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I have been using Flux Capacitor= to quantify transcript abundance for samples in my RNA-seq study. However,= for 2 of 126 samples, Flux Capacitor crashes with an out of memory error. = I have increased the java heap space to 16G using the environmental variabl= e FLUX_MEM=3D16G, but the error still occurs. The BAM file is about 2.4GB w= ith about 42 million paired end reads. Do you have any idea what the proble= m could be? Strangely, I am telling Flux Capacitor to use only 2 threads, b= ut it uses 22 threads on my server. So I wonder if it could be related to t= his?
/net/wonderland/home/cgillies/programs/f= lux-capacitor-1.6.1/bin/flux-capacitor -i /net/assembly/cgillies/data/NEPTU= NE/RNA-Seq/11_24_2015//25870//final.bam -a /net/assembly/cgillies/data/NEPT= UNE/RNA-Seq/11_24_2015/FLUX//gtf.filtered.sorted.gtf -m PAIRED -o /net/asse= mbly/cgillies/data/NEPTUNE/RNA-Seq/11_24_2015/FLUX//25870.gtf --count-eleme= nts SPLICE_JUNCTIONS,INTRONS --threads 2 --force --tmp-dir /net/assembly/cg= illies/data/NEPTUNE/RNA-Seq/11_24_2015/FLUX//25870_tmp/
[INFO] Flux-Capacitor v1.6.1 (Flux Libra= ry: 1.29)
[PRE-CHECK] I am checking availability o= f the required lpsolve JNI libs.
[PRE-CHECK] * successfully loaded lpsolve JNI (version 5.5,release 0,bu= ild 14)
Scanning annotation file Ch= ecking GTF ********** OK (00:00:09)
scanning OK (00:00:48)
[WARN] Skipped 268333 lines.
[INFO] &n= bsp;53182 loci, 215170 transcripts, 1306656 exons.
OK (00:00:48)
Scanning mapping file [SAM] Setting validation stringency to SILENT
[INFO] The Flux Capacitor is not using t= he SAM flags for counting the number of reads in the mapping file.= p>
[WARN] This process can be long for big = files!
OK (00:14:23)
[INFO] &n= bsp;85007194 mapped reads, 85007194 mappings: R-factor 1.0
[INFO] &n= bsp;76440206 entire, 8566988 split mappings (10.077957%)
OK (00:14:23)
[INFO] Annotation and mapping input chec= ked
[HEHO] We are set, so let's go!= p>
[ANNOTATION_FILE] /net/assembly/cgillies= /data/NEPTUNE/RNA-Seq/11_24_2015/FLUX/gtf.filtered.sorted.gtf
[MAPPING_FILE] /net/assembly/cgillies/da= ta/NEPTUNE/RNA-Seq/11_24_2015/25870/final.bam
[INFO] &n= bsp;minimum intron length 24
[SORT_IN_RAM] true
[TMP_DIR] /net/assembly/cgillies/data/NE= PTUNE/RNA-Seq/11_24_2015/FLUX/25870_tmp
[STDOUT_FILE] /net/assembly/cgillies/dat= a/NEPTUNE/RNA-Seq/11_24_2015/FLUX/25870.gtf
[INFO] &n= bsp;mate pairing information considered
[PROFILE] Loading profile
[PROFILE] Scanning the input and getting= the attributes.
profiling Exception in thread "Thread-5" java.lang.OutOfMemoryError: Ja= va heap space
at net.sf.samtools.DefaultSAMRecordFactory.createBAMRecord(DefaultSAMRe= cordFactory.java:30)
at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:201)
at net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileR= eader.java:557)
at net.sf.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAM= FileReader.java:664)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.= java:531)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.jav= a:521)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.jav= a:480)
at net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMF= ileReader.java:749)
at net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFile= Reader.java:719)
at net.sf.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFile= Reader.java:672)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.= java:664)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.= java:642)
at barna.io.sam.SAMMappingSortedIterator$1.run(SAMMappingSortedIterator.j= ava:103)
at java.lang.Thread.run(Thread.java:744)