ay-lab
commented
7 months ago Hi,
Generally an "ids_sample[[i]] out of bound" error will mean that there is a mismatch in the name of the files provided in the index file and the samples with actual fithic run. Let me try to debug this issue. Can you please share the input file description and the results generated under "DifferentialResult/folderName/fithic_run" directory. For example, this is a demo index file for me looks like -
ES_1_100Kb.matrix ES_1_100Kb_abs.bed ES_1_100Kb ES
ES_2_100Kb.matrix ES_2_100Kb_abs.bed ES_2_100Kb ES
ES_3_100Kb.matrix ES_3_100Kb_abs.bed ES_3_100Kb ES
ES_4_100Kb.matrix ES_4_100Kb_abs.bed ES_4_100Kb ES
NPC_2_100Kb.matrix NPC_2_100Kb_abs.bed NPC_2_100Kb NPC
NPC_3_100Kb.matrix NPC_3_100Kb_abs.bed NPC_3_100Kb NPC
NPC_4_100Kb.matrix NPC_4_100Kb_abs.bed NPC_4_100Kb NPCAnd my fithic_run directory looks like this -
For each replicate dchic will run the fithic calls and finally it will combine the replicate wise significant result to generate the FithicResult.txt file. This fill will look like this -
ES NPC
chr10_100000000_chr10_100000000 1 1
chr10_100000000_chr10_100100000 1 1
chr10_100000000_chr10_100400000 1 1
chr10_100000000_chr10_102200000 0 1
chr10_100000000_chr10_102300000 1 1
chr10_100000000_chr10_102400000 0 1
chr10_100000000_chr10_102500000 1 1While merging the replicates for a sample, it will use the names from the index.file. So, if there is a mismatch, then it can throw up an error.
kalavattam
Description
Encountered an error when running Step #4 of the dcHiC workflow, which involves determining statistically significant pairwise interactions using FitHiC prior to running dloop. The issue arises after the FitHiC analysis completes for each sample but fails during the subsequent processing stage with an "Error in ids_sample[[i]]: subscript out of bounds" message. I believe this pertains to lines 1617–1663 of dchicf.r.
Steps to Reproduce
Observe the error after the completion of FitHiC analysis for each sample.
Expected Behavior
The invocation of dchicf.r should complete the FitHiC analysis and proceed without errors.
Actual Behavior
The FitHiC analysis completes successfully for each sample, but the script halts with the following error:
Environment
Additional Context
Here's an excerpt from the terminal output showing the error:
Excerpt
```txt ❯ # Step 3 ❯ Rscript "${d_dcHiC}/dchicf.r" \ > --file "${f_infile}" \ > --pcatype analyze \ > --dirovwt T \ > --diffdir "${d_diff}" Running intra sample differential calls for D14 ctrl MM samples Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr1_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr10_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr11_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr12_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr13_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr14_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr15_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr16_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr17_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr18_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr19_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr2_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr20_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr21_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr22_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr3_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr4_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr5_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr6_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr7_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr8_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chr9_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/D14_data/intra_chrX_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr1_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr10_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr11_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr12_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr13_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr14_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr15_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr16_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr17_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr18_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr19_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr2_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr20_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr21_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr22_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr3_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr4_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr5_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr6_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr7_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr8_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