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RNA-Bloom v2.0.0
args: [-long, Input.fa, -stranded, -t, 8, -outdir, Output]
name: rnabloom
outdir: Output
Turning on option `-ntcard` to count k-mers
K-mer counting with ntCard...
Running command: `ntcard -t 8 -k 25 -c 65535 -p Output/rnabloom @Output/rnabloom.ntcard.readslist.txt`...
Parsing histogram file `Output/rnabloom_k25.hist`...
Unique k-mers (k=25): 57,234,431
Unique k-mers (k=25,c>1): 11,105,972
K-mer counting completed in 21.059s
Bloom filters Memory (GB)
====================================
de Bruijn graph: 0.12647936
k-mer counting: 0.19634001
====================================
Total: 0.32281935
> Stage 1: Construct graph from reads (k=25)
Parsing `Input.fa`...
Parsed 477,740 sequences in 1m 0s
DBG Bloom filter FPR: 1.06 %
Counting Bloom filter FPR: 1.17 %
> Stage 1 completed in 1m 1s
> Stage 2: Correct long reads for "rnabloom"
Parsing `Input.fa`...
Index -1 out of bounds for length 4
Index -1 out of bounds for length 4
java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 4
at rnabloom.util.SeqUtils.isLowComplexityLong(SeqUtils.java:619)
at rnabloom.util.SeqUtils.trimLowComplexityRegions(SeqUtils.java:848)
at rnabloom.RNABloom$LongReadCorrectionWorker.run(RNABloom.java:3791)
at java.base/java.lang.Thread.run(Thread.java:834)
java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 4
at rnabloom.util.SeqUtils.isLowComplexityLong(SeqUtils.java:619)
at rnabloom.util.SeqUtils.trimLowComplexityRegions(SeqUtils.java:848)
at rnabloom.RNABloom$LongReadCorrectionWorker.run(RNABloom.java:3791)
at java.base/java.lang.Thread.run(Thread.java:834)
null
java.lang.ArrayIndexOutOfBoundsException
null
java.lang.ArrayIndexOutOfBoundsException
null
java.lang.ArrayIndexOutOfBoundsException
null
java.lang.ArrayIndexOutOfBoundsException
Index -1 out of bounds for length 4
java.lang.ArrayIndexOutOfBoundsException: Index -1 out of bounds for length 4
at rnabloom.util.SeqUtils.isLowComplexityLong(SeqUtils.java:605)
at rnabloom.util.SeqUtils.trimLowComplexityRegions(SeqUtils.java:848)
at rnabloom.RNABloom$LongReadCorrectionWorker.run(RNABloom.java:3791)
at java.base/java.lang.Thread.run(Thread.java:834)
null
java.lang.ArrayIndexOutOfBoundsException
Corrected Read Lengths Sampling Distribution (n=4528)
min q1 med q3 max
239 776 1112 1635 5315
ERROR: null
java.lang.ArrayIndexOutOfBoundsException
Program version:
RNA-Bloom v2.0.0
openjdk version "11.0.1" 2018-10-16 LTS
OpenJDK Runtime Environment Zulu11.2+3 (build 11.0.1+13-LTS)
OpenJDK 64-Bit Server VM Zulu11.2+3 (build 11.0.1+13-LTS, mixed mode)
Any help that you can provide would be appreciated.
The text was updated successfully, but these errors were encountered:
Thank you very much @kmnip! I did not expect to have Ns in my reads either... direct reads were merged with Illumina reads (with fmlrc) and after that, I applied a second error correction method with transcript clean. The Ns probably were introduced after that step because some of the genomes that I am using are hard masked...
Anyway, thank you very much for noticing that you helped me a lot!
Dear author of RNA-Bloom
I am using your software to assemble some direct RNA reads for different species however I am obtaining different errors in some of them.
Input file and command:
The output that I get is the following:
Program version:
RNA-Bloom v2.0.0
openjdk version "11.0.1" 2018-10-16 LTS
OpenJDK Runtime Environment Zulu11.2+3 (build 11.0.1+13-LTS)
OpenJDK 64-Bit Server VM Zulu11.2+3 (build 11.0.1+13-LTS, mixed mode)
Any help that you can provide would be appreciated.
The text was updated successfully, but these errors were encountered: