bbduk fails with gzipped paired reads

[SethMusker]

versions 39.91 and 39.80 both fail below, while 39.50 works.

fasterq-dump --threads 1 --bufsize 10M --mem 3G --outdir raw_reads_temp --skip-technical --split-3 ERR10978319

#v39.80
bbduk.sh -Xmx20g in=raw_reads_temp/ERR10978319_1.fastq \
         in2=raw_reads_temp/ERR10978319_2.fastq \
         out=test_out.fq \
         ref=adaptors_combined.fasta \
         ktrim=r k=21 mink=11 hdist=2 minlength=21

noerror1.txt

pigz -p8 raw_reads_temp/*.fastq

# v39.80
bbduk.sh -Xmx20g in=raw_reads_temp/ERR10978319_1.fastq.gz \
         in2=raw_reads_temp/ERR10978319_2.fastq.gz \
         out=test_out.fq \
         ref=adaptors_combined.fasta \
         ktrim=r k=21 mink=11 hdist=2 minlength=21

error.txt

# v39.50
bbduk.sh -Xmx20g in=raw_reads_temp/ERR10978319_1.fastq.gz \
         in2=raw_reads_temp/ERR10978319_2.fastq.gz \
         out=test_out.fq \
         ref=adaptors_combined.fasta \
         ktrim=r k=21 mink=11 hdist=2 minlength=21

noerror2.txt

[EricDeveaud]

looks like #11

see:

Exception in thread "Thread-13" java.lang.AssertionError: List size mismatch: 99 vs 59
                                                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	at stream.PairStreamer.nextList(PairStreamer.java:88)
	at bbduk.BBDukProcessorS.process(BBDukProcessorS.java:743)
	at bbduk.BBDukS$ProcessThread.run(BBDukS.java:371)

[btpsj]

I'm setting up a test for this, but for now, @SethMusker would you be able to run on the latest version of BBTools? There was a big bug hunt over the last week, and some commits (most likely 31834d3) may have resolved the issue you are running into.

[SethMusker]

Still no luck. Now neither the raw nor the gzipped files work.

v39.93: unzipped:

bbduk.sh -Xmx20g in=raw_reads_temp/ERR10978319_1.fastq in2=raw_reads_temp/ERR10978319_2.fastq out=test_out1.fq out2=test_out2.fq  ref=adapters 
java -ea  --add-modules jdk.incubator.vector -Xmx20g -Xms20g -cp /home/seth/.local/bbmap/bbtools.jar bbduk.BBDukS -Xmx20g in=raw_reads_temp/ERR10978319_1.fastq in2=raw_reads_temp/ERR10978319_2.fastq out=test_out1.fq out2=test_out2.fq ref=adapters
WARNING: Using incubator modules: jdk.incubator.vector
Executing bbduk.BBDukS [-Xmx20g, in=raw_reads_temp/ERR10978319_1.fastq, in2=raw_reads_temp/ERR10978319_2.fastq, out=test_out1.fq, out2=test_out2.fq, ref=adapters]
Version 39.93

Allocating kmer table: 	Added 2970 kmers; time: 	0.046 seconds.
Memory: max=21474m, total=21474m, free=21297m, used=177m

Initial:
Memory: max=21474m, total=21474m, free=21297m, used=177m

Input is being processed as paired
Started output streams:	0.009 seconds.
Exception in thread "FastqStreamer-Worker-1" java.lang.RuntimeException: FastqStreamer worker 1 failed: raw_reads_temp/ERR10978319_1.fastq
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:359)
	at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:198)
Caused by: java.lang.AssertionError: 
Error in raw_reads_temp/ERR10978319_1.fastq, record 0, with these 4 lines: (missing plus)
@ERR10978319.1 ST-E00129:1164:HH5WCCCX2:5:1101:2331:2329 length=151
GATGGTGGAGGAAATGGAGGAGGGCGCACAGTGGAGATGGTGGAGAAGAAGAAGAAGAAGAAGATGACAAAGGACGGTGGGGGAGGACGGTGGTGGAGATGGTGGTGGAGATGGCGGAGGAAATGGAGGAAGAAGGTGGAGAGGAGAGTGA
+ERR10978319.1 ST-E00129:1164:HH5WCCCX2:5:1101:2331:2329 length=151
AA-F-F-AFFJFJJAAFAAF<AFJJF7AJFFJAFJF-<<FJJJFJJJF7JJ<FJFJJFFFJJAFJJJFFFF<<F-A<-AJ-<AAA-7-AFF-F7A-A<A7<-7-F77AJF7FJJF<J-A-FFF-7<AFJJJJFJJ7<JFFJF7JFF-A-77

	at stream.FASTQ.quadToReadVec(FASTQ.java:895)
	at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:425)
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:338)
	... 1 more
Exception in thread "FastqStreamer-Worker-1" java.lang.RuntimeException: FastqStreamer worker 1 failed: raw_reads_temp/ERR10978319_2.fastq
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:359)
	at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:198)
Caused by: java.lang.AssertionError: 
Error in raw_reads_temp/ERR10978319_2.fastq, record 0, with these 4 lines: (missing plus)
@ERR10978319.1 ST-E00129:1164:HH5WCCCX2:5:1101:2331:2329 length=151
CACTCTCTCTCTCTCTAAATCAAAATCGCAGATCTGATCTCCCTCTCTCACTCTCATCTCCACCTTCTGCCTCCATTTCCTCCGCCATCTCCACCACCATCTCCACCACCTTCCTCCACCACCGTCCTTTGTCAGCGTCTTCTTCTGCTTC
+ERR10978319.1 ST-E00129:1164:HH5WCCCX2:5:1101:2331:2329 length=151
AAAA<AJFJJJFFAJJFJJJJJJJJJJ<-<F7-<<-<-A-7-7-7A<FJ-F<--<-<FAFJ7-F<-A7-AAJ<-7<<FFJFJ<-F7-<<-FJ-JF<<F7-A-7<-JA7<---7AAF-AAJ-<F--<F-<7--7-----77-<-----<---

	at stream.FASTQ.quadToReadVec(FASTQ.java:895)
	at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:425)
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:338)
	... 1 more
Exception in thread "FastqStreamer-Worker-2" java.lang.RuntimeException: FastqStreamer worker 2 failed: raw_reads_temp/ERR10978319_1.fastq
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:359)
	at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:198)
Caused by: java.lang.AssertionError: 
Error in raw_reads_temp/ERR10978319_1.fastq, record 200, with these 4 lines: (missing plus)
@ERR10978319.201 ST-E00129:1164:HH5WCCCX2:5:1101:2960:2962 length=151
GTGTAATTAGGTGATAACCCTATGTTAGAGGCTGGCGGGACAAGATGCCAATGTGACAACAGTCCCTGTCTCTGTCTTGAGATTTACTCGTCAACTAACCCGATTCTTTCAGTGGACAAATGATGTTGCTGATAGATTGGCCTAGATCGGA
+ERR10978319.201 ST-E00129:1164:HH5WCCCX2:5:1101:2960:2962 length=151
<AAFFJJJJJAFAJJAJJJJJJ<AFJJJFJJJJJJFJJJJJJJJJJJAJ-FJFJJFJJAJJJJJFJJJJJJAFJFJJJJ7J-FJJFJFJAAJ<JJJJJJJFJFJJJJJJFJJJJJJJJJJJJJJJJJFJJFJAJJJFJJJ<FJJJJFAFJ<

	at stream.FASTQ.quadToReadVec(FASTQ.java:895)
	at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:425)
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:338)
	... 1 more
java.lang.Exception: Error reading FASTQ file (corrupt or truncated): raw_reads_temp/ERR10978319_1.fastq
	at shared.KillSwitch.kill(KillSwitch.java:128)
	at stream.FastqStreamer.nextList(FastqStreamer.java:141)
	at stream.PairStreamer.nextList(PairStreamer.java:80)
	at bbduk.BBDukProcessorS.process(BBDukProcessorS.java:743)
	at bbduk.BBDukS$ProcessThread.run(BBDukS.java:371)