chr9_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/ctrl_data/intra_chrX_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr1_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr10_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr11_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr12_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr13_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr14_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr15_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr16_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr17_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr18_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr19_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr2_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr20_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr21_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr22_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr3_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr4_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr5_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr6_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr7_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr8_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chr9_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote DifferentialResult/diff_D14_ctrl_MM_40000/MM_data/intra_chrX_combined.pcOri.bedGraph and pcQnm.bedGraph files Wrote intra_sample_chr1_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr10_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr11_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr12_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr13_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr14_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr15_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr16_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr17_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr18_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr19_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr2_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr20_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr21_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr22_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr3_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr4_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr5_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr6_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr7_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr8_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chr9_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote intra_sample_chrX_combined.pcOri.bedGraph & _combined.pcQnm.bedGraph files under DifferentialResult/diff_D14_ctrl_MM_40000/pcOri & DifferentialResult/diff_D14_ctrl_MM_40000/pcQnm folders Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr1_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr10_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr11_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr12_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr13_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr14_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr15_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr16_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr17_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr18_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr19_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr2_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr20_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr21_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr22_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr3_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr4_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr5_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr6_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr7_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr8_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chr9_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_chrX_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_combined.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_group.pcQnm.bedGraph file Wrote DifferentialResult/diff_D14_ctrl_MM_40000/fdr_result/differential.intra_sample_group.pcOri.bedGraph file ❯ # Step 4 ❯ Rscript "${d_dcHiC}/dchicf.r" \ > --file "${f_infile}" \ > --pcatype fithic \ > --dirovwt T \ > --diffdir "${d_diff}" \ > --fithicpath "${a_FitHiC}" \ > --pythonpath "python" Finding significant loops from intra sample D14 ctrl MM replicates Creating inputs for fithic run D14_no2_40000 Reading the bed and interaction matrix file A B C chr1 fragmentMid1 chr2 fragmentMid2 contactCount correct_A correct_B 11 4 4 1 chr1 140000 chr1 140000 1 4 4 29 5 5 1 chr1 180000 chr1 180000 1 5 5 59 7 7 2 chr1 260000 chr1 260000 2 7 7 85 8 8 2 chr1 300000 chr1 300000 2 8 8 111 15 15 1 chr1 580000 chr1 580000 1 15 15 112 15 17 1 chr1 580000 chr1 660000 1 15 17 Started calculating Marginalized Contact Count chr start end index extraField mappable mid correct_index marginalizedContactCount 1 chr1 0 40000 1 0 1 20000 1 0 2 chr1 40000 80000 2 0 1 60000 2 0 3 chr1 80000 120000 3 0 1 100000 3 0 4 chr1 120000 160000 4 0 1 140000 4 1 5 chr1 160000 200000 5 0 1 180000 5 1 6 chr1 200000 240000 6 0 1 220000 6 0 Creating inputs for fithic run D14_no7_40000 Reading the bed and interaction matrix file A B C chr1 fragmentMid1 chr2 fragmentMid2 contactCount correct_A correct_B 9 4 13 1 chr1 140000 chr1 500000 1 4 13 23 5 5 2 chr1 180000 chr1 180000 2 5 5 44 7 7 1 chr1 260000 chr1 260000 1 7 7 53 8 8 2 chr1 300000 chr1 300000 2 8 8 68 14 208 1 chr1 540000 chr1 8300000 1 14 208 71 15 16 1 chr1 580000 chr1 620000 1 15 16 Started calculating Marginalized Contact Count chr start end index extraField mappable mid correct_index marginalizedContactCount 1 chr1 0 40000 1 0 1 20000 1 0 2 chr1 40000 80000 2 0 1 60000 2 0 3 chr1 80000 120000 3 0 1 100000 3 0 4 chr1 120000 160000 4 0 1 140000 4 1 5 chr1 160000 200000 5 0 1 180000 5 2 6 chr1 200000 240000 6 0 1 220000 6 0 Creating inputs for fithic run ctrl_no2_40000 Reading the bed and interaction matrix file A B C chr1 fragmentMid1 chr2 fragmentMid2 contactCount correct_A correct_B 1 1 5 1 chr1 20000 chr1 180000 1 1 5 9 3 7 1 chr1 100000 chr1 260000 1 3 7 13 4 4 2 chr1 140000 chr1 140000 2 4 4 14 4 30 1 chr1 140000 chr1 1180000 1 4 30 30 5 5 4 chr1 180000 chr1 180000 4 5 5 47 7 7 7 chr1 260000 chr1 260000 7 7 7 Started calculating Marginalized Contact Count chr start end index extraField mappable mid correct_index marginalizedContactCount 1 chr1 0 40000 1 0 1 20000 1 1 2 chr1 40000 80000 2 0 1 60000 2 0 3 chr1 80000 120000 3 0 1 100000 3 1 4 chr1 120000 160000 4 0 1 140000 4 3 5 chr1 160000 200000 5 0 1 180000 5 5 6 chr1 200000 240000 6 0 1 220000 6 0 Creating inputs for fithic run ctrl_no7_40000 Reading the bed and interaction matrix file A B C chr1 fragmentMid1 chr2 fragmentMid2 contactCount correct_A correct_B 1 1 5 1 chr1 20000 chr1 180000 1 1 5 5 3 8 1 chr1 100000 chr1 300000 1 3 8 25 5 5 2 chr1 180000 chr1 180000 2 5 5 65 7 7 2 chr1 260000 chr1 260000 2 7 7 91 8 8 1 chr1 300000 chr1 300000 1 8 8 105 13 13 1 chr1 500000 chr1 500000 1 13 13 Started calculating Marginalized Contact Count chr start end index extraField mappable mid correct_index marginalizedContactCount 1 chr1 0 40000 1 0 1 20000 1 1 2 chr1 40000 80000 2 0 1 60000 2 0 3 chr1 80000 120000 3 0 1 100000 3 1 4 chr1 120000 160000 4 0 1 140000 4 0 5 chr1 160000 200000 5 0 1 180000 5 3 6 chr1 200000 240000 6 0 1 220000 6 0 Creating inputs for fithic run MM_no2_40000 Reading the bed and interaction matrix file A B C chr1 fragmentMid1 chr2 fragmentMid2 contactCount correct_A correct_B 2 2 2 1 chr1 60000 chr1 60000 1 2 2 3 3 3 1 chr1 100000 chr1 100000 1 3 3 4 3 7 1 chr1 100000 chr1 260000 1 3 7 8 4 4 2 chr1 140000 chr1 140000 2 4 4 13 5 5 3 chr1 180000 chr1 180000 3 5 5 34 7 7 2 chr1 260000 chr1 260000 2 7 7 Started calculating Marginalized Contact Count chr start end index extraField mappable mid correct_index marginalizedContactCount 1 chr1 0 40000 1 0 1 20000 1 0 2 chr1 40000 80000 2 0 1 60000 2 1 3 chr1 80000 120000 3 0 1 100000 3 2 4 chr1 120000 160000 4 0 1 140000 4 2 5 chr1 160000 200000 5 0 1 180000 5 3 6 chr1 200000 240000 6 0 1 220000 6 0 Creating inputs for fithic run MM_no7_40000 Reading the bed and interaction matrix file A B C chr1 fragmentMid1 chr2 fragmentMid2 contactCount correct_A correct_B 16 4 4 2 chr1 140000 chr1 140000 2 4 4 17 4 7 1 chr1 140000 chr1 260000 1 4 7 18 4 14 1 chr1 140000 chr1 540000 1 4 14 33 5 5 1 chr1 180000 chr1 180000 1 5 5 62 7 8 1 chr1 260000 chr1 300000 1 7 8 81 8 8 1 chr1 300000 chr1 300000 1 8 8 Started calculating Marginalized Contact Count chr start end index extraField mappable mid correct_index marginalizedContactCount 1 chr1 0 40000 1 0 1 20000 1 0 2 chr1 40000 80000 2 0 1 60000 2 0 3 chr1 80000 120000 3 0 1 100000 3 0 4 chr1 120000 160000 4 0 1 140000 4 4 5 chr1 160000 200000 5 0 1 180000 5 1 6 chr1 200000 240000 6 0 1 220000 6 0 Fithic requires a bias file. Please check the link for more details https://github.com/ay-lab/fithic Please generate the bias files for each sample provided in the input.txt file Create an additional folder 'biases' under current path and dump all the *.biases.gz files inside it Rerun the step again Error in FUN(X[[i]], ...) : Exit! Calls: fithicformat -> lapply -> FUN Execution halted ❯ cd "${d_base}/${d_proj}/${d_infile}/DifferentialResult/${d_diff}/fithic_run" \ > || echo "cd'ing failed; check on this" ❯ unset exps && typeset -a exps ❯ while IFS=" " read -r -d $'\0'; do > exps+=( "${REPLY}" ) > done < <(find . -type d -name "*_${res}_*" -print0 | sort -z) ❯ for exp in "${exps[@]}"; do > if [[ ! -f "${exp}/biases.txt.gz" ]]; then > python "${a_HiCKRy}" \ > -i "${exp}/interactions.txt.gz" \ > -f "${exp}/fragments.txt.gz" \ > -o "${exp}/biases.txt.gz" > echo "" > fi > done Creating sparse matrix... Sparse matrix creation took 2.4459965229034424 seconds Removing 0.05 percent of most sparse bins ... corresponds to 3789 total rows ... corresponds to all bins with less than or equal to 0.0 total interactions Sparse rows removed Initial matrix size: 75788 rows and 75788 columns New matrix size: 69830 rows and 69830 columns Normalizing with KR Algorithm WARNING... Bias vector has a median outside of typical range (0.5, 2). Consider running with a larger -x option if problems occur Mean 0.8427719427877771 Median 1.1189124367583258e-09 Std. Dev. 253.6527985474652 Creating sparse matrix... Sparse matrix creation took 2.881424903869629 seconds Removing 0.05 percent of most sparse bins ... corresponds to 3789 total rows ... corresponds to all bins with less than or equal to 0.0 total interactions Sparse rows removed Initial matrix size: 75788 rows and 75788 columns New matrix size: 69849 rows and 69849 columns Normalizing with KR Algorithm WARNING... Bias vector has a median outside of typical range (0.5, 2). Consider running with a larger -x option if problems occur Mean 0.8432733414260832 Median 6.088974504995514e-09 Std. Dev. 253.72096755584406 Creating sparse matrix... Sparse matrix creation took 2.408437490463257 seconds Removing 0.05 percent of most sparse bins ... corresponds to 3789 total rows ... corresponds to all bins with less than or equal to 0.0 total interactions Sparse rows removed Initial matrix size: 75788 rows and 75788 columns New matrix size: 69713 rows and 69713 columns Normalizing with KR Algorithm WARNING... Bias vector has a median outside of typical range (0.5, 2). Consider running with a larger -x option if problems occur Mean 0.8396843827518868 Median 2.6012449355303677e-09 Std. Dev. 222.08428426294967 Creating sparse matrix... Sparse matrix creation took 2.08026385307312 seconds Removing 0.05 percent of most sparse bins ... corresponds to 3789 total rows ... corresponds to all bins with less than or equal to 0.0 total interactions Sparse rows removed Initial matrix size: 75788 rows and 75788 columns New matrix size: 69476 rows and 69476 columns Normalizing with KR Algorithm WARNING... Bias vector has a median outside of typical range (0.5, 2). Consider running with a larger -x option if problems occur Mean 0.8334300944740592 Median 6.174390743383673e-09 Std. Dev. 252.36695742918135 Creating sparse matrix... Sparse matrix creation took 1.707571268081665 seconds Removing 0.05 percent of most sparse bins ... corresponds to 3789 total rows ... corresponds to all bins with less than or equal to 0.0 total interactions Sparse rows removed Initial matrix size: 75788 rows and 75788 columns New matrix size: 69610 rows and 69610 columns Normalizing with KR Algorithm WARNING... Bias vector has a median outside of typical range (0.5, 2). Consider running with a larger -x option if problems occur Mean 0.836966274344223 Median 5.184835662519182e-09 Std. Dev. 252.85294611927932 Creating sparse matrix... Sparse matrix creation took 2.4464430809020996 seconds Removing 0.05 percent of most sparse bins ... corresponds to 3789 total rows ... corresponds to all bins with less than or equal to 0.0 total interactions Sparse rows removed Initial matrix size: 75788 rows and 75788 columns New matrix size: 69700 rows and 69700 columns Normalizing with KR Algorithm WARNING... Bias vector has a median outside of typical range (0.5, 2). Consider running with a larger -x option if problems occur Mean 0.8393413205256771 Median 9.560161685721065e-09 Std. Dev. 253.1804869412731 ❯ if [[ ! -d "${d_base}/${d_proj}/${d_infile}/biases" ]]; then > mkdir -p "${d_base}/${d_proj}/${d_infile}/biases" > fi mkdir: created directory '/home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases' ❯ for exp in "${exps[@]}"; do > string_1="${exp#./}" # echo "${string}" > string_2="${string_1%_fithic}" # echo "${string}" > > if [[ ! -f "${d_base}/${d_proj}/${d_infile}/biases/${string_2}.biases.gz" ]]; then > cp \ > "${string_1}/biases.txt.gz" \ > "${d_base}/${d_proj}/${d_infile}/biases/${string_2}.biases.gz" > fi > done 'ctrl_no2_40000_fithic/biases.txt.gz' -> '/home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/ctrl_no2_40000.biases.gz' 'ctrl_no7_40000_fithic/biases.txt.gz' -> '/home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/ctrl_no7_40000.biases.gz' 'D14_no2_40000_fithic/biases.txt.gz' -> '/home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/D14_no2_40000.biases.gz' 'D14_no7_40000_fithic/biases.txt.gz' -> '/home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/D14_no7_40000.biases.gz' 'MM_no2_40000_fithic/biases.txt.gz' -> '/home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/MM_no2_40000.biases.gz' 'MM_no7_40000_fithic/biases.txt.gz' -> '/home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/MM_no7_40000.biases.gz' ❯ check_directory=true ❯ if ${check_directory}; then > ls -lhaFG "${d_base}/${d_proj}/${d_infile}/biases" > echo "" > fi total 7.2M drwxrws--- 2 kalavatt 246 Dec 7 