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庞林
Jul 28, 2013, 8:49:06 PM7/28/13
to meth...@googlegroups.com
Hi,
I am sorry that I cannot open the web "http://pastebin.com/" or the googlegroups.When I try to open it ,it says "Unable to display this page".Also the methylCRF Google Group in the web "http://methylcrf.wustl.edu/" cannot be displayed.The content of error file is :
Wed Jul 24 08:03:41 2013 format H1ESmrg_DIP.bed and H1ESmrg_MRE.bed
H1ESmrg_DIP.bed !!! not all parsed! Maybe croaked on score croaked
-rw-r--r-- 1 panglin bio 1007432426 Jul 23 20:21 cpg_H1ESmrg_DIP_read.bed
p75:5821541 P75cnt:11.000000
-rw-r--r-- 1 panglin bio 1674966247 Dec 27 2012 H1ESmrg_DIP.bed
-rw-r--r-- 1 panglin bio 1612711909 Jul 23 20:47 H1ESmrg_DIP.bed.norm.bed
-rw-r--r-- 1 panglin bio 59456634 Dec 28 2012 H1ESmrg_MRE.bed
Wed Jul 24 08:41:13 2013 make avg windows for H1ESmrg_DIP.bed and H1ESmrg_MRE.bed
0
10
100
1000
10000
0
10
100
1000
10000
28085155 56170310 494005998 H1ES_DIP_d0.cnt
28085155 56170310 494034461 H1ES_MRE_d0.cnt
28085155 56170310 494029512 H1ES_DIP_d10.cnt
28085155 56170310 494163561 H1ES_MRE_d10.cnt
28085155 56170310 495027124 H1ES_DIP_d100.cnt
28085155 56170310 495384134 H1ES_MRE_d100.cnt
28085155 56170310 509740530 H1ES_DIP_d1000.cnt
28085155 56170310 498366884 H1ES_MRE_d1000.cnt
28085155 56170310 533153252 H1ES_DIP_d10000.cnt
28085155 56170310 506330986 H1ES_MRE_d10000.cnt
H1ES_DIPMRE.cnt column numbers
11
Wed Jul 24 11:38:25 2013 making DIPMRE.cnt for H1ESmrg_DIP.bed and H1ESmrg_MRE.bed
H1ES_DIPMRE.cnt column numbers
11
Wed Jul 24 11:51:52 2013 make table
H1ES_cpgi.tbl
17
17
H1ES_cpgi_1kshore.tbl
17
17
H1ES_cpgi_2kshore.tbl
17
17
H1ES_distal_promoter.tbl
17
17
H1ES_proximal_promoter.tbl
17
17
H1ES_core_promoter.tbl
17
17
H1ES_utr5.tbl
17
17
H1ES_exon.tbl
17
17
H1ES_intron.tbl
17
17
H1ES_utr3.tbl
17
17
H1ES_gene_body.tbl
17
17
H1ES_rmsk_lowsimple.tbl
17
17
H1ES_rmsk_RNA.tbl
17
17
H1ES_rmsk_LTR.tbl
17
17
H1ES_rmsk_DNA.tbl
17
17
H1ES_rmsk_SINE.tbl
17
17
H1ES_rmsk_LINE.tbl
17
17
H1ES_rmsk_other.tbl
17
17
H1ES_notAnno.tbl
17
17
Wed Jul 24 14:09:05 2013 predict
predict: [cpgi] [h1es_mdl/cpgi.mdl]
-rw-r--r-- 1 panglin bio 10413040 Jul 24 02:23 H1ES_cpgi.tbl_h1es_mdl.out
predict: [cpgi_1kshore] [h1es_mdl/cpgi_1kshore.mdl]
-rw-r--r-- 1 panglin bio 7117289 Jul 24 02:29 H1ES_cpgi_1kshore.tbl_h1es_mdl.out
predict: [cpgi_2kshore] [h1es_mdl/cpgi_2kshore.mdl]
-rw-r--r-- 1 panglin bio 11600203 Jul 24 02:38 H1ES_cpgi_2kshore.tbl_h1es_mdl.out
predict: [distal_promoter] [h1es_mdl/distal_promoter.mdl]
-rw-r--r-- 1 panglin bio 6952612 Jul 24 02:44 H1ES_distal_promoter.tbl_h1es_mdl.out
predict: [proximal_promoter] [h1es_mdl/proximal_promoter.mdl]
-rw-r--r-- 1 panglin bio 1965235 Jul 24 02:45 H1ES_proximal_promoter.tbl_h1es_mdl.out
predict: [core_promoter] [h1es_mdl/core_promoter.mdl]
-rw-r--r-- 1 panglin bio 700040 Jul 24 02:46 H1ES_core_promoter.tbl_h1es_mdl.out
predict: [utr5] [h1es_mdl/utr5.mdl]
-rw-r--r-- 1 panglin bio 1726720 Jul 24 02:47 H1ES_utr5.tbl_h1es_mdl.out
predict: [exon] [h1es_mdl/exon.mdl]
-rw-r--r-- 1 panglin bio 9237975 Jul 24 02:54 H1ES_exon.tbl_h1es_mdl.out
predict: [intron] [h1es_mdl/intron.mdl]
-rw-r--r-- 1 panglin bio 0 Jul 24 02:55 H1ES_intron.tbl_h1es_mdl.out
predict: [utr3] [h1es_mdl/utr3.mdl]
-rw-r--r-- 1 panglin bio 1668445 Jul 24 03:08 H1ES_utr3.tbl_h1es_mdl.out
predict: [gene_body] [h1es_mdl/gene_body.mdl]
-rw-r--r-- 1 panglin bio 0 Jul 24 03:09 H1ES_gene_body.tbl_h1es_mdl.out
predict: [rmsk_lowsimple] [h1es_mdl/rmsk_lowsimple.mdl]
-rw-r--r-- 1 panglin bio 2113504 Jul 24 03:54 H1ES_rmsk_lowsimple.tbl_h1es_mdl.out
predict: [rmsk_RNA] [h1es_mdl/rmsk_RNA.mdl]
-rw-r--r-- 1 panglin bio 92039 Jul 24 03:54 H1ES_rmsk_RNA.tbl_h1es_mdl.out
predict: [rmsk_LTR] [h1es_mdl/rmsk_LTR.mdl]
-rw-r--r-- 1 panglin bio 10531615 Jul 24 04:04 H1ES_rmsk_LTR.tbl_h1es_mdl.out
predict: [rmsk_DNA] [h1es_mdl/rmsk_DNA.mdl]
-rw-r--r-- 1 panglin bio 3239180 Jul 24 04:07 H1ES_rmsk_DNA.tbl_h1es_mdl.out
predict: [rmsk_SINE] [h1es_mdl/rmsk_SINE.mdl]
-rw-r--r-- 1 panglin bio 0 Jul 24 04:07 H1ES_rmsk_SINE.tbl_h1es_mdl.out
predict: [rmsk_LINE] [h1es_mdl/rmsk_LINE.mdl]
-rw-r--r-- 1 panglin bio 17272300 Jul 24 04:58 H1ES_rmsk_LINE.tbl_h1es_mdl.out
predict: [rmsk_other] [h1es_mdl/rmsk_other.mdl]
-rw-r--r-- 1 panglin bio 1365510 Jul 24 05:00 H1ES_rmsk_other.tbl_h1es_mdl.out
predict: [notAnno] [h1es_mdl/notAnno.mdl]
-rw-r--r-- 1 panglin bio 0 Jul 24 05:00 H1ES_notAnno.tbl_h1es_mdl.out
Wed Jul 24 17:08:08 2013 making ensemble prediction
readline failed: [IO::File::AutoChomp=GLOB(0x1e066210)] () at ./methylCRF.pl line 33.
I'm sorry to trouble you so many times.(∩_∩)
michael
Jul 29, 2013, 5:36:37 PM7/29/13
to meth...@googlegroups.com, pang...@163.com
Hi,
No worries, that's what this group is for. :)
"H1ESmrg_DIP.bed !!! not all parsed! Maybe croaked on score croaked" indicates that there was a problem early on. It looks like maybe there's something about the MeDIP bed file. Can you check that the format is:
chr1 <begin> <begin+length> . 1 <strand>
Could you post the first 10 or so lines? And also run:
awk '(NF!=6)' yourDIP.bed |head
michael
No worries, that's what this group is for. :)
"H1ESmrg_DIP.bed !!! not all parsed! Maybe croaked on score croaked" indicates that there was a problem early on. It looks like maybe there's something about the MeDIP bed file. Can you check that the format is:
chr1 <begin> <begin+length> . 1 <strand>
Could you post the first 10 or so lines? And also run:
awk '(NF!=6)' yourDIP.bed |head
michael
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