The program crashes with the error for one of the four replicates (generated pro files).
[ERROR] Error while creating initial fragmentation: 0 is smaller than, or equal to, the minimum (0): m
org.apache.commons.math.exception.NotStrictlyPositiveException: 0 is smaller than, or equal to, the mi
at org.apache.commons.math.random.RandomDataImpl.nextExponential(RandomDataImpl.java:484)
at barna.flux.simulator.fragmentation.Fragmenter.processInitial(Fragmenter.java:847)
at barna.flux.simulator.fragmentation.Fragmenter.writeInitialFile(Fragmenter.java:714)
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:180)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:440)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Flux.main(Flux.java:198)
[ERROR] null
java.lang.NullPointerException
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:181)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:440)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Flux.main(Flux.java:198)
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3 Comments
Rory Kirchner
I also have this issue, both with 1.2.1 and the newest nightly release. This is my PAR file:
################################################File locations
REF_FILE_NAME /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/rnaseq/ref-transcripts.gtf
GEN_DIR /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/multi
###################################################Expression
NB_MOLECULES 5000000
TSS_MEAN 50
POLYA_SCALE 100
POLYA_SHAPE 1.5
EXPRESSION_K -0.1
EXPRESSION_X0 14500.0
EXPRESSION_X1 9.025E9
###############################################Fragmentation
FRAGMENTATION YES
FRAG_SUBSTRATE RNA
FRAG_METHOD UR
FRAG_UR_ETA 800
FRAG_UR_D0 100
RTRANSCRIPTION YES
RT_MOTIF default
RT_PRIMER RH
#########################################################PCR
PCR_DISTRIBUTION default
GC_MEAN NaN
PCR_PROBABILITY 0.05
FILTERING YES
SIZE_DISTRIBUTION N(400,50)
#################################################Sequencing
READ_NUMBER 2000000
READ_LENGTH 100
PAIRED_END YES
FASTA YES
ERR_FILE 76
UNIQUE_IDS YES
Gleb Speshilov
I've found the reason, my gtf contains 3 nt transcript. Since my simulation is comparative I have just removed it and now the program runs normally.
Micha Sammeth
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