demo.sh failed

[lmanchon]

--Hi,

i don't know what happened running demo.sh, files are empty:

This is a demo script for bisulfighter.

Let us consider that we have two human samples from different biological conditions,
and want to perform mC calling and DMR detection on the subset of the chromosome X.
We have bisulfite-converted reads for each of two samples: data/1.fastq and data/2.fastq,
and the reference chromosome: data/chrX.sub.fa

(1) Remove temporal files for previous demo.
done

(2) Perform mC calling for sample1. (take a few minutes)
invoking: ./bsf-call -o result/res.mc1 -W tmp.mc1 data/chrX.sub.fa data/1.fastq
done

(3) Perform mC calling for sample2. (take a few minutes)
invoking: ./bsf-call -o result/res.mc2 -W tmp.mc2 data/chrX.sub.fa data/2.fastq
done

(4) Prepare input files for DMR detection.
invoking: mkdir tmp.dmr
invoking: ../ComMet/util/Bsf2ComMetIn.pl result/res.mc1 result/res.mc2 > tmp.dmr/commet.in
\rm -f tmp.20647.1
\rm -f tmp.20647.2
done

(5) Perform DMR detection between sample1 and sample2.
invoking: ../ComMet/src/ComMet tmp.dmr/commet.in result/res.dmc result/res.dmr
ComMet v1.1 - identification of differentially methylated regions (DMRs)
load methylated bases
loading tmp.dmr/commet.in
calculate global statistics
.inner ab convergence
.inner w convergence
outer convergence
.inner ab convergence
.inner w convergence
outer convergence
beta mixture for sample 1:
high -nan -nan 1
high -nan 1 1
low -nan 1 -nan
low -nan 1 1

beta mixture for sample 2:
high -nan -nan 1
high -nan 1 1
low -nan 1 -nan
low -nan 1 1

construct a probability model
./demo.sh: line 14: 20650 Segmentation fault ../ComMet/src/ComMet tmp.dmr/commet.in result/res.dmc result/res.dmr
done

Demo finished. Results are following:
mC calling for sample1, result/res.mc1
mC calling for sample2, result/res.mc2
DMR detection, result/res.dmr
For more details of input/output formats and option tuning,
see ../bsf-call/bsf-call.txt and ../ComMet/README