run error

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Daofeng Li

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Aug 5, 2013, 2:39:06 PM8/5/13
to meth...@googlegroups.com
Hi Michael,

I encountered an error while running methylCRF. Here is the log:

Mon Aug  5 12:32:49 2013 format TW293_GM12878-10ng_MeDIP.extended.bed.crfdip and TW260_MRE.bed.nocontig
-rw-rw-r-- 1 dli dli 1039409431 Aug  5 12:36 cpg_TW293_GM12878-10ng_MeDIP.extended.crfdip_read.bed
p75:5003763 P75cnt:9.000000
-rw-rw-r-- 1 dli dli  43540874 Aug  5 11:14 TW260_MRE.bed.nocontig
-rw-rw-r-- 1 dli dli 838318243 Aug  5 12:32 TW293_GM12878-10ng_MeDIP.extended.bed.crfdip
-rw-rw-r-- 1 dli dli 959242730 Aug  5 12:40 TW293_GM12878-10ng_MeDIP.extended.bed.crfdip.norm.bed
Mon Aug  5 12:40:59 2013 make avg windows for TW293_GM12878-10ng_MeDIP.extended.bed.crfdip and TW260_MRE.bed.nocontig
0
10
100
1000
10000
0
10
100
1000
10000
 28085155  56170310 493984961 gm12878_DIP_d0.cnt
 28085155  56170310 494140312 gm12878_MRE_d0.cnt
 28085155  56170310 493990551 gm12878_DIP_d10.cnt
 28085155  56170310 494321537 gm12878_MRE_d10.cnt
 28085155  56170310 494211203 gm12878_DIP_d100.cnt
 28085155  56170310 495795868 gm12878_MRE_d100.cnt
 28085155  56170310 505270885 gm12878_DIP_d1000.cnt
 28085155  56170310 501026227 gm12878_MRE_d1000.cnt
 28085155  56170310 531652541 gm12878_DIP_d10000.cnt
 28085155  56170310 517557602 gm12878_MRE_d10000.cnt
gm12878_DIPMRE.cnt column numbers
11
Mon Aug  5 13:23:11 2013 making DIPMRE.cnt for TW293_GM12878-10ng_MeDIP.extended.bed.crfdip and TW260_MRE.bed.nocontig
gm12878_DIPMRE.cnt column numbers
11
Mon Aug  5 13:23:48 2013 make table
at cpg: chr1.1 (chr1.1 != chr1 != chr1.1) at /home/comp/twlab/dli/methylCRF/methylCRF.pl line 156, <GEN22> line 2.

Any thoughts? Thanks in advance!

Daofeng

michael

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Aug 5, 2013, 3:10:26 PM8/5/13
to meth...@googlegroups.com, lid...@gmail.com
Hi Daofeng,

This:
at cpg: chr1.1 (chr1.1 != chr1 != chr1.1)

means that the fragment file doesn't have cpg ids.  Can you check that you're using the right one?  Note that MRE_norm.pl and methylCRF.pl use different fragment files.

thx,
michael


Daofeng Li

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Aug 5, 2013, 3:16:08 PM8/5/13
to michael, meth...@googlegroups.com
Thanks Michael.

Yes, I think I might be using the wrong fragment file for methylCRF.pl. Do you have the MRE_5enz_4_6000.bin for download?
(For human hg19, thanks)

Thanks.

Daofeng

michael stevens

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Aug 5, 2013, 4:00:50 PM8/5/13
to Daofeng Li, meth...@googlegroups.com

sure:
http://methylcrf.wustl.edu/hg19/MRE_frags/MRE_3enz_4_6000_cpg.bin
or
http://methylcrf.wustl.edu/hg19/MRE_frags/MRE_5enz_4_6000_cpg.bin

