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no output from 'fermi clean' #7

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yunfeiguo opened this issue Mar 20, 2015 · 0 comments
Open

no output from 'fermi clean' #7

yunfeiguo opened this issue Mar 20, 2015 · 0 comments

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@yunfeiguo
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Dear Dr. Li,

I ran fermi with commands shown in documentation but failed at the 'fermi clean' step with no log info and no output. What are the possible reasons and how to troubleshoot? Thank you!

run-fermi.pl -ct12 -e ~/Downloads/fermi/fermi *.fastq.gz > ilmn_fermi_asbl.mak
make -f ilmn_fermi_asbl.mak -j 12 > ilmn_fermi_asbl.log 2>&1
  • Version: 1.1-r751-beta
  • input: illumina hiseq pe reads, 50x coverage human
  • memory on machine: 128Gb
$ du -h * #file size of all output files
44G     fmdef.ec.fmd
12K     fmdef.ec.fmd.log
134G    fmdef.ec.fq.gz
188K    fmdef.ec.fq.gz.log
20G     fmdef.ec.rank
4.0K    fmdef.ec.rank.log
4.0K    fmdef.fltuniq.log
531G    fmdef.p0.mag.gz
4.0K    fmdef.p0.mag.gz.log
0       fmdef.p1.mag.gz
0       fmdef.p1.mag.gz.log
4.0K    fmdef.p2.mag.gz
4.0K    fmdef.p2.mag.gz.log
4.0K    fmdef.p3.mag.gz
4.0K    fmdef.p3.mag.gz.log
4.0K    fmdef.p4.fa.gz
4.0K    fmdef.p4.fa.gz.log
4.0K    fmdef.p5.fq.gz
4.0K    fmdef.p5.fq.gz.log
68G     fmdef.raw.fmd
12K     fmdef.raw.fmd.log
4.0K    ilmn_fermi_asbl.log
8.0K    ilmn_fermi_asbl.mak
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