[modkit-logging/src/lib.rs::69][2026-07-15 20:01:40][DEBUG] command line: /home/eric/.cargo/bin/modkit pileup TSC_GFP_W3MECP2_merged_aln.sorted.MAPQ10.primary.bam ONT_TSC.MAPQ10.primary.5mC_CpG_combined.bed --reference /home/Resource/Genome/hg38/hg38.fa --modified-bases 5mC --cpg --combine-strands --threads 32 --log-filepath log_ONT_TSC.MAPQ10.primary.5mC_CpG_combined.modkit.txt [modkit-core/src/util.rs::535][2026-07-15 20:01:41][INFO] discarded 0 contigs with zero aligned reads [modkit-core/src/pileup/subcommand.rs::608][2026-07-15 20:01:41][INFO] parsed 1 base modification(s). Base modifications other than 'C:m' will be counted as 'N_other'. [modkit-core/src/pileup/subcommand.rs::621][2026-07-15 20:01:41][DEBUG] using optimized CpG combine strands processor [modkit-core/src/pileup/subcommand.rs::1170][2026-07-15 20:01:41][DEBUG] using standard file writer [modkit-core/src/command_utils.rs::416][2026-07-15 20:01:41][DEBUG] combining + and - strand counts [modkit-core/src/interval_chunks.rs::378][2026-07-15 20:01:41][DEBUG] there is 25 reference record(s) [modkit-core/src/interval_chunks.rs::401][2026-07-15 20:01:41][DEBUG] there are 25 contig(s) to work on (25 parts) [modkit-core/src/sample_probs/mod.rs::1704][2026-07-15 20:01:41][INFO] attempting to sample at least 10042 reads [modkit-core/src/sample_probs/mod.rs::1743][2026-07-15 20:01:41][DEBUG] sample schedule for 10042 reads +--------+------------------------+---------------+-----------------------+------------------------+ | contig | num_reads_per_interval | contig_length | intervals_over_contig | total_reads_per_contig | +--------+------------------------+---------------+-----------------------+------------------------+ | chr1 | 5 | 248956422 | 248 | 1240 | | chr10 | 5 | 133797422 | 133 | 665 | | chr11 | 5 | 135086622 | 135 | 675 | | chr12 | 5 | 133275309 | 133 | 665 | | chr13 | 5 | 114364328 | 114 | 570 | | chr14 | 5 | 107043718 | 107 | 535 | | chr15 | 5 | 101991189 | 101 | 505 | | chr16 | 5 | 90338345 | 90 | 450 | | chr17 | 5 | 83257441 | 83 | 415 | | chr18 | 5 | 80373285 | 80 | 400 | | chr19 | 5 | 58617616 | 58 | 290 | | chr2 | 5 | 242193529 | 242 | 1210 | | chr20 | 5 | 64444167 | 64 | 320 | | chr21 | 5 | 46709983 | 46 | 230 | | chr22 | 5 | 50818468 | 50 | 250 | | chr3 | 5 | 198295559 | 198 | 990 | | chr4 | 5 | 190214555 | 190 | 950 | | chr5 | 5 | 181538259 | 181 | 905 | | chr6 | 5 | 170805979 | 170 | 850 | | chr7 | 5 | 159345973 | 159 | 795 | | chr8 | 5 | 145138636 | 145 | 725 | | chr9 | 5 | 138394717 | 138 | 690 | | chrM | 1 | 16569 | 1 | 1 | | chrX | 5 | 156040895 | 156 | 780 | | chrY | 5 | 57227415 | 57 | 285 | +--------+------------------------+---------------+-----------------------+------------------------+ [modkit-core/src/pileup/subcommand.rs::786][2026-07-15 20:01:41][INFO] calculating threshold value with probabilities aligned to reference bases cytosines [modkit-core/src/interval_chunks.rs::428][2026-07-15 20:03:11][DEBUG] feeder is done [modkit-core/src/sample_probs/mod.rs::627][2026-07-15 20:03:14][INFO] setting threshold 0.8496094 (qual: 217) for base C, percentile 10, 1471893 total probabilites [modkit-core/src/pileup/subcommand.rs::1263][2026-07-15 20:03:14][INFO] using optimized genome workers, combining strands at CpG motifs [modkit-core/src/interval_chunks.rs::378][2026-07-15 20:03:15][DEBUG] there is 25 reference record(s) [modkit-core/src/interval_chunks.rs::401][2026-07-15 20:03:15][DEBUG] there are 25 contig(s) to work on (25 parts) [modkit-core/src/fasta.rs::256][2026-07-15 20:03:15][DEBUG] end_idx (1999998) hits a motif.. end=9000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:03:15][DEBUG] moved end_idx to 2000002, end=9000002 ref_end=248956422, contig=chr1, range=8000000..9000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:03:15][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:03:32][DEBUG] end_idx (1999998) hits a motif.. end=203000002 [modkit-core/src/fasta.rs::262][2026-07-15 20:03:32][DEBUG] moved