Assertion `check_sorted(raw_regions, false)' failed.

[Kristina]

Hi all,
Another question...I have run rseg without problem with a genome with
names "LG_1" through "LG_5", but am now getting this "Assertion
`check_sorted(raw_regions, false)' failed" error with a genome with
names shown below from my sorted bed file. is this a problem with my
contig names or something else? any suggestions are appreciated!

supercont10.1 0 35 ILLUMINA-20A1B2_0034_FC70GM3AAXX:5:72:6735:12226#0
0 +
supercont10.1 1 36 ILLUMINA-20A1B2_0034_FC70GM3AAXX:5:91:2015:10941#0
0 -
supercont10.1 1 36 ILLUMINA-20A1B2_0034_FC70GM3AAXX:5:86:19211:11923#0
0 +
supercont10.1 1 36 ILLUMINA-20A1B2_0034_FC70GM3AAXX:5:107:7636:19778#0
0 -
supercont10.1 1 36 ILLUMINA-20A1B2_0034_FC70GM3AAXX:5:50:9943:20531#0
0 -
supercont10.1 1 36 ILLUMINA-20A1B2_0034_FC70GM3AAXX:5:68:17571:10471#0
0 +
supercont10.1 1 36 ILLUMINA-20A1B2_0034_FC70GM3AAXX:5:44:8825:11672#0
0 -
supercont10.1 2 37 ILLUMINA-20A1B2_0034_FC70GM3AAXX:5:1:12368:5999#0
0 -

[Song, Qiang]

Hi Kristina,

First of all, make sure you sort all your input files with the sortbed program in the
rseg package. This should solve your problem.

Second, are you using the following file as chromosome size file or as the ChIP-Seq
input file?

Regards,
Song Qiang

[Kristina Smith]

Song, 

I did sort my input file with sortbed. the file below is my ChIP-seq input. since the error is for raw_regions and not raw_reads, i thought the problem might be the chromosome names. 

Kristina Smith

Oregon State University

Department of Biochemistry and Biophysics

ALS2034

Corvallis, OR 97331

541-737-4399 (lab)

541-223-1272 (cell)

[Song, Qiang]

Could you show me the command line you used to run this analysis?

[Kristina Smith]

i actually just found the problem. sortbed is sorting the contigs not in order from 1 to 21 as they are in my chromosome file. 

[Kristina Smith]

Song, 

I am getting a new error when i try to run rseg on a different genome. here is my command and error:

 /local/cluster/rseg/bin/rseg -c ../CASHX_2.3_Nc/Nc.txt -o rseg_K27ac -i 5 -v K27acs.bed

[PROCESSING] K27acs

[LOADING_DATA] chromosomes

[LOADING_DATA] reads

[LOADING_DATA] separating deserts

[Remove duplicate reads]

[Selecting bin size] use Hideaki's empirical method: ERROR: could not allocate memory

31.125u 53.748s 1:31.24 93.0% 0+0k 0+0io 10pf+0w

if i set a bin size, then the "could not allocate memory" error occurs during the binning reads step.

i don't understand why i would run out of memory when i have run rseg on a genome of the same size (40Mb) with data files of similar size.

any input would be greatly appreciated.

Kristina

On May 17, 2011, at 6:15 PM, Song, Qiang wrote:

[Song, Qiang]

Hi Kristina,

It seems the binning reads function does not work as expected in your cae.
But It is hard to pinpoint the exact cause of the error solely based on the information
you gave,  especially when it worked on some of your dataset.

If you are analysing any public dataset and have the same error, it would be
much helpful if you gave me the link to the specific dataset.

Best,
Song Qiang