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Segmentation fault (core dumped) #4

Closed tiramisutes closed 6 years ago

tiramisutes commented 6 years ago

Hello, I want to use the CscoreTool for compartment analysis and have some confusion when preparing the input.summary file. In HOMER software, the runHiCpca.pl script input file is a directory from makeTagDirectory resulted, but I can't find a file that same as the Test.summary. Finally, I find the hicup2homer from HiCUP can conversion the HiCUP bam file to homer format that same as the Test.summary: 

Column1: index number (integer 1, 2, 3,..)
Column2: forward read chromosome name
Column3: forward read position
Column4: forward read strand (0 = positive strand, 1 = negative strand)
Column5: reverse read chromosome name 
Column6: reverse read position
Column7: reverse read strand (0 = positive strand, 1 = negative strand)

But, I get follows error stdout when using this homer format file: 

dmin=75
0
read VLWs File
VLWs sorted
Segmentation fault (core dumped)

Any help is much appreciated. Thanks.

scoutzxb commented 6 years ago

Hi,

It seems that the problem doesn't come from the summar file, instead, no genomic windows had been read from the windows bed file, so that file must has a problem. You can look at it.

Best,

Xiaobin

On Wed, Apr 4, 2018 at 4:02 AM, hope notifications@github.com wrote:

Hello, I want to use the CscoreTool for compartment analysis and have some confusion when preparing the input.summary file. In HOMER software, the runHiCpca.pl script input file is a directory from makeTagDirectory resulted, but I can't find a file that same as the Test.summary. Finally, I find the hicup2homer from HiCUP https://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ can conversion the HiCUP bam file to homer format that same as the Test.summary:

Column1: index number (integer 1, 2, 3,..) Column2: forward read chromosome name Column3: forward read position Column4: forward read strand (0 = positive strand, 1 = negative strand) Column5: reverse read chromosome name Column6: reverse read position Column7: reverse read strand (0 = positive strand, 1 = negative strand)

But, I get follows error stdout when using this homer format file:

dmin=75 0 read VLWs File VLWs sorted Segmentation fault (core dumped)

Any help is much appreciated. Thanks.

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tiramisutes commented 6 years ago

Hi, This is my command

/public/home/software/CscoreTool/CscoreTool1.1 genome_10k.bed ../HiCUP/RHC00720_L1_1_2.hicup.bam.homer RHC00720_L1_1_2.hicup_10k 1 1000000

And I have genome_10k.bed file as follows:

fragScaff_scaffold_0    1       10000
fragScaff_scaffold_0    10001   20000
fragScaff_scaffold_0    20001   30000
fragScaff_scaffold_0    30001   40000
fragScaff_scaffold_0    40001   50000
fragScaff_scaffold_0    50001   60000
fragScaff_scaffold_0    60001   70000
fragScaff_scaffold_0    70001   80000
fragScaff_scaffold_0    80001   90000
fragScaff_scaffold_0    90001   100000
fragScaff_scaffold_0    100001  110000
fragScaff_scaffold_0    110001  120000
fragScaff_scaffold_0    120001  130000
fragScaff_scaffold_0    130001  140000
fragScaff_scaffold_0    140001  150000
......

The different is I used all genome data, not just one chromosome as the hg19_chr1_10k.bed show.

scoutzxb commented 6 years ago

The genome_10k.bed file needs to be tab-delimited, not by space, and in the current version, my program needs the chromosome name to start with "chr". You can check if these are the possible reason.

Best,

Xiaobin

On Wed, Apr 4, 2018 at 10:30 PM, hope notifications@github.com wrote:

Hi, This is my command

/public/home/software/CscoreTool/CscoreTool1.1 genome_10k.bed ../HiCUP/RHC00720_L1_1_2.hicup.bam.homer RHC00720_L1_1_2.hicup_10k 1 1000000

And I have genome_10k.bed file as follows:

fragScaff_scaffold_0 1 10000 fragScaff_scaffold_0 10001 20000 fragScaff_scaffold_0 20001 30000 fragScaff_scaffold_0 30001 40000 fragScaff_scaffold_0 40001 50000 fragScaff_scaffold_0 50001 60000 fragScaff_scaffold_0 60001 70000 fragScaff_scaffold_0 70001 80000 fragScaff_scaffold_0 80001 90000 fragScaff_scaffold_0 90001 100000 fragScaff_scaffold_0 100001 110000 fragScaff_scaffold_0 110001 120000 fragScaff_scaffold_0 120001 130000 fragScaff_scaffold_0 130001 140000 fragScaff_scaffold_0 140001 150000 ......

The different is I used all genome data, not just one chromosome as the hg19_chr1_10k.bed show.

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tiramisutes commented 6 years ago

Hi, what is the L value in the stdout?

dmin=75
24926
read VLWs File
VLWs sorted
chr ranges assigned
1000000
L=-2119757.1923734471   maxdevc=0
L=-2033362.8908567722   maxdevc=2.1227826948561694

But, in my command, the L is zero.

dmin=50
70479
read VLWs File
VLWs sorted
chr ranges assigned
1000000
2000000
3000000
4000000
5000000
6000000
7000000
8000000
9000000
10000000
11000000
12000000
13000000
14000000
15000000
16000000
17000000
18000000
19000000
L=0     maxdevc=0
L=0     maxdevc=0
scoutzxb commented 6 years ago

L is the log-likelihood. So if it's zero, most likely no valid reads were found in your summary file. One possible reason for this is that your .summary file isn't tab-delimited, another possible reason is the chromosome name of the summary file doesn't match the chromosome name in the genome_10k.bed file. In this version, the program doesn't support calculating the Cscore of all chromosomes together, and this could cause unknown problems. So you can run each chromosome one by one, by simply add the chromosome name at the end of the command, then reads involving other chromosomes would be ignored.

Best,

Xiaobin

On Thu, Apr 5, 2018 at 12:25 AM, hope notifications@github.com wrote:

Hi, what is the L value in the stdout?

dmin=75 24926 read VLWs File VLWs sorted chr ranges assigned 1000000 L=-2119757.1923734471 maxdevc=0 L=-2033362.8908567722 maxdevc=2.1227826948561694

But, in my command, the L is zero.

dmin=50 70479 read VLWs File VLWs sorted chr ranges assigned 1000000 2000000 3000000 4000000 5000000 6000000 7000000 8000000 9000000 10000000 11000000 12000000 13000000 14000000 15000000 16000000 17000000 18000000 19000000 L=0 maxdevc=0 L=0 maxdevc=0

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tiramisutes commented 6 years ago

Yes, It's working. Thanks.

Drosophilid commented 4 years ago

Hi, I am facing the same problem as above, I already checked that input file (Dpse-M-larvae_Dpse.03Run.chr.fa.bwt2pairs.bam.v3.chr2.homer) is tab-delimited and chromosome name is matching with genome10kb bed file.

/apps/cscoretool/1.1/CscoreTool1.1 Dpse.03Run.chr.fa.size.10kb.v2.chr2.bed Dpse-M-larvae_Dpse.03Run.chr.fa.bwt2pairs.bam.v3.chr2.homer Dpse.03Run.chr.fa.size.10kb.Lm chr2 1000000 dmin=75 3309 read VLWs File VLWs sorted chr ranges assigned 1000000 2000000 3000000 4000000 5000000 6000000 7000000 8000000 9000000 10000000 11000000 12000000 13000000 14000000 15000000 L=0 maxdevc=0 L=0 maxdevc=0