On 08/05/2013 02:16 PM, Daofeng Li wrote:
> Thanks Michael.
>
> Yes, I think I might be using the wrong fragment file for methylCRF.pl.
> Do you have the MRE_5enz_4_6000.bin for download?
> (For human hg19, thanks)
>
> Thanks.
>
> Daofeng
>
>
> On Mon, Aug 5, 2013 at 2:10 PM, michael <ste...@cse.wustl.edu
> <mailto:ste...@cse.wustl.edu>> wrote:
>
> Hi Daofeng,
>
> This:
> at cpg: chr1.1 (chr1.1 != chr1 != chr1.1)
>
> means that the fragment file doesn't have cpg ids. Can you check
> that you're using the right one? Note that MRE_norm.pl and
> methylCRF.pl use different fragment files.
>
> thx,
> michael
>
>
> On Monday, August 5, 2013 1:39:06 PM UTC-5, Daofeng Li wrote:
>
> Hi Michael,
>
> I encountered an error while running methylCRF. Here is the log:
>
> Mon Aug 5 12:32:49 2013 format
> TW293_GM12878-10ng_MeDIP.__extended.bed.crfdip and
> TW260_MRE.bed.nocontig
> -rw-rw-r-- 1 dli dli 1039409431 Aug 5 12:36
> cpg_TW293_GM12878-10ng_MeDIP.__extended.crfdip_read.bed
> p75:5003763 P75cnt:9.000000
> -rw-rw-r-- 1 dli dli 43540874 Aug 5 11:14 TW260_MRE.bed.nocontig
> -rw-rw-r-- 1 dli dli 838318243 Aug 5 12:32
> TW293_GM12878-10ng_MeDIP.__extended.bed.crfdip
> -rw-rw-r-- 1 dli dli 959242730 Aug 5 12:40
> TW293_GM12878-10ng_MeDIP.__extended.bed.crfdip.norm.bed
> Mon Aug 5 12:40:59 2013 make avg windows for
> TW293_GM12878-10ng_MeDIP.__extended.bed.crfdip and
> TW260_MRE.bed.nocontig
> 0
> 10
> 100
> 1000
> 10000
> 0
> 10
> 100
> 1000
> 10000
> 28085155 56170310 493984961 gm12878_DIP_d0.cnt
> 28085155 56170310 494140312 gm12878_MRE_d0.cnt
> 28085155 56170310 493990551 gm12878_DIP_d10.cnt
> 28085155 56170310 494321537 gm12878_MRE_d10.cnt
> 28085155 56170310 494211203 gm12878_DIP_d100.cnt
> 28085155 56170310 495795868 gm12878_MRE_d100.cnt
> 28085155 56170310 505270885 gm12878_DIP_d1000.cnt
> 28085155 56170310 501026227 gm12878_MRE_d1000.cnt
> 28085155 56170310 531652541 gm12878_DIP_d10000.cnt
> 28085155 56170310 517557602 gm12878_MRE_d10000.cnt
> gm12878_DIPMRE.cnt column numbers
> 11
> Mon Aug 5 13:23:11 2013 making DIPMRE.cnt for
> TW293_GM12878-10ng_MeDIP.__extended.bed.crfdip and
> TW260_MRE.bed.nocontig
> gm12878_DIPMRE.cnt column numbers
> 11
> Mon Aug 5 13:23:48 2013 make table
> at cpg: chr1.1 (chr1.1 != chr1 != chr1.1) at
> /home/comp/twlab/dli/__methylCRF/methylCRF.pl line 156, <GEN22>

Daofeng Li

unread,
Aug 5, 2013, 4:06:31 PM8/5/13
to michael stevens, meth...@googlegroups.com
hmm, actually you didn't have that file at the location you mentioned...
I used http://methylcrf.wustl.edu/hg19/MRE_frags/MRE_5enz_50_300.bed.bin instead.
What's the difference use 50_300 or 100_300 bin here?

Thanks a lot.

Daofeng

michael stevens

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Aug 5, 2013, 4:13:28 PM8/5/13
to meth...@googlegroups.com


The smaller frag files are historical. I've switched everything to use
the more lenient 4-6000bp fragment sizes. It didn't make much
difference in the results and has the benefit of no longer trying to
guess the true fragment ranges.

Thanks for pointing that out. The file is there now.

michael


On 08/05/2013 03:06 PM, Daofeng Li wrote:
> hmm, actually you didn't have that file at the location you mentioned...
> I used http://methylcrf.wustl.edu/hg19/MRE_frags/MRE_5enz_50_300.bed.bin
> instead.
> What's the difference use 50_300 or 100_300 bin here?
>
> Thanks a lot.
>
> Daofeng
>
>
> On Mon, Aug 5, 2013 at 3:00 PM, michael stevens <ste...@cse.wustl.edu
> <mailto:ste...@cse.wustl.edu>> wrote:
>
>
> sure:
> http://methylcrf.wustl.edu/__hg19/MRE_frags/MRE_3enz_4___6000_cpg.bin <http://methylcrf.wustl.edu/hg19/MRE_frags/MRE_3enz_4_6000_cpg.bin>
> or
> http://methylcrf.wustl.edu/__hg19/MRE_frags/MRE_5enz_4___6000_cpg.bin <http://methylcrf.wustl.edu/hg19/MRE_frags/MRE_5enz_4_6000_cpg.bin>
>
>
> On 08/05/2013 02:16 PM, Daofeng Li wrote:
>
> Thanks Michael.
>
> Yes, I think I might be using the wrong fragment file for
> methylCRF.pl.
> Do you have the MRE_5enz_4_6000.bin for download?
> (For human hg19, thanks)
>
> Thanks.
>
> Daofeng
>
>
> On Mon, Aug 5, 2013 at 2:10 PM, michael <ste...@cse.wustl.edu
> <mailto:ste...@cse.wustl.edu>
> <mailto:ste...@cse.wustl.edu <mailto:ste...@cse.wustl.edu>>__>
> wrote:
>
> Hi Daofeng,
>
> This:
> at cpg: chr1.1 (chr1.1 != chr1 != chr1.1)
>
> means that the fragment file doesn't have cpg ids. Can you
> check
> that you're using the right one? Note that MRE_norm.pl and
> methylCRF.pl use different fragment files.
>
> thx,
> michael
>
>
> On Monday, August 5, 2013 1:39:06 PM UTC-5, Daofeng Li wrote:
>
> Hi Michael,
>
> I encountered an error while running methylCRF. Here is
> the log:
>
> Mon Aug 5 12:32:49 2013 format
> TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip and
>
> TW260_MRE.bed.nocontig
> -rw-rw-r-- 1 dli dli 1039409431 Aug 5 12:36
> cpg_TW293_GM12878-10ng_MeDIP.____extended.crfdip_read.bed
>
> p75:5003763 P75cnt:9.000000
> -rw-rw-r-- 1 dli dli 43540874 Aug 5 11:14
> TW260_MRE.bed.nocontig
> -rw-rw-r-- 1 dli dli 838318243 Aug 5 12:32
> TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip
>
> -rw-rw-r-- 1 dli dli 959242730 Aug 5 12:40
> TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip.norm.bed
>
> Mon Aug 5 12:40:59 2013 make avg windows for
> TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip and
>
> TW260_MRE.bed.nocontig
> 0
> 10
> 100
> 1000
> 10000
> 0
> 10
> 100
> 1000
> 10000
> 28085155 56170310 493984961 gm12878_DIP_d0.cnt
> 28085155 56170310 494140312 gm12878_MRE_d0.cnt
> 28085155 56170310 493990551 gm12878_DIP_d10.cnt
> 28085155 56170310 494321537 gm12878_MRE_d10.cnt
> 28085155 56170310 494211203 gm12878_DIP_d100.cnt
> 28085155 56170310 495795868 gm12878_MRE_d100.cnt
> 28085155 56170310 505270885 gm12878_DIP_d1000.cnt
> 28085155 56170310 501026227 gm12878_MRE_d1000.cnt
> 28085155 56170310 531652541 gm12878_DIP_d10000.cnt
> 28085155 56170310 517557602 gm12878_MRE_d10000.cnt
> gm12878_DIPMRE.cnt column numbers
> 11
> Mon Aug 5 13:23:11 2013 making DIPMRE.cnt for
> TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip and
>
> TW260_MRE.bed.nocontig
> gm12878_DIPMRE.cnt column numbers
> 11
> Mon Aug 5 13:23:48 2013 make table
> at cpg: chr1.1 (chr1.1 != chr1 != chr1.1) at
> /home/comp/twlab/dli/____methylCRF/methylCRF.pl line
> 156, <GEN22>
>
> line 2.
>
> Any thoughts? Thanks in advance!
>
> Daofeng
>
>
>
>
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>

Daofeng Li

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Aug 5, 2013, 4:24:06 PM8/5/13
to michael stevens, meth...@googlegroups.com
cool. Thanks a lot.