Zipped:

bbduk.sh -Xmx20g in=raw_reads_temp/ERR10978319_1.fastq.gz in2=raw_reads_temp/ERR10978319_2.fastq.gz out=test_out1.fq.gz out2=test_out2.fq.gz  ref=adapters 
java -ea  --add-modules jdk.incubator.vector -Xmx20g -Xms20g -cp /home/seth/.local/bbmap/bbtools.jar bbduk.BBDukS -Xmx20g in=raw_reads_temp/ERR10978319_1.fastq.gz in2=raw_reads_temp/ERR10978319_2.fastq.gz out=test_out1.fq.gz out2=test_out2.fq.gz ref=adapters
WARNING: Using incubator modules: jdk.incubator.vector
Executing bbduk.BBDukS [-Xmx20g, in=raw_reads_temp/ERR10978319_1.fastq.gz, in2=raw_reads_temp/ERR10978319_2.fastq.gz, out=test_out1.fq.gz, out2=test_out2.fq.gz, ref=adapters]
Version 39.93

Allocating kmer table: 	Added 2970 kmers; time: 	0.046 seconds.
Memory: max=21474m, total=21474m, free=21297m, used=177m

Initial:
Memory: max=21474m, total=21474m, free=21297m, used=177m

Input is being processed as paired
Exception in thread "FastqStreamer-Worker-1" java.lang.RuntimeException: FastqStreamer worker 1 failed: raw_reads_temp/ERR10978319_2.fastq.gz
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:359)
	at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:198)
Caused by: java.lang.AssertionError: 
Error in raw_reads_temp/ERR10978319_2.fastq.gz, record 0, with these 4 lines: (missing plus)
@ERR10978319.1 ST-E00129:1164:HH5WCCCX2:5:1101:2331:2329 length=151
CACTCTCTCTCTCTCTAAATCAAAATCGCAGATCTGATCTCCCTCTCTCACTCTCATCTCCACCTTCTGCCTCCATTTCCTCCGCCATCTCCACCACCATCTCCACCACCTTCCTCCACCACCGTCCTTTGTCAGCGTCTTCTTCTGCTTC
+ERR10978319.1 ST-E00129:1164:HH5WCCCX2:5:1101:2331:2329 length=151
AAAA<AJFJJJFFAJJFJJJJJJJJJJ<-<F7-<<-<-A-7-7-7A<FJ-F<--<-<FAFJ7-F<-A7-AAJ<-7<<FFJFJ<-F7-<<-FJ-JF<<F7-A-7<-JA7<---7AAF-AAJ-<F--<F-<7--7-----77-<-----<---

	at stream.FASTQ.quadToReadVec(FASTQ.java:895)
	at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:425)
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:338)
	... 1 more
Exception in thread "FastqStreamer-Worker-1" java.lang.RuntimeException: FastqStreamer worker 1 failed: raw_reads_temp/ERR10978319_1.fastq.gz
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:359)
	at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:198)
Caused by: java.lang.AssertionError: 
Error in raw_reads_temp/ERR10978319_1.fastq.gz, record 0, with these 4 lines: (missing plus)
@ERR10978319.1 ST-E00129:1164:HH5WCCCX2:5:1101:2331:2329 length=151
GATGGTGGAGGAAATGGAGGAGGGCGCACAGTGGAGATGGTGGAGAAGAAGAAGAAGAAGAAGATGACAAAGGACGGTGGGGGAGGACGGTGGTGGAGATGGTGGTGGAGATGGCGGAGGAAATGGAGGAAGAAGGTGGAGAGGAGAGTGA
+ERR10978319.1 ST-E00129:1164:HH5WCCCX2:5:1101:2331:2329 length=151
AA-F-F-AFFJFJJAAFAAF<AFJJF7AJFFJAFJF-<<FJJJFJJJF7JJ<FJFJJFFFJJAFJJJFFFF<<F-A<-AJ-<AAA-7-AFF-F7A-A<A7<-7-F77AJF7FJJF<J-A-FFF-7<AFJJJJFJJ7<JFFJF7JFF-A-77