10:08 ./ drwxrws--- 11 kalavatt 1.3K Dec 7 10:08 ../ -rw-rw---- 1 kalavatt 828K Dec 7 10:08 ctrl_no2_40000.biases.gz -rw-rw---- 1 kalavatt 826K Dec 7 10:08 ctrl_no7_40000.biases.gz -rw-rw---- 1 kalavatt 826K Dec 7 10:08 D14_no2_40000.biases.gz -rw-rw---- 1 kalavatt 823K Dec 7 10:08 D14_no7_40000.biases.gz -rw-rw---- 1 kalavatt 818K Dec 7 10:08 MM_no2_40000.biases.gz -rw-rw---- 1 kalavatt 835K Dec 7 10:08 MM_no7_40000.biases.gz ❯ cd "${d_base}/${d_proj}/${d_infile}" \ > || echo "cd'ing failed; check on this" ❯ Rscript "${d_dcHiC}/dchicf.r" \ > --file "${f_infile}" \ > --pcatype fithic \ > --dirovwt T \ > --diffdir "diff_D14_ctrl_MM_${res}" \ > --fithicpath "${a_FitHiC}" \ > --pythonpath "python" Finding significant loops from intra sample D14 ctrl MM replicates [1] "folder exists" Fithic file already exists for D14_no2_40000 , skipping [1] "folder exists" Fithic file already exists for D14_no7_40000 , skipping [1] "folder exists" Fithic file already exists for ctrl_no2_40000 , skipping [1] "folder exists" Fithic file already exists for ctrl_no7_40000 , skipping [1] "folder exists" Fithic file already exists for MM_no2_40000 , skipping [1] "folder exists" Fithic file already exists for MM_no7_40000 , skipping python /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/src/fithic/fithic/fithic.py -i DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no2_40000_fithic/interactions.txt.gz -f DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no2_40000_fithic/fragments.txt.gz -t /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/D14_no2_40000.biases.gz -U 2000000 -o DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no2_40000_fithic/fithic_result -r 40000 GIVEN FIT-HI-C ARGUMENTS ========================= Reading fragments file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no2_40000_fithic/fragments.txt.gz Reading interactions file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no2_40000_fithic/interactions.txt.gz Output path created DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no2_40000_fithic/fithic_result Fixed size option detected... Fast version of FitHiC will be used Resolution is 40.0 kb Reading bias file from: /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/D14_no2_40000.biases.gz The number of spline passes is 1 The number of bins is 100 The number of reads required to consider an interaction is 1 The name of the library for outputted files will be FitHiC Upper Distance threshold is 2000000 Lower Distance threshold is 0 Only intra-chromosomal regions will be analyzed Lower bound of bias values is 0.5 Upper bound of bias values is 2 All arguments processed. Running FitHiC now... ========================= Reading the contact counts file to generate bins... Interactions file read. Time took 5.3157219886779785 Fragments file read. Time took 0.1039571762084961 Bias file read. Time took 0.2922706604003906 Writing DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no2_40000_fithic/fithic_result/FitHiC.fithic_pass1.res40000.txt Spline fit Pass 1 starting... Outlier threshold is... 1.418022154043717e-07 Writing p-values and q-values to file DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no2_40000_fithic/fithic_result/FitHiC.spline_pass1.significances.txt Number of outliers is... 0 Spline fit Pass 1 completed. Time took 21.363317251205444 ========================= Fit-Hi-C completed successfully python /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/src/fithic/fithic/fithic.py -i DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no7_40000_fithic/interactions.txt.gz -f DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no7_40000_fithic/fragments.txt.gz -t /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/D14_no7_40000.biases.gz -U 2000000 -o DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no7_40000_fithic/fithic_result -r 40000 GIVEN FIT-HI-C ARGUMENTS ========================= Reading fragments file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no7_40000_fithic/fragments.txt.gz Reading interactions file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no7_40000_fithic/interactions.txt.gz Output path created DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no7_40000_fithic/fithic_result Fixed size option detected... Fast version of FitHiC will be used Resolution is 40.0 kb Reading bias file from: /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/D14_no7_40000.biases.gz The number of spline passes is 1 The number of bins is 100 The number of reads required to consider an interaction is 1 The name of the library for outputted files will be FitHiC Upper Distance threshold is 2000000 Lower Distance threshold is 0 Only intra-chromosomal regions will be analyzed Lower bound of bias values is 0.5 Upper bound of bias values is 2 All arguments processed. Running FitHiC now... ========================= Reading the contact counts file to generate bins... Interactions file read. Time took 4.570132255554199 Fragments file read. Time took 0.12056660652160645 Bias file read. Time took 