Daofeng


On Mon, Aug 5, 2013 at 3:13 PM, michael stevens <ste...@cse.wustl.edu> wrote:

The smaller frag files are historical.  I've switched everything to use the more lenient 4-6000bp fragment sizes.  It didn't make much difference in the results and has the benefit of no longer trying to guess the true fragment ranges.

Thanks for pointing that out.  The file is there now.

michael


On 08/05/2013 03:06 PM, Daofeng Li wrote:
hmm, actually you didn't have that file at the location you mentioned...
I used http://methylcrf.wustl.edu/hg19/MRE_frags/MRE_5enz_50_300.bed.bin
instead.
What's the difference use 50_300 or 100_300 bin here?

Thanks a lot.

Daofeng


On Mon, Aug 5, 2013 at 3:00 PM, michael stevens <ste...@cse.wustl.edu



    On 08/05/2013 02:16 PM, Daofeng Li wrote:

        Thanks Michael.

        Yes, I think I might be using the wrong fragment file for
        methylCRF.pl.
        Do you have the MRE_5enz_4_6000.bin for download?
        (For human hg19, thanks)

        Thanks.

        Daofeng


        On Mon, Aug 5, 2013 at 2:10 PM, michael <ste...@cse.wustl.edu
        <mailto:ste...@cse.wustl.edu>
        <mailto:ste...@cse.wustl.edu <mailto:ste...@cse.wustl.edu>>__>
        wrote:

             Hi Daofeng,

             This:
             at cpg: chr1.1 (chr1.1 != chr1 != chr1.1)

             means that the fragment file doesn't have cpg ids.  Can you
        check
             that you're using the right one?  Note that MRE_norm.pl and
             methylCRF.pl use different fragment files.

             thx,
             michael


             On Monday, August 5, 2013 1:39:06 PM UTC-5, Daofeng Li wrote:

                 Hi Michael,

                 I encountered an error while running methylCRF. Here is
        the log:

                 Mon Aug  5 12:32:49 2013 format
                 TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip and


                 TW260_MRE.bed.nocontig
                 -rw-rw-r-- 1 dli dli 1039409431 Aug  5 12:36
                 cpg_TW293_GM12878-10ng_MeDIP.____extended.crfdip_read.bed


                 p75:5003763 P75cnt:9.000000
                 -rw-rw-r-- 1 dli dli  43540874 Aug  5 11:14
        TW260_MRE.bed.nocontig
                 -rw-rw-r-- 1 dli dli 838318243 Aug  5 12:32
                 TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip


                 -rw-rw-r-- 1 dli dli 959242730 Aug  5 12:40
                 TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip.norm.bed


                 Mon Aug  5 12:40:59 2013 make avg windows for
                 TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip and


                 TW260_MRE.bed.nocontig
                 0
                 10
                 100
                 1000
                 10000
                 0
                 10
                 100
                 1000
                 10000
                   28085155  56170310 493984961 gm12878_DIP_d0.cnt
                   28085155  56170310 494140312 gm12878_MRE_d0.cnt
                   28085155  56170310 493990551 gm12878_DIP_d10.cnt
                   28085155  56170310 494321537 gm12878_MRE_d10.cnt
                   28085155  56170310 494211203 gm12878_DIP_d100.cnt
                   28085155  56170310 495795868 gm12878_MRE_d100.cnt
                   28085155  56170310 505270885 gm12878_DIP_d1000.cnt
                   28085155  56170310 501026227 gm12878_MRE_d1000.cnt
                   28085155  56170310 531652541 gm12878_DIP_d10000.cnt
                   28085155  56170310 517557602 gm12878_MRE_d10000.cnt
                 gm12878_DIPMRE.cnt column numbers
                 11
                 Mon Aug  5 13:23:11 2013 making DIPMRE.cnt for
                 TW293_GM12878-10ng_MeDIP.____extended.bed.crfdip and


                 TW260_MRE.bed.nocontig
                 gm12878_DIPMRE.cnt column numbers
                 11
                 Mon Aug  5 13:23:48 2013 make table
                 at cpg: chr1.1 (chr1.1 != chr1 != chr1.1) at
                 /home/comp/twlab/dli/____methylCRF/methylCRF.pl line

        156, <GEN22>

                 line 2.

                 Any thoughts? Thanks in advance!

                 Daofeng



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