ChromHMM segmenting only 1 chromosome

Question

[Venados]

I have been trying ChromHMM but after running LearnModel my segmentation file has only 1 chromosome without information for the rest. It looks like this:

chr10_GL383545v1_alt    0   13800   E1
chr10_GL383545v1_alt    13800   14400   E12
chr10_GL383545v1_alt    14400   34600   E1
chr10_GL383545v1_alt    34600   35200   E3
chr10_GL383545v1_alt    35200   71600   E1
chr10_GL383545v1_alt    71600   72200   E3
chr10_GL383545v1_alt    72200   81200   E1
chr10_GL383545v1_alt    81200   81800   E6
chr10_GL383545v1_alt    81800   117000  E1
chr10_GL383545v1_alt    117000  117200  E6
chr10_GL383545v1_alt    117200  164800  E1
chr10_GL383545v1_alt    164800  165000  E6
chr10_GL383545v1_alt    165000  175400  E1
chr10_GL383545v1_alt    175400  179200  E6

That is literally the entire segment file.

The commands ran without any error and are as follow: java -mx22000M -jar ChromHMM.jar BinarizeBam hg38.chrom.sizes bam/ input_matrix.txt binarizedBAM java -mx52000M -jar ChromHMM.jar LearnModel -p 0 binarizedBAM/ LearnModel/ 10 hg38

Where the input_matrix.txt looks like this:

NT          H3K27ac     NT_H3K27ac_rmdup.bam            NT_input_rmdup.bam
NT          H3K4me3     NT_H3K4me3_rmdup.bam            NT_input_rmdup.bam
NT          H3K27me3    NT_H3K27me3_rmdup.bam           NT_input_rmdup.bam
NT          H3K9me3     NT_H3K9me3_rmdup.bam            NT_input_rmdup.bam
P53         H3K27ac     P53_H3K27ac_rmdup.bam           P53+ACTD_input_rmdup.bam
P53         H3K4me3     P53_H3K4me3_rmdup.bam           P53+ACTD_input_rmdup.bam
P53         H3K27me3    P53_H3K27me3_rmdup.bam          P53+ACTD_input_rmdup.bam
P53         H3K9me3     P53_H3K9me3_rmdup.bam           P53+ACTD_input_rmdup.bam
P53+ACTD    H3K27ac     P53+ACTD_H3K27ac_rmdup.bam      P53+ACTD_input_rmdup.bam
P53+ACTD    H3K4me3     P53+ACTD_H3K4me3_rmdup.bam      P53+ACTD_input_rmdup.bam
P53+ACTD    H3K27me3    P53+ACTD_H3K27me3_rmdup.bam     P53+ACTD_input_rmdup.bam
P53+ACTD    H3K9me3     P53+ACTD_H3K9me3_rmdup.bam      P53+ACTD_input_rmdup.bam

I also checked the output of BinarizedBam and there are files for all sample+mark combination for all the chromosomes.

Any idea what might be going on?

Thanks a lot in advance for the help!!

[Rashedul Islam]

Can I see the 'hg38.chrom.sizes' file header? Try changing the -p to at least 1 instead of 0; see here.

[Venados]

Thanks for your comments! there was a small bug in version 1.16 but it got fixed in version 1.17

Answer 1

[Venados]

Hello everyone,

I talked to the developer of ChromHMM there was a small bug introduced in the version 1.16, if anyone is experiencing the same error please update to version 1.17 https://github.com/jernst98/ChromHMM/

Thanks!