	at stream.FASTQ.quadToReadVec(FASTQ.java:895)
	at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:425)
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:338)
	... 1 more
Exception in thread "FastqStreamer-Worker-2" java.lang.RuntimeException: FastqStreamer worker 2 failed: raw_reads_temp/ERR10978319_2.fastq.gz
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:359)
	at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:198)
Caused by: java.lang.AssertionError: 
Error in raw_reads_temp/ERR10978319_2.fastq.gz, record 200, with these 4 lines: (missing plus)
@ERR10978319.201 ST-E00129:1164:HH5WCCCX2:5:1101:2960:2962 length=151
AGGCCAATCTATCAGCAACATCATTTGTCCACTGAAAGAATCGGGTTAGTTGACGAGTAAATCTCAAGACAGAGACAGGGACTGTTGTCACTTTGGCATCTTGTCCCGCCAGCCTCTAACATAGGGTTATCACCTAATTACACAGATCGGA
+ERR10978319.201 ST-E00129:1164:HH5WCCCX2:5:1101:2960:2962 length=151
AAFFFJJJJJJAJFF<FAJ-FF7JJJJFAAJAJJFFJJJJJJJJJJJJJJJFFJFJFJFJFJ<F-<AJJ<JJAFFFJF<FFJJJJFFJAJJ-7FA<FFJJJJFA<AJ<F--A<JJJFJJJFJA-7FJFJJFA-F7-FFFAF<JJJJ---<-

	at stream.FASTQ.quadToReadVec(FASTQ.java:895)
	at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:425)
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:338)
	... 1 more
Exception in thread "FastqStreamer-Worker-2" java.lang.RuntimeException: FastqStreamer worker 2 failed: raw_reads_temp/ERR10978319_1.fastq.gz
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:359)
	at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:198)
Caused by: java.lang.AssertionError: 
Error in raw_reads_temp/ERR10978319_1.fastq.gz, record 200, with these 4 lines: (missing plus)
@ERR10978319.201 ST-E00129:1164:HH5WCCCX2:5:1101:2960:2962 length=151
GTGTAATTAGGTGATAACCCTATGTTAGAGGCTGGCGGGACAAGATGCCAATGTGACAACAGTCCCTGTCTCTGTCTTGAGATTTACTCGTCAACTAACCCGATTCTTTCAGTGGACAAATGATGTTGCTGATAGATTGGCCTAGATCGGA
+ERR10978319.201 ST-E00129:1164:HH5WCCCX2:5:1101:2960:2962 length=151
<AAFFJJJJJAFAJJAJJJJJJ<AFJJJFJJJJJJFJJJJJJJJJJJAJ-FJFJJFJJAJJJJJFJJJJJJAFJFJJJJ7J-FJJFJFJAAJ<JJJJJJJFJFJJJJJJFJJJJJJJJJJJJJJJJJFJJFJAJJJFJJJ<FJJJJFAFJ<

	at stream.FASTQ.quadToReadVec(FASTQ.java:895)
	at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:425)
	at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:338)
	... 1 more
Started output streams:	0.087 seconds.
java.lang.Exception: Error reading FASTQ file (corrupt or truncated): raw_reads_temp/ERR10978319_1.fastq.gz
	at shared.KillSwitch.kill(KillSwitch.java:128)
	at stream.FastqStreamer.nextList(FastqStreamer.java:141)
	at stream.PairStreamer.nextList(PairStreamer.java:80)
	at bbduk.BBDukProcessorS.process(BBDukProcessorS.java:743)
	at bbduk.BBDukS$ProcessThread.run(BBDukS.java:371)

v39.60:

~/Downloads/bbmap/bbduk.sh -Xmx20g in=raw_reads_temp/ERR10978319_1.fastq.gz in2=raw_reads_temp/ERR10978319_2.fastq.gz out=test_out1.fq.gz out2=test_out2.fq.gz  ref=adapters 
java -ea  --add-modules jdk.incubator.vector -Xmx20g -Xms20g -cp /home/seth/Downloads/bbmap/current/ jgi.BBDuk -Xmx20g in=raw_reads_temp/ERR10978319_1.fastq.gz in2=raw_reads_temp/ERR10978319_2.fastq.gz out=test_out1.fq.gz out2=test_out2.fq.gz ref=adapters
WARNING: Using incubator modules: jdk.incubator.vector
Executing jgi.BBDuk [-Xmx20g, in=raw_reads_temp/ERR10978319_1.fastq.gz, in2=raw_reads_temp/ERR10978319_2.fastq.gz, out=test_out1.fq.gz, out2=test_out2.fq.gz, ref=adapters]
Version 39.60

Allocating kmer table: 	0.016 seconds.
Initial:
Memory: max=21474m, total=21474m, free=21389m, used=85m

Added 2970 kmers; time: 	0.044 seconds.
Memory: max=21474m, total=21474m, free=21305m, used=169m

Input is being processed as paired
Started output streams:	0.021 seconds.
Processing time:   		12.391 seconds.

Input:                  	6871010 reads 		1037522510 bases.
Contaminants:           	893440 reads (13.00%) 	134909440 bases (13.00%)
Total Removed:          	893440 reads (13.00%) 	134909440 bases (13.00%)
Result:                 	5977570 reads (87.00%) 	902613070 bases (87.00%)

Time:                         	12.460 seconds.
Reads Processed:       6871k 	551.46k reads/sec
Bases Processed:       1037m 	83.27m bases/sec

[btpsj]

Thanks @SethMusker ! I'm able to replicate the error you are getting on a smaller dataset, and post some cleaned up replication notes a little later.

From what I can tell so far, the issue seems that BBDuk will use different fastq parser implementations based on the number of threads. If the number of threads is greater than 8, it uses a more recent fastq parser implementation that has this issue, and if you don't set t= parameter, it infers the thread count based on the number of logical CPUs. Is it correct that you are running this on a machine with more than 8 cores?

So based on the above, one last thing to try that can get you unblocked while this is getting fixed is that you can add t=8 as a parameter to bbduk. If that works, but is too slow, the other thing you can do instead is add tin=0. This is an alias for the threadsIn parameter, and really shouldn't be used for anything, and its mainly to force BBDuk to use the other working parser but still keep the inferred thread count as high as it can be.

[btpsj]

The latest commit (d31d5d3) should fix the parsing for both gzipped and regular fastqs. Below is the set of commands I've used to recreate the error path with BBTools and bash commands, and validate it works on the latest commit. If there error still persists, please comment with it below and any other info about the inputs.

