Request CpG methylation detection command
liuyang2006 opened this issue · 2 comments
liuyang2006 commented
Issue Report
My output is not CpG, all Cs have been reported. Not what I want.
Steps to reproduce the issue:
My script:
dorado basecaller hac,5mC_5hmC $indir/ \
-x auto --verbose \
--reference $ref \
--output-dir $outdir
Please list any steps to reproduce the issue.
As you can see in below IGV for BAM output, all Cs reported, but I only need CpG results, exclude non-CpG output. Thank you!
Logs
- Please provide output trace of dorado (run dorado with -v, or -vv on a small subset)
+ dorado basecaller hac,5mC_5hmC /project/sli68423_1316/users/yang/to_be_delete/guppy_test/pod5_five/ -x auto --verbose --reference /project/sli68423_1316/users/yang/reference/chm13v2.0/chm13v2.0.fa --output-dir /project/sli68423_1316/users/yang/to_be_delete/guppy_test/pod5_five_dorado_basecall
[2024-10-27 19:34:57.246] [info] