DMRfind generates thousands of chunk.tsv files

Hi Yupeng,

I'm running into some issues with the results generated by DMRfind. I have EM-seq reads from two different organisms to use in my DMR analysis. I've run DMRfind (methylpy 1.4.7) on Arabidopsis with the simplified command below with success:

methylpy DMRfind \
    --allc-files /allc_Arabidopsis_1_merged.tsv.gz /allc_Arabidopsis_2_merged.tsv.gz
    --samples A1 A2 \
    --mc-type "CGN" \
    --chroms 1 2 3 4 5 \
    --num-procs 10 \
    --output-prefix /results/CGN_DMR_A1_A2_merged

Results:

CGN_DMR_A1_A2_merged_rms_results.tsv.gz
CGN_DMR_A1_A2_merged_rms_results_collapsed.tsv
CGN_DMR_A1_A2_merged_rms_results_collapsed.tsv.DMR.bed
CGN_DMR_A1_A2_merged_rms_results_collapsed.tsv.DMS.bed

However, running this similar command on another organism (with a scaffold genome) led to the generation of thousands of scaffold#_chunk#.tsv files in the results directory:

methylpy DMRfind \
    --allc-files /allc_Sample_1_merged.tsv.gz /allc_Sample_2_merged.tsv.gz
    --samples S1 S2 \
    --mc-type "CGN" \
    --num-procs 10 \
    --output-prefix /results/CGN_DMR_S1_S2_merged

Results:

CGN_DMR_S1_S2_merged_rms_results.tsv.gz
CGN_DMR_S1_S2_merged_rms_results_collapsed.tsv
CGN_DMR_S1_S2_merged_rms_results_collapsed.tsv.DMR.bed
CGN_DMR_S1_S2_merged_rms_results_collapsed.tsv.DMS.bed
CGN_DMR_S1_S2_merged_rms_results_for_organism_scaffold1_chunk_0.tsv
CGN_DMR_S1_S2_merged_rms_results_for_organism_scaffold1_chunk_1.tsv
CGN_DMR_S1_S2_merged_rms_results_for_organism_scaffold1_chunk_2.tsv
thousands more of the rms chunk files

It's interesting because there was no obvious error in the output file and some of the DMRs seem to have compiled in the top four files.

Thank you for your help, and please let me know if you need any more information for troubleshooting this issue.

yupenghe / methylpy

DMRfind generates thousands of chunk.tsv files #94