Exception in thread "main" java.lang.AssertionError:

[Rbeinart]

Hello,
I'm having the below problem with BBsplit. If I run the bbsplit.sh just to make the reference indexes, it runs fine. It's only when I try to do the mapping, or combine the reference building with the mapping, that I get the below error. I've tried deleting the ref/ directory and re-doing it a few times with no success. I also tried implementing it with the command: java -Xmx14g -cp /Applications/bbmap/current/align2.BBSplitter, and get the same error.

Thanks!
-Roxanne-

/Applications/bbmap/bbsplit.sh ref=Desulfobact-contigs.fa,Desulfobulb-contigs.fa in=/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.1.filtered.fastq.gz in2==/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.2.filtered.fastq.gz ambiguous=best ambiguous2=best basename=out_%.fq
Max memory cannot be determined. Attempting to use 3200 MB.
If this fails, please add the -Xmx flag (e.g. -Xmx24g) to your command,
or run this program qsubbed or from a qlogin session on Genepool, or set ulimit to an appropriate value.
java -Djava.library.path=/Applications/bbmap/jni/ -ea -Xmx3200m -cp /Applications/bbmap/current/ align2.BBSplitter ow=t fastareadlen=500 minhits=1 minratio=0.56 maxindel=20 qtrim=rl untrim=t trimq=6 ref=Desulfobact-contigs.fa,Desulfobulb-contigs.fa in=/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.1.filtered.fastq.gz in2==/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.2.filtered.fastq.gz ambiguous=best ambiguous2=best basename=out_%.fq
Executing align2.BBSplitter [ow=t, fastareadlen=500, minhits=1, minratio=0.56, maxindel=20, qtrim=rl, untrim=t, trimq=6, ref=Desulfobact-contigs.fa,Desulfobulb-contigs.fa, in=/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.1.filtered.fastq.gz, in2==/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.2.filtered.fastq.gz, ambiguous=best, ambiguous2=best, basename=out_%.fq]

Converted arguments to [ow=t, fastareadlen=500, minhits=1, minratio=0.56, maxindel=20, qtrim=rl, untrim=t, trimq=6, in=/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.1.filtered.fastq.gz, in2==/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.2.filtered.fastq.gz, ambiguous=best, ambiguous2=best, basename=out_%.fq, ref_Desulfobact-contigs=Desulfobact-contigs.fa, ref_Desulfobulb-contigs=Desulfobulb-contigs.fa]
Creating merged reference file ref/genome/1/merged_ref_2951985054197617.fa.gz
Ref merge time: 0.283 seconds.
Executing align2.BBMap [ow=t, fastareadlen=500, minhits=1, minratio=0.56, maxindel=20, qtrim=rl, untrim=t, trimq=6, in=/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.1.filtered.fastq.gz, in2==/Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metatranscriptome/filtered/MMETSP1317-Unknown-Unknown-.2.filtered.fastq.gz, ambiguous=best, ambiguous2=best, ref=ref/genome/1/merged_ref_2951985054197617.fa.gz, out_Desulfobact-contigs=out_Desulfobact-contigs.fq, out_Desulfobulb-contigs=out_Desulfobulb-contigs.fq]

BBMap version 36.14
Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.560
Retaining first best site only for ambiguous mappings.
NOTE: Deleting contents of ref/genome/1 because reference is specified and overwrite=true
Writing reference.
Executing dna.FastaToChromArrays2 [ref/genome/1/merged_ref_2951985054197617.fa.gz, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false]

Set genScaffoldInfo=true
Writing chunk 1
Set genome to 1

Loaded Reference: 0.017 seconds.
Loading index for chunk 1-1, build 1
No index available; generating from reference genome: /Volumes/Beinart_Seagate/Sequence_data/Brown_Ciliate/Brown_ciliate_metagenome/BBsplit/Anvio_bins/ref/index/1/chr1_index_k13_c7_b1.block
Indexing threads started for block 0-1
Indexing threads finished for block 0-1
Generated Index: 2.481 seconds.
Analyzed Index: 2.188 seconds.
Reads that map to multiple references will be written to the first reference's stream only.
Exception in thread "main" java.lang.AssertionError:
at fileIO.FileFormat.<init>(FileFormat.java:159)
at fileIO.FileFormat.testInput(FileFormat.java:116)
at align2.AbstractMapper.getReadInputStream(AbstractMapper.java:977)
at align2.AbstractMapper.openStreams(AbstractMapper.java:813)
at align2.BBMap.testSpeed(BBMap.java:433)
at align2.BBMap.main(BBMap.java:33)
at align2.BBSplitter.main(BBSplitter.java:45)