end_idx to 2000002, end=203000004 ref_end=248956422, contig=chr1, range=202000002..203000002 [modkit-core/src/fasta.rs::273][2026-07-15 20:03:32][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:03:32][DEBUG] end_idx (2000002) hits a motif.. end=203000004 [modkit-core/src/fasta.rs::262][2026-07-15 20:03:32][DEBUG] moved end_idx to 2000006, end=203000006 ref_end=248956422, contig=chr1, range=202000002..203000002 [modkit-core/src/fasta.rs::273][2026-07-15 20:03:32][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:04:06][DEBUG] end_idx (1999998) hits a motif.. end=124000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:04:06][DEBUG] moved end_idx to 2000002, end=124000002 ref_end=133797422, contig=chr10, range=123000000..124000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:04:06][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:04:15][DEBUG] end_idx (1999998) hits a motif.. end=61000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:04:15][DEBUG] moved end_idx to 2000002, end=61000002 ref_end=135086622, contig=chr11, range=60000000..61000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:04:15][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:04:28][DEBUG] end_idx (1999998) hits a motif.. end=27000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:04:28][DEBUG] moved end_idx to 2000002, end=27000002 ref_end=133275309, contig=chr12, range=26000000..27000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:04:28][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:04:40][DEBUG] end_idx (1999998) hits a motif.. end=132000002 [modkit-core/src/fasta.rs::262][2026-07-15 20:04:40][DEBUG] moved end_idx to 2000002, end=132000004 ref_end=133275309, contig=chr12, range=131000002..132000002 [modkit-core/src/fasta.rs::273][2026-07-15 20:04:40][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:04:49][DEBUG] end_idx (1999998) hits a motif.. end=76000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:04:49][DEBUG] moved end_idx to 2000002, end=76000002 ref_end=114364328, contig=chr13, range=75000000..76000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:04:49][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:05:15][DEBUG] end_idx (1999998) hits a motif.. end=22000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:05:15][DEBUG] moved end_idx to 2000002, end=22000002 ref_end=90338345, contig=chr16, range=21000000..22000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:05:15][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:05:18][DEBUG] end_idx (1999998) hits a motif.. end=32000002 [modkit-core/src/fasta.rs::262][2026-07-15 20:05:18][DEBUG] moved end_idx to 2000002, end=32000004 ref_end=90338345, contig=chr16, range=31000002..32000002 [modkit-core/src/fasta.rs::273][2026-07-15 20:05:18][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:05:24][DEBUG] end_idx (1999998) hits a motif.. end=89000004 [modkit-core/src/fasta.rs::262][2026-07-15 20:05:24][DEBUG] moved end_idx to 2000002, end=89000006 ref_end=90338345, contig=chr16, range=88000004..89000004 [modkit-core/src/fasta.rs::273][2026-07-15 20:05:24][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:05:50][DEBUG] end_idx (1999998) hits a motif.. end=11000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:05:50][DEBUG] moved end_idx to 2000002, end=11000002 ref_end=58617616, contig=chr19, range=10000000..11000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:05:50][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:05:53][DEBUG] end_idx (1999998) hits a motif.. end=42000002 [modkit-core/src/fasta.rs::262][2026-07-15 20:05:53][DEBUG] moved end_idx to 2000002, end=42000004 ref_end=58617616, contig=chr19, range=41000002..42000002 [modkit-core/src/fasta.rs::273][2026-07-15 20:05:53][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:06:05][DEBUG] end_idx (1999998) hits a motif.. end=69000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:06:05][DEBUG] moved end_idx to 