Description
Hello,
I am using modkit pileup to create a bedmethyl file for modified basecalling.
I basecalled with Dorado, afterwards I sorted the bam file.
However when using modkit, i get an empty bed file.
Output:
[src/logging.rs::54][2023-12-14 08:35:36][DEBUG] command line: modkit pileup vip_fam0_FAW14788_sorted.bam vip_fam0_FAW14788_cpg.bed --cpg --ref ./resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --only-tabs --log-filepath vip_fam0_FAW14788_modkit.log
[src/pileup/subcommand.rs::386][2023-12-14 08:35:36][INFO] calculated chunk size: 6, interval size 100000, processing 600000 positions concurrently
[src/pileup/subcommand.rs::493][2023-12-14 08:35:36][INFO] filtering to only CpG motifs
[src/command_utils.rs::67][2023-12-14 08:35:36][INFO] attempting to sample 10042 reads
[src/reads_sampler/mod.rs::41][2023-12-14 08:35:36][DEBUG] found BAM index, sampling reads in 1000000 base pair chunks
[src/reads_sampler/sampling_schedule.rs::127][2023-12-14 08:35:36][DEBUG] derived sampling schedule, sampling total 10179 reads from 191 contigs, 0 unmapped reads
[src/reads_sampler/sampling_schedule.rs::137][2023-12-14 08:35:36][DEBUG] schedule: SQ: 0, 1020 reads SQ: 1, 722 reads SQ: 3, 674 reads SQ: 2, 584 reads SQ: 4, 559 reads SQ: 5, 501 reads SQ: 6, 468 reads SQ: 9, 465 reads SQ: 8, 448 reads SQ: 7, 439 reads SQ: 12, 380 reads SQ: 11, 373 reads SQ: 10, 370 reads SQ: 15, 336 reads SQ: 14, 289 reads SQ: 16, 287 reads SQ: 23, 265 reads SQ: 17, 256 reads SQ: 13, 255 reads SQ: 19, 252 reads SQ: 22, 241 reads SQ: 20, 212 reads SQ: 18, 163 reads SQ: 21, 154 reads SQ: 96, 44 reads SQ: 45, 27 reads SQ: 170, 26 reads SQ: 59, 24 reads SQ: 192, 18 reads SQ: 28, 17 reads SQ: 132, 12 reads SQ: 55, 11 reads SQ: 62, 11 reads SQ: 53, 10 reads SQ: 176, 9 reads SQ: 190, 8 reads SQ: 171, 7 reads SQ: 60, 7 reads SQ: 91, 7 reads SQ: 191, 6 reads SQ: 37, 6 reads SQ: 183, 5 reads SQ: 44, 5 reads SQ: 94, 5 reads SQ: 175, 5 reads SQ: 36, 5 reads SQ: 47, 4 reads SQ: 25, 4 reads SQ: 56, 4 reads SQ: 173, 4 reads SQ: 31, 3 reads SQ: 57, 3 reads SQ: 186, 3 reads SQ: 52, 3 reads SQ: 193, 3 reads SQ: 54, 3 reads SQ: 137, 3 reads SQ: 168, 3 reads SQ: 41, 3 reads SQ: 189, 2 reads SQ: 50, 2 reads SQ: 136, 2 reads SQ: 179, 2 reads SQ: 95, 2 reads SQ: 181, 2 reads SQ: 169, 2 reads SQ: 35, 2 reads SQ: 188, 2 reads SQ: 61, 2 reads SQ: 104, 2 reads SQ: 92, 2 reads SQ: 63, 2 reads SQ: 180, 2 reads SQ: 46, 2 reads SQ: 182, 2 reads SQ: 122, 1 reads SQ: 177, 1 reads SQ: 110, 1 reads SQ: 43, 1 reads SQ: 165, 1 reads SQ: 98, 1 reads SQ: 86, 1 reads SQ: 141, 1 reads SQ: 74, 1 reads SQ: 129, 1 reads SQ: 117, 1 reads SQ: 172, 1 reads SQ: 105, 1 reads SQ: 38, 1 reads SQ: 160, 1 reads SQ: 93, 1 reads SQ: 26, 1 reads SQ: 148, 1 reads SQ: 81, 1 reads SQ: 69, 1 reads SQ: 124, 1 reads SQ: 112, 1 reads SQ: 167, 1 reads SQ: 100, 1 reads SQ: 33, 1 reads SQ: 155, 1 reads SQ: 88, 1 reads SQ: 143, 1 reads SQ: 76, 1 reads SQ: 131, 1 reads SQ: 64, 1 reads SQ: 119, 1 reads SQ: 174, 1 reads SQ: 107, 1 reads SQ: 40, 1 reads SQ: 162, 1 reads SQ: 150, 1 reads SQ: 83, 1 reads SQ: 138, 1 reads SQ: 71, 1 reads SQ: 126, 1 reads SQ: 114, 1 reads SQ: 102, 1 reads SQ: 157, 1 reads SQ: 90, 1 reads SQ: 145, 1 reads SQ: 78, 1 reads SQ: 133, 1 reads SQ: 66, 1 reads SQ: 121, 1 reads SQ: 109, 1 reads SQ: 42, 1 reads SQ: 164, 1 reads SQ: 97, 1 reads SQ: 30, 1 reads SQ: 152, 1 reads SQ: 85, 1 reads SQ: 140, 1 reads SQ: 73, 1 reads SQ: 128, 1 reads SQ: 116, 1 reads SQ: 49, 1 reads SQ: 159, 1 reads SQ: 147, 1 reads SQ: 80, 1 reads SQ: 135, 1 reads SQ: 68, 1 reads SQ: 123, 1 reads SQ: 178, 1 reads SQ: 111, 1 reads SQ: 166, 1 reads SQ: 99, 1 reads SQ: 32, 1 reads SQ: 154, 1 reads SQ: 87, 1 reads SQ: 142, 1 reads SQ: 75, 1 reads SQ: 130, 1 reads SQ: 185, 1 reads SQ: 118, 1 reads SQ: 51, 1 reads SQ: 106, 1 reads SQ: 39, 1 reads SQ: 161, 1 reads SQ: 27, 1 reads SQ: 149, 1 reads SQ: 82, 1 reads SQ: 70, 1 reads SQ: 125, 1 reads SQ: 58, 1 reads SQ: 101, 1 reads SQ: 34, 1 reads SQ: 156, 1 reads SQ: 89, 1 reads SQ: 144, 1 reads SQ: 77, 1 reads SQ: 65, 1 reads SQ: 187, 1 reads SQ: 120, 1 reads SQ: 108, 1 reads SQ: 163, 1 reads SQ: 29, 1 reads SQ: 151, 1 reads SQ: 84, 1 reads SQ: 139, 1 reads SQ: 72, 1 reads SQ: 127, 1 reads SQ: 115, 1 reads SQ: 48, 1 reads SQ: 103, 1 reads SQ: 158, 1 reads SQ: 24, 1 reads SQ: 146, 1 reads SQ: 79, 1 reads SQ: 134, 1 reads SQ: 67, 1 reads
[src/reads_sampler/mod.rs::110][2023-12-14 08:36:57][DEBUG] sampled 10979 records
[src/command_utils.rs::88][2023-12-14 08:36:57][DEBUG] estimated pass threshold 0.7246094 for primary sequence base C
[src/pileup/subcommand.rs::633][2023-12-14 08:36:57][INFO] Using filter threshold 0.7246094 for C.
[src/pileup/subcommand.rs::787][2023-12-14 08:36:57][INFO] Done, processed 0 rows. Processed ~0 reads and skipped zero reads.
can you help me? i am using version 0.2.0