$ git clone https://github.com/bbushnell/BBTools.git
$ git -C BBTools log --oneline -1
d31d5d36 (HEAD -> master, origin/master, origin/HEAD) Bughunt on var2, stream, hiseq, fun, cardinality, barcode.
$ BBTools/randomreads.sh ref=BBTools/resources/phix174_ill.ref.fa.gz     out=raw_r1.fq out2=raw_r2.fq     len=151 reads=200 paired=t illuminanames=t overwrite=t
# Modify quality header to be the same as the sequence header
$ for f in raw_r1 raw_r2; do   awk 'NR%4==1{h=$0; print; next} NR%4==3{print "+" substr(h,2); next} {print}'     "$f.fq" > "repeated_${f#raw_}.fq"; done
$ BBTools/bbduk.sh -Xmx1g t=9 in=repeated_r1.fq in2=repeated_r2.fq     out=out1_t9.fq out2=out2_t9.fq ref=BBTools/resources/adapters.fa overwrite=t
# ... Completes with regular output

With gzipped versions

$ pigz -c repeated_r1.fq >repeated_r1.fq.gz
$ pigz -c repeated_r1.fq >repeated_r1.fq.gz
$ BBTools/bbduk.sh -Xmx1g t=9 in=repeated_r1.fq.gz in2=repeated_r2.fq.gz     out=out1_t9.fq out2=out2_t9.fq ref=BBTools/resources/adapters.fa overwrite=t
# .. Completes with regular output

Checking out the old version gives the observed error

$ git -C BBTools checkout HEAD~1
$ BBTools/bbduk.sh -Xmx1g t=9 in=repeated_r1.fq in2=repeated_r2.fq     out=out1_t9.fq out2=out2_t9.fq ref=BBTools/resources/adapters.fa overwrite=t
# .. skipped
Exception in thread "FastqStreamer-Worker-2" Exception in thread "FastqStreamer-Worker-1" java.lang.RuntimeException: FastqStreamer worker 2 failed: repeated_r2.fq
        at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:359)
        at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:198)
Caused by: java.lang.AssertionError: 
Error in repeated_r2.fq, record 0, with these 4 lines: (missing plus)
@0 2:
AGACATGGCGCCACCAGCAAGAGCAGAAGCAATACCGCCAGCAATAGCACCAAACATAAATCACCTCACTTAAGTGGCTGGAGACAAATAATCTCTTTAATAACCTGATTCAGCGAAACCAATCCGCGGCATTTAGTAGCGGTAAAGTTAG
+0 2:
9379;;9;;;??8BBBCA@@CAAB?BCABBBA@@ABC??>BBB@ACA@AA@?A??B@AA@BA?AA@>B@>?B=A???@@?@5A>A=>>>@A?B:A:?@AA@=@:??=?=B;=?B<>A=??@C=<AB=@<@A@A<<<::883;365;;;335

        at stream.FASTQ.quadToReadVec(FASTQ.java:895)
        at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:425)
        at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:338)
        ... 1 more
# ... cutoff the rest
$ BBTools/bbduk.sh -Xmx1g t=9 in=repeated_r1.fq.gz in2=repeated_r2.fq.gz     out=out1_t9.fq out2=out2_t9.fq ref=BBTools/resources/adapters.fa overwrite=t
# ... skipped
Exception in thread "FastqStreamer-Worker-1" java.lang.RuntimeException: FastqStreamer worker 1 failed: repeated_r1.fq.gz
        at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:359)
        at stream.FastqStreamer$ProcessThread.run(FastqStreamer.java:198)
Caused by: java.lang.AssertionError: 
Error in repeated_r1.fq.gz, record 0, with these 4 lines: (missing plus)
@0 1:
TCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGGATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCTCGTACGCCGGGCAATAATGGTTATGTT
+0 1:
4;9;9::<<;@@@@BDBA@B=BA@CAACCA@@AABDB?@BBABD@AC@AC>BD@=BABB@>B;AB?D@>C>B?@A?@>A=?@?<<?@8?:=?C=>=>@@=>@<A>@=@@=@;CB8>A?;>;8:B<=@B8>?=;8;@<B448556444:444

        at stream.FASTQ.quadToReadVec(FASTQ.java:895)
        at stream.FastqStreamer$ProcessThread.quadToRead(FastqStreamer.java:425)
        at stream.FastqStreamer$ProcessThread.makeReadsSingle(FastqStreamer.java:338)
        ... 1 more