bbmap seal.sh error

Question

[amitpande74]

HI,

While working with chipseq data I am getting this error on some chipseq fastq files:

seal.sh in=/media/usr/LaCie/chip_seq/brain_chipseq/SRR823888_GSM1119239_Region_80_-_Pons_rostral_part_Brain2_H3K27ac_ChIP_Homo_sapiens_ChIP-Seq.fastq.gz ref=transcriptome.fa stats=Ventral_Anterior_Thalamic_Nucleus.sealstats.txt rpkm=Ventral_Anterior_Thalamic_Nucleus.rpkm.txt ambig=random


java -ea -Xmx23714m -Xms23714m -cp /home/usr/miniconda3/opt/bbmap-38.79-0/current/ jgi.Seal in=/media/usr/LaCie/chip_seq/brain_chipseq/SRR823888_GSM1119239_Region_80_-_Pons_rostral_part_Brain2_H3K27ac_ChIP_Homo_sapiens_ChIP-Seq.fastq.gz ref=transcriptome.fa stats=Ventral_Anterior_Thalamic_Nucleus.sealstats.txt rpkm=Ventral_Anterior_Thalamic_Nucleus.rpkm.txt ambig=random

Executing jgi.Seal [in=/media/usr/LaCie/chip_seq/brain_chipseq/SRR823888_GSM1119239_Region_80_-_Pons_rostral_part_Brain2_H3K27ac_ChIP_Homo_sapiens_ChIP-Seq.fastq.gz, ref=transcriptome.fa, stats=Ventral_Anterior_Thalamic_Nucleus.sealstats.txt, rpkm=Ventral_Anterior_Thalamic_Nucleus.rpkm.txt, ambig=random]
Version 38.79

0.013 seconds.
Initial:
Memory: max=23830m, total=23830m, free=23333m, used=497m

Added 75906666 kmers; time:     14.105 seconds.
Memory: max=23830m, total=23830m, free=16811m, used=7019m

Exception in thread "main" java.lang.NoSuchMethodError: java.lang.Process.isAlive()Z
    at dna.Data.testExecute(Data.java:1776)
    at dna.Data.BGZIP(Data.java:1516)
    at fileIO.ReadWrite.getGZipInputStream(ReadWrite.java:1024)
    at fileIO.ReadWrite.getInputStream(ReadWrite.java:848)
    at fileIO.ByteFile1.open(ByteFile1.java:330)
    at fileIO.ByteFile1.<init>(ByteFile1.java:100)
    at fileIO.ByteFile2$BF1Thread.<init>(ByteFile2.java:237)
    at fileIO.ByteFile2.open(ByteFile2.java:215)
    at fileIO.ByteFile2.<init>(ByteFile2.java:86)
    at fileIO.ByteFile.makeByteFile(ByteFile.java:35)
    at fileIO.ByteFile.makeByteFile(ByteFile.java:27)
    at stream.FastqReadInputStream.<init>(FastqReadInputStream.java:59)
    at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:116)
    at stream.ConcurrentReadInputStream.getReadInputStream(ConcurrentReadInputStream.java:69)
    at jgi.Seal.spawnProcessThreads(Seal.java:1437)
    at jgi.Seal.process2(Seal.java:707)
    at jgi.Seal.process(Seal.java:628)
    at jgi.Seal.main(Seal.java:69)

Has someone come across something similar with seal.sh. Kindly advise.

[h.mon]

The key error message here is:

Exception in thread "main" java.lang.NoSuchMethodError: java.lang.Process.isAlive()Z

This error indicates there is a problem with the BBTools install, the most common problems being it was compiled with a different version of Java than the one running it now; or some classes are missing or conflicting. As you are running Seal from within a miniconda directory, I guess you used Conda to install it.

The version of BBTools (38.79) you are running is somewhat old, and it seems you installed it at your base Conda environment. Maybe something got updated later and broke BBTools. It is recommended to create separate environments to install bioinformatic tools, to avoid conflicts and breakages when one tools updates its library dependencies and another doesn't.