2000002, end=69000002 ref_end=242193529, contig=chr2, range=68000000..69000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:06:05][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:06:33][DEBUG] end_idx (1999998) hits a motif.. end=59000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:06:33][DEBUG] moved end_idx to 2000002, end=59000002 ref_end=64444167, contig=chr20, range=58000000..59000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:06:33][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:07:02][DEBUG] end_idx (1999998) hits a motif.. end=75000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:07:02][DEBUG] moved end_idx to 2000002, end=75000002 ref_end=198295559, contig=chr3, range=74000000..75000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:07:02][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:07:06][DEBUG] end_idx (1999998) hits a motif.. end=127000002 [modkit-core/src/fasta.rs::262][2026-07-15 20:07:06][DEBUG] moved end_idx to 2000002, end=127000004 ref_end=198295559, contig=chr3, range=126000002..127000002 [modkit-core/src/fasta.rs::273][2026-07-15 20:07:06][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:07:09][DEBUG] end_idx (1999998) hits a motif.. end=137000004 [modkit-core/src/fasta.rs::262][2026-07-15 20:07:09][DEBUG] moved end_idx to 2000002, end=137000006 ref_end=198295559, contig=chr3, range=136000004..137000004 [modkit-core/src/fasta.rs::273][2026-07-15 20:07:09][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:07:11][DEBUG] end_idx (1999998) hits a motif.. end=164000006 [modkit-core/src/fasta.rs::262][2026-07-15 20:07:11][DEBUG] moved end_idx to 2000002, end=164000008 ref_end=198295559, contig=chr3, range=163000006..164000006 [modkit-core/src/fasta.rs::273][2026-07-15 20:07:11][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:07:49][DEBUG] end_idx (1999998) hits a motif.. end=68000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:07:49][DEBUG] moved end_idx to 2000002, end=68000002 ref_end=181538259, contig=chr5, range=67000000..68000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:07:49][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:07:59][DEBUG] end_idx (1999998) hits a motif.. end=160000002 [modkit-core/src/fasta.rs::262][2026-07-15 20:07:59][DEBUG] moved end_idx to 2000002, end=160000004 ref_end=181538259, contig=chr5, range=159000002..160000002 [modkit-core/src/fasta.rs::273][2026-07-15 20:07:59][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:08:05][DEBUG] end_idx (1999998) hits a motif.. end=26000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:08:05][DEBUG] moved end_idx to 2000002, end=26000002 ref_end=170805979, contig=chr6, range=25000000..26000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:08:05][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:08:43][DEBUG] end_idx (1999998) hits a motif.. end=157000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:08:43][DEBUG] moved end_idx to 2000002, end=157000002 ref_end=159345973, contig=chr7, range=156000000..157000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:08:43][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:08:59][DEBUG] end_idx (1999998) hits a motif.. end=114000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:08:59][DEBUG] moved end_idx to 2000002, end=114000002 ref_end=145138636, contig=chr8, range=113000000..114000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:08:59][DEBUG] re-check.. [modkit-core/src/fasta.rs::256][2026-07-15 20:09:14][DEBUG] end_idx (1999998) hits a motif.. end=124000000 [modkit-core/src/fasta.rs::262][2026-07-15 20:09:14][DEBUG] moved end_idx to 2000002, end=124000002 ref_end=138394717, contig=chr9, range=123000000..124000000 [modkit-core/src/fasta.rs::273][2026-07-15 20:09:14][DEBUG] re-check.. [modkit-core/src/interval_chunks.rs::428][2026-07-15 20:09:38][DEBUG] feeder is done [modkit-core/src/pileup/subcommand.rs::1642][2026-07-15 20:09:41][INFO] Done, processed 28049909 rows.