ERROR: For input string: "9223372036854775808"
schorlton opened this issue · 6 comments
schorlton commented
Another error which seems to be from too few/too short reads as input? But pretty cryptic. Thanks again!!
root@633c29844365:/data/retry# rnabloom -outdir rnabloom_out -t 8 -long filtered.fastq -ntcard
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`...
ERROR: For input string: "9223372036854775808"
java.lang.NumberFormatException: For input string: "9223372036854775808"
at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.base/java.lang.Long.parseLong(Long.java:696)
at java.base/java.lang.Long.parseLong(Long.java:817)
at rnabloom.util.NTCardHistogram.<init>(NTCardHistogram.java:44)
at rnabloom.RNABloom.getNTCardHistogram(RNABloom.java:5568)
at rnabloom.RNABloom.main(RNABloom.java:6631)
- version of RNA-Bloom with
java -jar RNA-Bloom.jar -version
- version of java with
java -version
root@633c29844365:/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
kmnip commented
Can you please print the first few lines of rnabloom_k17.hist
? e.g.
head rnabloom_out/rnabloom_k17.hist
kmnip commented
This number 9223372036854775808
is just larger than the largest 64-bit long integer in Java, i.e. 9,223,372,036,854,775,807
.
Can you please report your ntCard version?
ntcard --version
schorlton commented
>ntcard --version
ntCard 1.2.2
>head rnabloom_out/rnabloom_k17.hist
F1 270
F0 0
1 9223372036854775808
2 9223372036854775808
3 9223372036854775808
4 9223372036854775808
5 9223372036854775808
6 9223372036854775808
7 9223372036854775808
8 9223372036854775808
kmnip commented
This looks like a bug in ntCard. Can you share your read sequences with me?
schorlton commented
Done! Emailed kmnip@bcgsc.ca. Let me know if you need it to be sent somewhere else.
kmnip commented
Thanks, I got your email and I was able to replicate the same issue.
I created an issue for this in ntCard:
bcgsc/ntCard#73