java -Djava.library.path=/home/Simulation/revision/bbmap/jni/ -ea -Xmx101g -cp /home/Simulation/revision/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=/home/Simulation/real_genomes/Mmul_new/Mmul_long.fa nodisk in=/home/Simulation/revision/realGenomes/100SE/Mmul/fastq/Mmul.100SE.rep1.fastq.gz unpigz=t maxindel=200000 local=t threads=1 ambiguous=best out=/home/Simulation/revision/realGenomes/100SE/Mmul/bams/self_Mmul.100SE.rep1.bam pigz=t showprogress=1000000 sam=1.3 nhtag=t nmtag=t statsfile=/home/Simulation/revision/realGenomes/100SE/Mmul/bams/self_Mmul.100SE.rep1.stats -Xmx101g
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=/home/Simulation/real_genomes/Mmul_new/Mmul_long.fa, nodisk, in=/home/Simulation/revision/realGenomes/100SE/Mmul/fastq/Mmul.100SE.rep1.fastq.gz, unpigz=t, maxindel=200000, local=t, threads=1, ambiguous=best, out=/home/Simulation/revision/realGenomes/100SE/Mmul/bams/self_Mmul.100SE.rep1.bam, pigz=t, showprogress=1000000, sam=1.3, nhtag=t, nmtag=t, statsfile=/home/Simulation/revision/realGenomes/100SE/Mmul/bams/self_Mmul.100SE.rep1.stats, -Xmx101g]
Version 38.02 [build=1, overwrite=true, fastareadlen=500, ref=/home/Simulation/real_genomes/Mmul_new/Mmul_long.fa, nodisk, in=/home/Simulation/revision/realGenomes/100SE/Mmul/fastq/Mmul.100SE.rep1.fastq.gz, unpigz=t, maxindel=200000, local=t, threads=1, ambiguous=best, out=/home/Simulation/revision/realGenomes/100SE/Mmul/bams/self_Mmul.100SE.rep1.bam, pigz=t, showprogress=1000000, sam=1.3, nhtag=t, nmtag=t, statsfile=/home/Simulation/revision/realGenomes/100SE/Mmul/bams/self_Mmul.100SE.rep1.stats, -Xmx101g]

Set threads to 1
Retaining first best site only for ambiguous mappings.
Executing dna.FastaToChromArrays2 [/home/Simulation/real_genomes/Mmul_new/Mmul_long.fa, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=false, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=true]

Set genScaffoldInfo=true
Set genome to 1

Loaded Reference:	0.004 seconds.
Loading index for chunk 1-7, build 1
Indexing threads started for block 0-3
Indexing threads finished for block 0-3
Indexing threads started for block 4-7
Indexing threads finished for block 4-7
Generated Index:	512.669 seconds.
Analyzed Index:   	17.231 seconds.
Found samtools 1.8
Started output stream:	0.151 seconds.
Cleared Memory:    	4.581 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 1 mapping thread.
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)
Detecting finished threads: 0

**************************************************************************
Warning!  1 mapping thread did not terminate normally.
Check the error log; the output may be corrupt or incomplete.
Please submit the full stderr output as a bug report, not just this message.
**************************************************************************




   ------------------   Results   ------------------   

Genome:                	1
Key Length:            	13
Max Indel:             	200000
Minimum Score Ratio:  	0.56
Mapping Mode:         	normal
Exception in thread "main" java.lang.AssertionError: 
The number of reads out does not add up to the number of reads in.
This may indicate that a mapping thread crashed.
If you submit a bug report, include the entire console output, not just this error message.
48746+48232+0+503+0 = 97481 != 97482
	at align2.AbstractMapper.printOutputStats(AbstractMapper.java:1924)
	at align2.AbstractMapper.printOutput(AbstractMapper.java:1053)
	at align2.BBMap.testSpeed(BBMap.java:499)
	at align2.BBMap.main(BBMap.java:35)