repair.sh java.lang.AssertionError

I have downloaded paired end fastq files from NCBI which contains different number of the reads. So I tried to repair using bbtools repair.sh But I am seeing following errors:

java -ea -Xmx320196m \
  -cp /igm/apps/bbmap_38/bbmap/current/ jgi.SplitPairsAndSingles rp fint=f \
  in1=/igm/projects/Aiman_RNASeq_Project/GATA4/Fastq/SRR4032134_1.fastq.gz \
  in2=/igm/projects/Aiman_RNASeq_Project/GATA4/Fastq/SRR4032134_2.fastq.gz \
  out1=SRR4032134_1.fastq.gz z
  out2=SRR4032134_2.fastq.gz \
  outsingle=SRR4032134_1.fastq.gz_singletons.fq.gz

Executing jgi.SplitPairsAndSingles [rp, fint=f, in1=/igm/projects/Aiman_RNASeq_Project/GATA4/Fastq/SRR4032134_1.fastq.gz, in2=/igm/projects/Aiman_RNASeq_Project/GATA4/Fastq/SRR4032134_2.fastq.gz, out1=SRR4032134_1.fastq.gz, out2=SRR4032134_2.fastq.gz, outsingle=SRR4032134_1.fastq.gz_singletons.fq.gz]

Set INTERLEAVED to false Started output stream.
Exception in thread "Thread-5"
Exception in thread "Thread-4"
java.lang.AssertionError: Somehow the list became null for /igm/projects/Aiman_RNASeq_Project/GATA4/Fastq/SRR4032134_1.fastq.gz at line 673000
java.lang.AssertionError: Somehow the list became null for /igm/projects/Aiman_RNASeq_Project/GATA4/Fastq/SRR4032134_2.fastq.gz at line 673000
at fileIO.ByteFile2$BF1Thread.run(ByteFile2.java:276)
at fileIO.ByteFile2$BF1Thread.run(ByteFile2.java:276)

Can someone tell me what the issue and how I can resolve it.

repair.sh bbtools

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updated 3.2 years ago by Ram

• written 3.7 years ago by aimanbarki •

Can you show us your actual repair.sh command? It is advisable to use the wrapper scripts @Brian includes rather than running the java commands directly. If you did not do that try using the wrapper script.

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written 3.7 years ago by GenoMax

Thanks for response. Yes, I am submitting it in the form of bash script. Previously I just posted output file of one run. repair.sh command is as follows:

 qsub -q all.q -pe smp 12 -cwd -V -j y -b y -S /bin/bash -N "C"_${filename_r1} /igm/apps/bbmap_38/bbmap/repair.sh fint=f in1=$R1 in2=$R2 out1=$filename_r1 out2=$filename_r2 outsingle=${filename_r1%}_singletons.fq.gz

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updated 3.7 years ago by GenoMax

• written 3.7 years ago by aimanbarki •

Be sure to add a memory specification like repair.sh -Xmx20g (just an example depending on size of your data you will need to adjust this number) and then a corresponding request on qsub side that matches.

If this does not work then next thing to check would be to make sure your fastq files are not corrupt.

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written 3.7 years ago by GenoMax

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