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Old 05-23-2014, 07:20 AM   #42
WhatsOEver
Senior Member
 
Location: Germany

Join Date: Apr 2012
Posts: 215
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Dear Brian,

I have yet another issue

Looking through the readme I saw that the standard state for stoptag and idtag is true. However, looking at my sam file I couldn't find any YS or YI fields. I therefore tried to set the parameter explicitly in the start command, but this resulted in an error:

Quote:
/projects/bbmap$ ./bbmap ../bbAlign/DNAseq_140306.fastq
java -ea -Xmx56g -cp /projects/bbmap/current/ align2.BBMapPacBio build=1 overwrite=true minratio=0.40 fastareadlen=6000 ambiguous=best minscaf=100 startpad=10000 stoppad=10000 midpad=6000 k=14 t=16 in=../bbAlign/DNAseq_140306.fastq out=/projects/bbAlign/bbmap_DNAseq_140306_mapped.sam xstag=unstranded xmtag=t stoptag=t idtag=t ambig=all maxindel=10 qin=33 samversion=1.4 qhist=/projects/bbAlign/bb_qhist.txt mhist=/projects/bbAlign/bb_mhist.txt qahist=/projects/bbAlign/qahist.txt ihist=/projects/bbAlign/ihist.txt bhist=/projects/bbAlign/bhist.txt scafstats=/projects/bbAlign/scafStats refStats=/projects/bbAlign/refStats.txt -Xmx56g
Executing align2.BBMapPacBio [build=1, overwrite=true, minratio=0.40, fastareadlen=6000, ambiguous=best, minscaf=100, startpad=10000, stoppad=10000, midpad=6000, k=14, t=16, in=../bbAlign/DNAseq_140306.fastq, out=/projects/bbAlign/bbmap_DNAseq_140306_mapped.sam, xstag=unstranded, xmtag=t, stoptag=t, idtag=t, ambig=all, maxindel=10, qin=33, samversion=1.4, qhist=/projects/bbAlign/bb_qhist.txt, mhist=/projects/bbAlign/bb_mhist.txt, qahist=/projects/bbAlign/qahist.txt, ihist=/projects/bbAlign/ihist.txt, bhist=/projects/bbAlign/bhist.txt, scafstats=/projects/bbAlign/scafStats, refStats=/projects/bbAlign/refStats.txt, -Xmx56g]

BBMap version 32.14
Set overwrite to true
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.400
Set threads to 16
Set fastq input ASCII offset to 33
Set quality histogram output to /projects/bbAlign/bb_qhist.txt
Set match histogram output to /projects/bbAlign/bb_mhist.txt
Set quality accuracy histogram output to /projects/bbAlign/qahist.txt
Set insert size histogram output to /projects/bbAlign/ihist.txt
Set base content histogram output to /projects/bbAlign/bhist.txt
Scaffold statistics will be written to /projects/bbAlign/scafStats
Reference set statistics will be written to /projects/bbAlign/refStats.txt
Retaining all best sites for ambiguous mappings.
Set genome to 1

Loaded Reference: 6.389 seconds.
Loading index for chunk 1-7, build 1
Generated Index: 8.479 seconds.
Analyzed Index: 23.584 seconds.
Started output stream: 0.014 seconds.
Creating scaffold statistics table: 0.001 seconds.
Cleared Memory: 0.506 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 16 mapping threads.
Exception in thread "Thread-11" java.lang.NullPointerException
at stream.SamLine.<init>(SamLine.java:1130)
at stream.ReadStreamByteWriter.run2(ReadStreamByteWriter.java:154)
at stream.ReadStreamByteWriter.run(ReadStreamByteWriter.java:19)
Exception in thread "Thread-24" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-21" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-19" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-12" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Detecting finished threads: 0Exception in thread "Thread-25" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-18" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-23" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-27" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-15" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-17" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-20" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-13" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
, 1Exception in thread "Thread-26" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-22" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
Exception in thread "Thread-14" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
, 2, 3Exception in thread "Thread-16" java.lang.RuntimeException: Writing to a terminated thread.
at stream.RTextOutputStream3.write(RTextOutputStream3.java:121)
at stream.RTextOutputStream3.addDisordered(RTextOutputStream3.java:116)
at stream.RTextOutputStream3.add(RTextOutputStream3.java:90)
at align2.AbstractMapThread.writeList(AbstractMapThread.java:394)
at align2.AbstractMapThread.run(AbstractMapThread.java:320)
, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15

**************************************************************************

Warning! 16 mapping threads did not terminate normally.
Please check the error log; the output may be corrupt or incomplete.

**************************************************************************




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

Genome: 1
Key Length: 14
Max Indel: 10
Minimum Score Ratio: 0.4
Mapping Mode: normal
Reads Used: 850 (150375 bases)

Mapping: 16.779 seconds.
Reads/sec: 50.66
kBases/sec: 8.96


Read 1 data: pct reads num reads pct bases num bases

mapped: 71.8824% 611 84.5406% 127128
unambiguous: 63.6471% 541 75.8251% 114022
ambiguous: 8.2353% 70 8.7155% 13106
low-Q discards: 0.0000% 0 0.0000% 0

perfect best site: 0.0000% 0 0.0000% 0
semiperfect site: 0.0000% 0 0.0000% 0

Match Rate: NA NA 24.8088% 109654
Error Rate: 73.7923% 611 75.1826% 332304
Sub Rate: 72.9469% 604 1.8880% 8345
Del Rate: 59.6618% 494 71.2368% 314864
Ins Rate: 71.9807% 596 2.0577% 9095
N Rate: 4.1063% 34 0.0086% 38
Splice Rate: 14.8551% 123 (splices at least 10 bp)
Exception in thread "main" java.lang.RuntimeException: BBMap terminated in an error state; the output may be corrupt.
at align2.BBMapPacBio.testSpeed(BBMapPacBio.java:407)
at align2.BBMapPacBio.main(BBMapPacBio.java:33)
When I run it without both parameters, everything works fine. My dataset includes 1.6M single end 454 reads if this is important.
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