the version of the version_tools.jar installed (from https://github.com/aidenlab/juicer/wiki/Download).
The output of just running juicer_tools (in the common directory) with juicer_tools.1.6.2_jcuda.0.7.0.jar installed is:
$ juicer_tools
Juicer Tools Version 1.6.2
Usage:
dump <observed/oe> <NONE/VC/VC_SQRT/KR> <hicFile(s)>
[:x1:x2] [:y1:y2] <BP/FRAG> [outfile] dump <norm/expected> <NONE/VC/VC_SQRT/KR> <hicFile(s)>
<BP/FRAG> [outfile] dump <loops/domains>
[outfile] pre [options]
addNorm
pearsons [-p] <NONE/VC/VC_SQRT/KR> <hicFile(s)>
<BP/FRAG> [outfile] eigenvector -p <NONE/VC/VC_SQRT/KR> <hicFile(s)>
<BP/FRAG> [outfile] apa <hicFile(s)>
arrowhead <hicFile(s)>
hiccups
hiccupsdiff
validate
-h, --help print help
-v, --verbose verbose mode
-V, --version print version
Type juicer_tools
for more detailed usage instructions
So clearly, there is no LibraryComplexity command available. I also tried juicer_tools_1.19.02.jar and juicer_tools_0.7.0.jar; neither has such command.
Following immediately the above error line, I found the following (unrelated?) error line:
sort: cannot create temporary file in ‘/home/project/fastq/sample1/HIC_tmp’: No such file or directory
Which is odd because HIC_tmp had been created earlier (I saw the directory soon after the juicer.sh run started) but obviously was deleted at a later step in the script.
In the end, the .hic files were created OK, and I assume these are correct.
Thank you.
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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org
edfajardo
Line 453 of the juicer.sh script (version 1.6 in CPU directory) results in the following error:
The offending line in juicer.sh is:
This error is not dependent on the version of the version_tools.jar installed (from https://github.com/aidenlab/juicer/wiki/Download).
The output of just running juicer_tools (in the common directory) with juicer_tools.1.6.2_jcuda.0.7.0.jar installed is:
So clearly, there is no LibraryComplexity command available. I also tried juicer_tools_1.19.02.jar and juicer_tools_0.7.0.jar; neither has such command.
Following immediately the above error line, I found the following (unrelated?) error line:
Which is odd because HIC_tmp had been created earlier (I saw the directory soon after the juicer.sh run started) but obviously was deleted at a later step in the script.
In the end, the .hic files were created OK, and I assume these are correct.
Thank you.