0.28597235679626465 Writing DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no7_40000_fithic/fithic_result/FitHiC.fithic_pass1.res40000.txt Spline fit Pass 1 starting... Outlier threshold is... 1.4228997501672618e-07 Writing p-values and q-values to file DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no7_40000_fithic/fithic_result/FitHiC.spline_pass1.significances.txt Number of outliers is... 0 Spline fit Pass 1 completed. Time took 17.940237760543823 ========================= Fit-Hi-C completed successfully python /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/src/fithic/fithic/fithic.py -i DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no2_40000_fithic/interactions.txt.gz -f DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no2_40000_fithic/fragments.txt.gz -t /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/ctrl_no2_40000.biases.gz -U 2000000 -o DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no2_40000_fithic/fithic_result -r 40000 GIVEN FIT-HI-C ARGUMENTS ========================= Reading fragments file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no2_40000_fithic/fragments.txt.gz Reading interactions file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no2_40000_fithic/interactions.txt.gz Output path created DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no2_40000_fithic/fithic_result Fixed size option detected... Fast version of FitHiC will be used Resolution is 40.0 kb Reading bias file from: /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/ctrl_no2_40000.biases.gz The number of spline passes is 1 The number of bins is 100 The number of reads required to consider an interaction is 1 The name of the library for outputted files will be FitHiC Upper Distance threshold is 2000000 Lower Distance threshold is 0 Only intra-chromosomal regions will be analyzed Lower bound of bias values is 0.5 Upper bound of bias values is 2 All arguments processed. Running FitHiC now... ========================= Reading the contact counts file to generate bins... Interactions file read. Time took 5.569983005523682 Fragments file read. Time took 0.11757349967956543 Bias file read. Time took 0.29406166076660156 Writing DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no2_40000_fithic/fithic_result/FitHiC.fithic_pass1.res40000.txt Spline fit Pass 1 starting... Outlier threshold is... 1.415626535070024e-07 Writing p-values and q-values to file DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no2_40000_fithic/fithic_result/FitHiC.spline_pass1.significances.txt Number of outliers is... 0 Spline fit Pass 1 completed. Time took 22.050061464309692 ========================= Fit-Hi-C completed successfully python /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/src/fithic/fithic/fithic.py -i DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no7_40000_fithic/interactions.txt.gz -f DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no7_40000_fithic/fragments.txt.gz -t /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/ctrl_no7_40000.biases.gz -U 2000000 -o DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no7_40000_fithic/fithic_result -r 40000 GIVEN FIT-HI-C ARGUMENTS ========================= Reading fragments file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no7_40000_fithic/fragments.txt.gz Reading interactions file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no7_40000_fithic/interactions.txt.gz Output path created DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no7_40000_fithic/fithic_result Fixed size option detected... Fast version of FitHiC will be used Resolution is 40.0 kb Reading bias file from: /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/ctrl_no7_40000.biases.gz The number of spline passes is 1 The number of bins is 100 The number of reads required to consider an interaction is 1 The name of the library for outputted files will be FitHiC Upper Distance threshold is 2000000 Lower Distance threshold is 0 Only intra-chromosomal regions will be analyzed Lower bound of bias values is 0.5 Upper bound of bias values is 2 All arguments processed. Running FitHiC now... ========================= Reading the contact counts file to generate bins... Interactions file read. Time took 6.58297324180603 Fragments file read. Time took 0.10645461082458496 Bias file read. Time took 0.29202890396118164 Writing DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no7_40000_fithic/fithic_result/FitHiC.fithic_pass1.res40000.txt Spline fit Pass 1 starting... Outlier threshold is... 1.4152382666841024e-07 Writing p-values and q-values to file DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/ctrl_no7_40000_fithic/fithic_result/FitHiC.spline_pass1.significances.txt Number of outliers is... 0 Spline fit Pass 1 completed. Time took 25.76362919807434 ========================= Fit-Hi-C completed successfully python /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/src/fithic/fithic/fithic.py -i DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no2_40000_fithic/interactions.txt.gz -f DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no2_40000_fithic/fragments.txt.gz -t /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/MM_no2_40000.biases.gz -U 2000000 -o DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no2_40000_fithic/fithic_result -r 40000 GIVEN FIT-HI-C ARGUMENTS ========================= Reading fragments file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no2_40000_fithic/fragments.txt.gz Reading interactions file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no2_40000_fithic/interactions.txt.gz Output path created DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no2_40000_fithic/fithic_result Fixed size option detected... Fast version of FitHiC will be used Resolution is 40.0 kb Reading bias file from: /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/MM_no2_40000.biases.gz The number of spline passes is 1 The number of bins is 100 The number of reads required to consider an interaction is 1 The name of the library for outputted files will be FitHiC Upper Distance threshold is 2000000 Lower Distance threshold is 0 Only intra-chromosomal regions will be analyzed Lower bound of bias values is 0.5 Upper bound of bias values is 2 All arguments processed. Running FitHiC now... ========================= Reading the contact counts file to generate bins... Interactions file read. Time took 3.753464698791504 Fragments file read. Time took 0.10889172554016113 Bias file read. Time took 0.2916555404663086 Writing DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no2_40000_fithic/fithic_result/FitHiC.fithic_pass1.res40000.txt Spline fit Pass 1 starting... Outlier threshold is... 1.4201378385786125e-07 Writing p-values and q-values to file DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no2_40000_fithic/fithic_result/FitHiC.spline_pass1.significances.txt Number of outliers is... 0 Spline fit Pass 1 completed. Time took 14.641690492630005 ========================= Fit-Hi-C completed successfully python /home/kalavatt/tsukiyamalab/kalavatt/2023_rDNA/src/fithic/fithic/fithic.py -i DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no7_40000_fithic/interactions.txt.gz -f DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no7_40000_fithic/fragments.txt.gz -t /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/MM_no7_40000.biases.gz -U 2000000 -o DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no7_40000_fithic/fithic_result -r 40000 GIVEN FIT-HI-C ARGUMENTS ========================= Reading fragments file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no7_40000_fithic/fragments.txt.gz Reading interactions file from: DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no7_40000_fithic/interactions.txt.gz Output path created DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no7_40000_fithic/fithic_result Fixed size option detected... Fast version of FitHiC will be used Resolution is 40.0 kb Reading bias file from: /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/09_dcHiC/biases/MM_no7_40000.biases.gz The number of spline passes is 1 The number of bins is 100 The number of reads required to consider an interaction is 1 The name of the library for outputted files will be FitHiC Upper Distance threshold is 2000000 Lower Distance threshold is 0 Only intra-chromosomal regions will be analyzed Lower bound of bias values is 0.5 Upper bound of bias values is 2 All arguments processed. Running FitHiC now... ========================= Reading the contact counts file to generate bins... Interactions file read. Time took 5.746699333190918 Fragments file read. Time took 0.10715699195861816 Bias file read. Time took 0.2898731231689453 Writing DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no7_40000_fithic/fithic_result/FitHiC.fithic_pass1.res40000.txt Spline fit Pass 1 starting... Outlier threshold is... 1.4182888345211502e-07 Writing p-values and q-values to file DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/MM_no7_40000_fithic/fithic_result/FitHiC.spline_pass1.significances.txt Number of outliers is... 0 Spline fit Pass 1 completed. Time took 22.723848819732666 ========================= Fit-Hi-C completed successfully [1] 1 Taking input= as a system command ('gzip -dc DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no2_40000_fithic/fithic_result/FitHiC.spline_pass1.res40000.significances.txt.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Taking input= as a system command ('gzip -dc DifferentialResult/diff_D14_ctrl_MM_40000/fithic_run/D14_no7_40000_fithic/fithic_result/FitHiC.spline_pass1.res40000.significances.txt.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message. Error in ids_sample[[i]] : subscript out of bounds Calls: fithicformat Execution halted ```The issue seems to occur after FitHiC successfully completes its analysis for each sample but fails during the subsequent processing stage. It appears to be related to the handling of sample IDs or indices in the script.
Any insights or guidance on how to resolve this issue would be greatly appreciated.