bbnorm Java error?
I'm trying to use bbnorm to normalize my reads; I ran it first to just generate the kmer histogram, and now I'm trying to run it to normalize. However in the first stage, I'm getting 'java.lang.AssertionError' for each thread. Any suggestions? I realized I set my min and max from the k=31 default histogram, so probably I should redo the histogram with k=43. Here's the command
bbnorm.sh k=43 mindepth=10 maxdepth=45 prefilter=t threads=60 hist=index6_input.hist histout=index6_norm.hist in=HK7M5ALXX_s3_1_illumina12index_6_SL254531.fastq.gz in2=HK7M5ALXX_s3_2_illumina12index_6_SL254531.fastq.gz out=bbnorm_s3_1_index_6.fastq.gz out2=bbnorm_s3_2_index_6.fastq.gz outt=bbnorm_toss_s3_12_index_6.fastq.gz
and the echoed command:
Executing jgi.KmerNormalize [bits=32, k=43, mindepth=10, maxdepth=45, prefilter=t, threads=60, hist=index6_input.hist, histout=index6_norm.hist, in=HK7M5ALXX_s3_1_illumina12index_6_SL254531.fastq.gz, in2=HK7M5ALXX_s3_2_illumina12index_6_SL254531.fastq.gz, out=bbnorm_s3_1_index_6.fastq.gz, out2=bbnorm_s3_2_index_6.fastq.gz, outt=bbnorm_toss_s3_12_index_6.fastq.gz]
and then the beginning of the errrors:
Exception in thread "Thread-5" java.lang.AssertionError
at kmer.KmerCount7MTA$CountThread.fillKmerArrayLong(KmerCount7MTA.java:800)
at kmer.KmerCount7MTA$CountThread.fillKmerArray(KmerCount7MTA.java:731)
at kmer.KmerCount7MTA$CountThread.addRead_Advanced(KmerCount7MTA.java:705)
at kmer.KmerCount7MTA$CountThread.count(KmerCount7MTA.java:502)
at kmer.KmerCount7MTA$CountThread.run(KmerCount7MTA.java:461)
Exception in thread "Thread-64" java.lang.AssertionError
at kmer.KmerCount7MTA$CountThread.fillKmerArrayLong(KmerCount7MTA.java:800)
at kmer.KmerCount7MTA$CountThread.fillKmerArray(KmerCount7MTA.java:731)
at kmer.KmerCount7MTA$CountThread.addRead_Advanced(KmerCount7MTA.java:705)
at kmer.KmerCount7MTA$CountThread.count(KmerCount7MTA.java:502)
at kmer.KmerCount7MTA$CountThread.run(KmerCount7MTA.java:461)
Exception in thread "Thread-63" java.lang.AssertionError
at kmer.KmerCount7MTA$CountThread.fillKmerArrayLong(KmerCount7MTA.java:800)
at kmer.KmerCount7MTA$CountThread.fillKmerArray(KmerCount7MTA.java:731)
at kmer.KmerCount7MTA$CountThread.addRead_Advanced(KmerCount7MTA.java:705)
at kmer.KmerCount7MTA$CountThread.count(KmerCount7MTA.java:502)
at kmer.KmerCount7MTA$CountThread.run(KmerCount7MTA.java:461)
Exception in thread "Thread-62" Exception in thread "Thread-61" java.lang.AssertionError
at kmer.KmerCount7MTA$CountThread.fillKmerArrayLong(KmerCount7MTA.java:800)
at kmer.KmerCount7MTA$CountThread.fillKmerArray(KmerCount7MTA.java:731)
at kmer.KmerCount7MTA$CountThread.addRead_Advanced(KmerCount7MTA.java:705)
at kmer.KmerCount7MTA$CountThread.count(KmerCount7MTA.java:502)
at kmer.KmerCount7MTA$CountThread.run(KmerCount7MTA.java:461)
0 answers
No answers yet.
Log in to answer this question.
which version is it ?
Tagging: Brian Bushnell
@Brian validates BBMap only using Java 1.7 and above.
I'm on 1.8:
The weird thing is, even just trying to make the histogram with k=43 fails, but the default (k=31) succeeds. I'm trying the normalization with default k now.
Aggh. I moved this to a comment but lost the RAM question. Java is getting 371.5Gb, machine has 512 so I could conceivably give it more. Annnd, I've hit the post limit for noobs. Version 34.82 of bbtools.
The memory is not a problem; BBNorm doesn't run out of memory. And by default it tries to use most, but not all, memory because our computers are configured to kill processes that use more than... ~85% of physical memory, for some reason. Some is reserved for caching, and some for the OS, so it's probably best to not try to use 100% of the memory in any case.
The latest version of BBTools is 37.32, so I suggest you try that and see if the error persists.
I was asking for the version of bbnorm
I'm on 1.8:
The weird thing is, even just trying to make the histogram with k=43 fails, but the default (k=31) succeeds. I'm trying the normalization with default k now.
How much RAM are you assigning to this job?
Please use
ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized.Oops ok sorry about that! Java is getting 371.5 Gb, machine has 512 installed so I could push it up to maybe 490-500Gb?