java.lang.AssertionError with forcemerge=t
BBMap short read aligner, and other bioinformatic tools.
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#72 java.lang.AssertionError with forcemerge=t
Hi,
We recently updated to the lateset 39.15 version but when running BBMerge with the forcemerge=t option, I am getting the attached java.lang.AssertionError. This issue does not exist on the version we had previously been using (38.90).
Thank you for your help and the great, actively maintained tool! Let me know if there is anything else I can do to help.
Best,
- Jared
java -ea -Xmx1000m -Xms1000m -Djava.library.path=/opt/conda/opt/bbmap-39.15-0/jni/ -cp /opt/conda/opt/bbmap-39.15-0/current/ jgi.BBMerge forcemerge=t in=S6_L001_R1_001.fastq.gz in2=S6_L001_R2_001.fastq.gz out=sample.fq
Executing jgi.BBMerge [forcemerge=t, in=S6_L001_R1_001.fastq.gz, in2=S6_L001_R2_001.fastq.gz, out=sample.fq]
Version 39.15
Writing mergable reads merged.
Started output threads.
0, null
*22, false, 0, [1.1, 1.7334083, 0.4341722, 0.51, 0.51, 0.76400006, 0.68944097, 0.54545456, 0.2, 0.03918919, 0.5555556, 1.0600001, 0.42528737, 0.84555984, 0.2, 0.57972974, 0.8148148, 1.520156, 1.7711866, 0.0, 0.7516779, 0.1]
400, null
*22, false, 400, [1.5, 0.02252334, 0.064615756, 0.51, 0.51, 0.772, 0.6855346, 0.2, 0.2, 0.0050458717, 0.2, 1.164, 0.18032786, 0.5897436, 0.2, 0.4818182, 0.5, 1.4743787, 0.59375, 0.0, 0.90909094, 0.1]
1200, null
*22, false, 1200, [1.5, 0.024115011, 0.023431044, 0.51, 0.51, 0.776, 0.6835443, 0.2, 0.2, 0.005092593, 0.2, 1.1680001, 0.16666667, 0.5897436, 0.2, 0.53000003, 0.5, 1.5222478, 0.59375, 0.0, 0.9159664, 0.1]
800, null
*22, false, 800, [1.3000001, 0.024304846, 0.022640742, 0.51, 0.51, 0.768, 0.6875, 0.2, 0.2, 0.005, 0.2, 1.1400001, 0.25373134, 0.65665233, 0.2, 0.4235294, 0.5833333, 1.4164472, 0.83124995, 0.0, 0.8671875, 0.1]
Exception in thread "Thread-4" java.lang.AssertionError
at jgi.BBMerge$MateThread.mateByOverlap(BBMerge.java:2455)
at jgi.BBMerge$MateThread.processReadPair_inner(BBMerge.java:2774)
at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2576)
at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1853)
at jgi.BBMerge$MateThread.processReads(BBMerge.java:1774)
at jgi.BBMerge$MateThread.run(BBMerge.java:1748)
Exception in thread "Thread-6" java.lang.AssertionError
at jgi.BBMerge$MateThread.mateByOverlap(BBMerge.java:2455)
at jgi.BBMerge$MateThread.processReadPair_inner(BBMerge.java:2774)
at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2576)
at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1853)
at jgi.BBMerge$MateThread.processReads(BBMerge.java:1774)
at jgi.BBMerge$MateThread.run(BBMerge.java:1748)
Exception in thread "Thread-7" java.lang.AssertionError
at jgi.BBMerge$MateThread.mateByOverlap(BBMerge.java:2455)
at jgi.BBMerge$MateThread.processReadPair_inner(BBMerge.java:2774)
at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2576)
at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1853)
at jgi.BBMerge$MateThread.processReads(BBMerge.java:1774)
at jgi.BBMerge$MateThread.run(BBMerge.java:1748)
Exception in thread "Thread-5" java.lang.AssertionError
at jgi.BBMerge$MateThread.mateByOverlap(BBMerge.java:2455)
at jgi.BBMerge$MateThread.processReadPair_inner(BBMerge.java:2774)
at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2576)
at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1853)
at jgi.BBMerge$MateThread.processReads(BBMerge.java:1774)
at jgi.BBMerge$MateThread.run(BBMerge.java:1748)
Total time: 0.814 seconds.
Pairs: 4
Joined: 0 0.000%
Ambiguous: 0 0.000%
No Solution: 0 0.000%
Too Short: 0 0.000%
Avg Insert: NaN
Standard Deviation: 0.0
Mode: 0
Insert range: 999999999 - 0
90th percentile: 0
75th percentile: 0
50th percentile: 0
25th percentile: 0
10th percentile: 0