FASTQC causes a problem - can we fix?

[markziemann]

lesize
37373f16385ca2678ac1a3373f2c7e59 SRR29972717.sra
SRR29972717.sra file validated
SRR29972717 diagnose basespace colorspace, single/paired-end and read length
Read 81 spots for SRR29972717.sra
Written 81 spots for SRR29972717.sra
SRR29972717 is single end

Starting FastQC analysis of SRR29972717_1.fastq
Started analysis of SRR29972717_1.fastq
Exception in thread "Thread-1" java.lang.OutOfMemoryError: Java heap space
at uk.ac.babraham.FastQC.Utilities.QualityCount.(QualityCount.java:33)
at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.processSequence(PerBaseQualityScores.java:141)
at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:88)
at java.lang.Thread.run(Thread.java:748)
^C/dee2/code/volunteer_pipeline.sh: line 569: [: ==: unary operator expected
/dee2/code/volunteer_pipeline.sh: line 572: [: ==: unary operator expected
Unable to determine if colorspace or basespace. Quitting.
rm: cannot remove '*tsv': No such file or directory
adding: SRR29972717/ (stored 0%)
adding: SRR29972717/SRR29972717.log (deflated 33%)
adding: SRR29972717/SRR29972717.attempts.txt (deflated 6%)
adding: SRR29972717/volunteer_pipeline.sh (deflated 77%)
Starting pipeline with species athaliana and SRA file /dee2/mnt/athaliana_SRR30125856.sra
athaliana
mkdir: cannot create directory 'SRR30125856': File exists
Starting /dee2/code/volunteer_pipeline.sh SRR30125856
current disk space = 584507416
free memory = 61183292
SRR30125856 check if SRA file exists and download if neccessary
^C