error running psg_prepare_reference

[Zhenhua Wu]

here is the command I used: ~/data/rnaSeq.pipeline/psg$ psg_prepare_reference.py -k 1 -g ../fasta/hg19/ -a ../knownGene-06-30-2013.gtf hg19.knownGene.063013

The output is:

Using 64 cores

Reading transcripts from GTF-formatted file...

Processing chromosome chrUn_gl000218...

        Creating PSGs

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chrUn_gl000218/uc011mfn.2.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chrUn_gl000218/uc003jai.3.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chrUn_gl000218/uc003jaj.2.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chrUn_gl000218/uc003jah.2.psg 100

Processing chromosome chr9_gl000201_random...

        Creating PSGs

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr9_gl000201_random/uc004con.1.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr9_gl000201_random/uc011mfg.1.psg 100

Processing chromosome chr17_gl000205_random...

        Creating PSGs

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr17_gl000205_random/uc002kgk.4.psg 100

Processing chromosome chr6_apd_hap1...

        Creating PSGs

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc011enc.2.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc011enn.1.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc011esk.1.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc011epd.2.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc021zis.1.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc031srp.1.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc011eiq.2.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc011eib.2.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc011elx.2.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc021ziu.1.psg 100

Error: Command was terminated or failed:

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6_apd_hap1/uc011eje.1.psg 100

The error message is not informative. Could you help me identify what went wrong?

Jeremy

[Zhenhua Wu]

the error message file report:

#

# There is insufficient memory for the Java Runtime Environment to continue.

# Cannot create GC thread. Out of system resources.

# Possible reasons:

#   The system is out of physical RAM or swap space

#   In 32 bit mode, the process size limit was hit

# Possible solutions:

#   Reduce memory load on the system

#   Increase physical memory or swap space

#   Check if swap backing store is full

#   Use 64 bit Java on a 64 bit OS

#   Decrease Java heap size (-Xmx/-Xms)

#   Decrease number of Java threads

#   Decrease Java thread stack sizes (-Xss)

#   Set larger code cache with -XX:ReservedCodeCacheSize=

# This output file may be truncated or incomplete.

#

#  Out of Memory Error (gcTaskThread.cpp:45), pid=58744, tid=140021640898304

#

# JRE version: 6.0_24-b24

# Java VM: OpenJDK 64-Bit Server VM (20.0-b12 mixed mode linux-amd64 compressed oops)

# Derivative: IcedTea6 1.11.4

# Distribution: Red Hat Enterprise Linux Server release 6.3 (Santiago), package rhel-1.49.1.11.4.el6_3-x86_64

However, there are still > 80G RAM. How much does PSG need? It runs 64 cores by default. Is there a way to reduce the number of cores PSG uses?

Jeremy

[Zhenhua Wu]

The problem I found is that psg_prepare_reference.py automatically use the maximum number of core. Each java thread actually takes 33g memory. In my case, we have 64 core, so the code tried to allocate 63 * 33G > 2TB memory, that's why it fails. I think you should add an option to allow user to specify the number of core they want to use.

Jeremy

On Wednesday, August 21, 2013 4:46:42 PM UTC-4, Zhenhua Wu wrote:

[Zhenhua Wu]

Now I got another error after it runs for 2 hours:

... (many lines that are not shown here)

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc003nkq.2.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc003pgf.3.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc021yva.1.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc010kkp.3.psg 100

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr6/uc003odo.1.psg 100

Exception in thread "main" java.lang.NullPointerException

        at SpliceGraph.<init>(SpliceGraph.java:57)

        at MakeFastaStdOut.main(MakeFastaStdOut.java:14)

Exception in thread "main" java.lang.NullPointerException

        at SpliceGraph.<init>(SpliceGraph.java:57)

        at MakeFastaStdOut.main(MakeFastaStdOut.java:14)

Exception in thread "main" java.lang.NullPointerException

        at SpliceGraph.<init>(SpliceGraph.java:57)

        at MakeFastaStdOut.main(MakeFastaStdOut.java:14)

Error: Command was terminated or failed:

java -cp /data/tools/psginfer-1.1.3/LearnPSG MakeFastaStdOut hg19.knownGene.063013/chr5/uc021yer.1.psg 100

I found that "hg19.knownGene.063013/chr5/uc021yer.1.psg" file is empty. For chr5, there are many .psg files that are empty (with size 0). For other chromosomes like chr6, there is no empty .psg file Why does this happen  to 'chr5'?

The .gtf file is downloaded from ucsc table, using ucsc gene, known gene.

Jeremy