bbmap aborts after mapping some reads
Hello Brian,
we are using bbmap to see in how far it is possible to quantify gene expression by mapping Illumina RNA-seq reads to the genome of a closely related species, e.g. map chimpanzee reads to human or as in this example Macaque reads.
To this end, we generated Macaque Illumina SE reads using flux-simulator and map them to
hg38 and for comparison we were also trying also Mmul8, downloaded from ensembl (wget ftp://ftp.ensembl.org/pub/release-92...toplevel.fa.gz).
Everything mapped fine to hg38, but not to Mmul8.
Exception in thread "Thread-12" java.lang.AssertionError
at align2.BBIndex.extendScore(BBIndex.java:2612)
at align2.BBIndex.slowWalk3(BBIndex.java:1389)
at align2.BBIndex.find(BBIndex.java:777)
at align2.BBIndex.find(BBIndex.java:623)
at align2.BBIndex.findAdvanced(BBIndex.java:400)
at align2.AbstractMapThread.quickMap(AbstractMapThread.java:750)
at align2.BBMapThread.processRead(BBMapThread.java:408)
at align2.AbstractMapThread.run(AbstractMapThread.java:508)
I tried to run on one thread, increased memory to 101G, removed small contigs of <100kb ... but the error message remains the same.
We are running a Debian system with java version "1.8.0_181" and have BBMap version 38.02 -- the detailed error output is in the attached file.
The false Mapping Rates of bbmap are so much better than for STAR & GSNAP, that we definitely want to use bbmap for our paper and we are nearly done all other species (marmoset, gorilla, chimpanzee and orangutan) and the simulations ran through -- the only missing piece is the mapping to the Mmul8.
Any help would be greatly appreciated.
Best, Ines
Hello Brian,
we are using bbmap to see in how far it is possible to quantify gene expression by mapping Illumina RNA-seq reads to the genome of a closely related species, e.g. map chimpanzee reads to human or as in this example Macaque reads.
To this end, we generated Macaque Illumina SE reads using flux-simulator and map them to
hg38 and for comparison we were also trying also Mmul8, downloaded from ensembl (wget ftp://ftp.ensembl.org/pub/release-92...toplevel.fa.gz).
Everything mapped fine to hg38, but not to Mmul8.
Exception in thread "Thread-12" java.lang.AssertionError
at align2.BBIndex.extendScore(BBIndex.java:2612)
at align2.BBIndex.slowWalk3(BBIndex.java:1389)
at align2.BBIndex.find(BBIndex.java:777)
at align2.BBIndex.find(BBIndex.java:623)
at align2.BBIndex.findAdvanced(BBIndex.java:400)
at align2.AbstractMapThread.quickMap(AbstractMapThread.java:750)
at align2.BBMapThread.processRead(BBMapThread.java:408)
at align2.AbstractMapThread.run(AbstractMapThread.java:508)
I tried to run on one thread, increased memory to 101G, removed small contigs of <100kb ... but the error message remains the same.
We are running a Debian system with java version "1.8.0_181" and have BBMap version 38.02 -- the detailed error output is in the attached file.
The false Mapping Rates of bbmap are so much better than for STAR & GSNAP, that we definitely want to use bbmap for our paper and we are nearly done all other species (marmoset, gorilla, chimpanzee and orangutan) and the simulations ran through -- the only missing piece is the mapping to the Mmul8.
Any help would be greatly appreciated.
Best, Ines
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