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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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hicpro2juicebox.sh error #471

Closed csijcs closed 3 years ago

csijcs commented 3 years ago

Thanks for the great tool(s).

I've used this script before without issue, but recently I receive the following error: Warning : Java version must be > 1.8.0 to use Juicebox - 11.0.1 detected HiC-Pro format > 2.7.5 detected ... Generating Juicebox input files ... Running Juicebox ... WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. WARN [2021-08-17T12:40:54,131] [Globals.java:138] [main] Development mode is enabled Problem with creating fragment-delimited maps, NullPointerException. This could be due to a null fragment map or to a mismatch in the chromosome name in the fragment map vis-a-vis the input file or chrom.sizes file. Exiting. done !

I am sure that I am using the same chrom.sizes file that was used in processing.

After receiving the error I updated to the 3.1.0 version, reprocessed, ran the script again and received the same error.

Any idea what is causing this or how to fix it?

csijcs commented 3 years ago

Nevermind, I fixed it. I had no pairs mapping to the Y chromosome, so I removed it from the chrom.sizes file and it runs fine