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Old 01-27-2019, 05:17 AM   #49
mayabritstein
Junior Member
 
Location: Israel

Join Date: Nov 2015
Posts: 2
Default Exception in thread "Thread-175" java.lang.AssertionError:

Hello,

Thanks for the great software!

I want to use bbnorm to normalize single end RNAseq library reads.

I'm using the software on my university cluster (linux)

this is the exception message I get:

Exception in thread "Thread-175" java.lang.AssertionError:
NB501112:39:HKM3VBGXY:4:11401:7344:1020 1:N:0:CCAGTT 1 -1 + -1 -1 1000000000000000000 1 0 0 CTTTACATCAAATCCTAATGTAGTTACAGGTGATTCAATTAATCTATCACCTAATGATTGTGAACGTTG EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEE . 35 . .

null
at stream.ReadStreamByteWriter.writeFastq(ReadStreamByteWriter.java:460)
at stream.ReadStreamByteWriter.processJobs(ReadStreamByteWriter.java:97)
at stream.ReadStreamByteWriter.run2(ReadStreamByteWriter.java:42)
at stream.ReadStreamByteWriter.run(ReadStreamByteWriter.java:28)


this is the script I used:
#!/bin/bash
#SBATCH -N 1
#SBATCH -n 24
#SBATCH -p hive7d
#SBATCH -J ecc_bbnormSE # Job name
#SBATCH --mem=128000
#SBATCH --time=2-23:00:00 # Runtime in D-HH:MM:SS
#SBATCH --mail-type=ALL # Type of email notification- BEGIN,END,FAIL,ALL
#SBATCH --mail-user=mayabritstein@gmail.com # Email to send notifications to

. /etc/profile.d/modules.sh
module purge
module load java/jre1.8.0

export PATH=/data/home/steindler/mbritstei/programs/anaconda2/bin:$PATH

source activate bbtools

fastq_DATA=/data/home/steindler/mbritstei/Petrosia_transcriptomes/transcriptome_assembly/All_Single_end


bbnorm.sh in=$fastq_DATA/petrosia_SE.fastq out= out2=petrosia_SE_normalized_ecc.fastq target=100 min=5 ecc prefilter


source deactivate



## Can you please tell me what is wrong?

# thanks!!

Maya
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