You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Thanks for the great tool! Hitting a bit of an error...I suspect it may be because I have so few reads or they're too short but it's a bit cryptic...
root@f069f7fa8f9e:/data/retry# rnabloom -outdir rnabloom_out -t 8 -long filtered.fastq -ntcard [58/423]
RNA-Bloom v1.4.3
args: [-outdir, rnabloom_out, -t, 8, -long, filtered.fastq, -ntcard]
name: rnabloom
outdir: rnabloom_out
WARNING: Output directory does not exist!
Created output directory at `rnabloom_out`
K-mer counting with ntCard...
Running command: `ntcard -t 8 -k 17 -c 65535 -p rnabloom_out/rnabloom @rnabloom_out/rnabloom.ntcard.readslist.txt`...
Parsing histogram file `rnabloom_out/rnabloom_k17.hist`...
Unique k-mers (k=17): 1,600
Unique k-mers (k=17,c>1): 0
K-mer counting completed in 3.977s
Bloom filters Memory (GB)
====================================
de Bruijn graph: 3.5357662E-6
====================================
Total: 3.5357662E-6
> Stage 1: Construct graph from reads (k=17)
Parsing `filtered.fastq`...
Exception in thread "Thread-6" Exception in thread "Thread-5" Exception in thread "Thread-3" Exception in thread "Thread-2" java.lang.RuntimeException: java.lang.Arithme$
icException: / by zero
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:617)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ArithmeticException: / by zero
at rnabloom.bloom.CountingBloomFilter.getIndex(CountingBloomFilter.java:103)
at rnabloom.bloom.CountingBloomFilter.increment(CountingBloomFilter.java:132)
at rnabloom.graph.BloomFilterDeBruijnGraph.add(BloomFilterDeBruijnGraph.java:411)
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:606)
... 1 more
Exception in thread "Thread-7" Exception in thread "Thread-0" java.lang.RuntimeException: java.lang.ArithmeticException: / by zero
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:617)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ArithmeticException: / by zero
at rnabloom.bloom.CountingBloomFilter.getIndex(CountingBloomFilter.java:103)
at rnabloom.bloom.CountingBloomFilter.increment(CountingBloomFilter.java:132)
at rnabloom.graph.BloomFilterDeBruijnGraph.add(BloomFilterDeBruijnGraph.java:411)
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:606)
... 1 more
Exception in thread "Thread-4" Exception in thread "Thread-1" java.lang.RuntimeException: java.lang.ArithmeticException: / by zero
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:617)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ArithmeticException: / by zero
at rnabloom.bloom.CountingBloomFilter.getIndex(CountingBloomFilter.java:103)
at rnabloom.bloom.CountingBloomFilter.increment(CountingBloomFilter.java:132)
at rnabloom.graph.BloomFilterDeBruijnGraph.add(BloomFilterDeBruijnGraph.java:411)
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:606)
... 1 more
java.lang.RuntimeException: java.lang.ArithmeticException: / by zero
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:617)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ArithmeticException: / by zero
at rnabloom.bloom.CountingBloomFilter.getIndex(CountingBloomFilter.java:103)
at rnabloom.bloom.CountingBloomFilter.increment(CountingBloomFilter.java:132)
at rnabloom.graph.BloomFilterDeBruijnGraph.add(BloomFilterDeBruijnGraph.java:411)
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:606)
... 1 more
java.lang.RuntimeException: java.lang.ArithmeticException: / by zero
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:617)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ArithmeticException: / by zero
at rnabloom.bloom.CountingBloomFilter.getIndex(CountingBloomFilter.java:103)
at rnabloom.bloom.CountingBloomFilter.increment(CountingBloomFilter.java:132)
at rnabloom.graph.BloomFilterDeBruijnGraph.add(BloomFilterDeBruijnGraph.java:411)
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:606)
... 1 more
java.lang.RuntimeException: java.lang.ArithmeticException: / by zero
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:617)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ArithmeticException: / by zero
at rnabloom.bloom.CountingBloomFilter.getIndex(CountingBloomFilter.java:103)
at rnabloom.bloom.CountingBloomFilter.increment(CountingBloomFilter.java:132)
at rnabloom.graph.BloomFilterDeBruijnGraph.add(BloomFilterDeBruijnGraph.java:411)
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:606)
... 1 more
java.lang.RuntimeException: java.lang.ArithmeticException: / by zero
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:617)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ArithmeticException: / by zero
at rnabloom.bloom.CountingBloomFilter.getIndex(CountingBloomFilter.java:103)
at rnabloom.bloom.CountingBloomFilter.increment(CountingBloomFilter.java:132)
at rnabloom.graph.BloomFilterDeBruijnGraph.add(BloomFilterDeBruijnGraph.java:411)
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:606)
... 1 more
java.lang.RuntimeException: java.lang.ArithmeticException: / by zero
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:617)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.ArithmeticException: / by zero
at rnabloom.bloom.CountingBloomFilter.getIndex(CountingBloomFilter.java:103)
at rnabloom.bloom.CountingBloomFilter.increment(CountingBloomFilter.java:132)
at rnabloom.graph.BloomFilterDeBruijnGraph.add(BloomFilterDeBruijnGraph.java:411)
at rnabloom.RNABloom$FastqToGraphWorker.run(RNABloom.java:606)
... 1 more
Parsed 3 sequences in 0.015s
DBG Bloom filter FPR: 0.0452 %
DBG Bloom filter FPR: 0.0452 %
ERROR: Infinite or NaN
java.lang.NumberFormatException: Infinite or NaN
at java.base/java.math.BigDecimal.<init>(BigDecimal.java:923)
at java.base/java.math.BigDecimal.<init>(BigDecimal.java:900)
at rnabloom.util.Common.roundToSigFigs(Common.java:36)
at rnabloom.util.Common.convertToRoundedPercent(Common.java:32)
at rnabloom.RNABloom.populateGraph2(RNABloom.java:1322)
at rnabloom.RNABloom.main(RNABloom.java:6823)
version of RNA-Bloom with java -jar RNA-Bloom.jar -version
version of java with java -version
root@f069f7fa8f9e:/data/retry# java --version
openjdk 11.0.9.1-internal 2020-11-04
OpenJDK Runtime Environment (build 11.0.9.1-internal+0-adhoc..src)
OpenJDK 64-Bit Server VM (build 11.0.9.1-internal+0-adhoc..src, mixed mode)
exact command used to run RNA-Bloom
The text was updated successfully, but these errors were encountered:
Thanks for your report!
This is indeed a bug where there are too few reads. I will fix it for the next release.
For such a small FASTQ file, you can bypass the bug by using this option -mem 0.5 instead of -ntcard.
Thanks for the great tool! Hitting a bit of an error...I suspect it may be because I have so few reads or they're too short but it's a bit cryptic...
java -jar RNA-Bloom.jar -version
java -version
The text was updated successfully, but these errors were encountered: