Bad hash size error in Jellyfish

[BethMH]

Hi all,

I'm using Trinity for the first time on some data we've been sent by a colleague. I'm getting this error during the Jellyfish stage - I wondered if any of you have any insights?

Here's the error:

perl Trinity.pl --seqType fq --JM 30G --single ../../../../data/Easp_VT.fastq --CPU 4
Current settings:
time(seconds) unlimited
file(blocks) unlimited
data(kbytes) unlimited
stack(kbytes) 8192
coredump(blocks) 0
memory(kbytes) unlimited
locked memory(kbytes) 64
process unlimited
nofiles 1024
vmemory(kbytes) unlimited
locks unlimited


-since butterfly will eventually be run, lets test for proper execution of java
#######################################
Running Java Tests
Thursday, January 23, 2014: 10:05:30 CMD: java -Xmx64m -jar /Trinity/util/ExitTester.jar 0
CMD finished (0 seconds)
Thursday, January 23, 2014: 10:05:30 CMD: java -Xmx64m -jar /Trinity/util/ExitTester.jar 1
-we properly captured the java failure status, as needed. Looking good.
Java tests succeeded.
###################################

-------------------------------------------
----------- Jellyfish --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

Thursday, January 23, 2014: 10:05:55 CMD: /Trinity/trinity-plugins/jellyfish/bin/jellyfish count -t 4 -m 25 -s 409974768 single.fa
CMD finished (2344 seconds)
Thursday, January 23, 2014: 10:44:59 CMD: /Trinity/trinity-plugins/jellyfish/bin/jellyfish merge -o jellyfish.kmer.db mer_counts_0 mer_counts_1 mer_counts_2 mer_counts_3 mer_counts_4 mer_counts_5 mer_counts_6 mer_counts_7 mer_counts_8 mer_counts_9
terminate called after throwing an instance of 'jellyfish::compacted_hash::ErrorReading'
what(): 'mer_counts_0': Bad hash size '4467145872', expected '4494027120' bytes
Error, cmd: /Trinity/trinity-plugins/jellyfish/bin/jellyfish merge -o jellyfish.kmer.db mer_counts_0 mer_counts_1 mer_counts_2 mer_counts_3 mer_counts_4 mer_counts_5 mer_counts_6 mer_counts_7 mer_counts_8 mer_counts_9 died with ret 6 at Trinity.pl line 1793.

[westerman]

You *may* be running out of memory. What is the memory size in your system? Using a small '-JM' size could be useful. It should only increase the time to run Jellyfish by a small amount.

[vivek_]

I'd also check the version of perl, some older versions have a memory cap.

[BethMH]

Thanks, it does appear to have been a memory problem and reducing the -Jm seems to have solved it.