Error: chromosome combination 1_10 appears in multiple blocks

[Vanessa Roy]

Hi all!

I've been running into issues when running mega.sh, and would greatly appreciate if you could take a look at what's going on here.

I've been trying to run both the SLURM and CPU version of juicer2 with juicer_tools v2.20, however, whenever I try to run mega.sh (CPU or SLURM), I get an error that I haven't been able to resolve, even after trying to sort the files (I pre-processed the replicates separately using juicer, and this works, the inter.hic and inter_30.hic for individual replicated are being created, so it is strange that there is a sorting problem when using mega.sh). 

Here is the output I get when I use the CPU version, which also cannot recognize the string 50% - 50% while creating the merged stats file (although the stats file is being created), followed by the error: 'Error: the chromosome combination 1_10 appears in multiple blocks'

Coreutils9.0 has been activated

gatk-4.2.3.0-java8 has been activated

java.lang.NumberFormatException: For input string: "50% - 50%"

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.lang.Long.parseLong(Long.java:589)

at java.lang.Long.parseLong(Long.java:631)

at sfh.merger.StatsMerger.processLine(StatsMerger.java:41)

at sfh.merger.StatsMerger.parse(StatsMerger.java:16)

at sfh.StatsUtils.merge(StatsUtils.java:10)

at sfh.MergeStats.main(MergeStats.java:50)

java.lang.NumberFormatException: For input string: "50% - 50%"

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.lang.Long.parseLong(Long.java:589)

at java.lang.Long.parseLong(Long.java:631)

at sfh.merger.StatsMerger.processLine(StatsMerger.java:41)

at sfh.merger.StatsMerger.parse(StatsMerger.java:16)

at sfh.StatsUtils.merge(StatsUtils.java:10)

at sfh.MergeStats.main(MergeStats.java:50)

java.lang.NumberFormatException: For input string: "50% - 50%"

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.lang.Long.parseLong(Long.java:589)

at java.lang.Long.parseLong(Long.java:631)

at sfh.merger.StatsMerger.processLine(StatsMerger.java:41)

at sfh.merger.StatsMerger.parse(StatsMerger.java:16)

at sfh.StatsUtils.merge(StatsUtils.java:10)

at sfh.MergeStats.main(MergeStats.java:50)

java.lang.NumberFormatException: For input string: "50% - 50%"

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.lang.Long.parseLong(Long.java:589)

at java.lang.Long.parseLong(Long.java:631)

at sfh.merger.StatsMerger.processLine(StatsMerger.java:41)

at sfh.merger.StatsMerger.parse(StatsMerger.java:16)

at sfh.StatsUtils.merge(StatsUtils.java:10)

at sfh.MergeStats.main(MergeStats.java:50)

java.lang.NumberFormatException: For input string: "50% - 50%"

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.lang.Long.parseLong(Long.java:589)

at java.lang.Long.parseLong(Long.java:631)

at sfh.merger.StatsMerger.processLine(StatsMerger.java:41)

at sfh.merger.StatsMerger.parse(StatsMerger.java:16)

at sfh.StatsUtils.merge(StatsUtils.java:10)

at sfh.MergeStats.main(MergeStats.java:50)

java.lang.NumberFormatException: For input string: "50% - 50%"

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

at java.lang.Long.parseLong(Long.java:589)

at java.lang.Long.parseLong(Long.java:631)

at sfh.merger.StatsMerger.processLine(StatsMerger.java:41)

at sfh.merger.StatsMerger.parse(StatsMerger.java:16)

at sfh.StatsUtils.merge(StatsUtils.java:10)

at sfh.MergeStats.main(MergeStats.java:50)

(-: Finished creating top stats files.

(-: Finished sorting all files into a single merge.

Using 1 CPU thread(s) for primary task

Using 10 CPU thread(s) for secondary task

Not including fragment map

Start preprocess

Writing header

Writing body

......................................................................................Error: the chromosome combination 1_10 appears in multiple blocks

---

When I run the SLURM version, this is what I get (from the hic1-xyz.err file):

head hic1-4883.err

Picked up _JAVA_OPTIONS: -Xms150000m -Xmx150000m

Error: the chromosome combination 1_10 appears in multiple blocks

---

Upon the 'Error: the chromosome combination 1_10 appears in multiple blocks' errors, the hic file generation stops and the files are removed, so the downstream scripts also give me the error that it cannot find the inter.hic or inter_30.hic files.

I haven't been able to figure out what the problem is here. I would be very grateful for any pointers!

Many thanks!

Best wishes,

Vanessa 

[Bishal Shrestha]

I have the same issue, has anyone encountered the same issue and solved it?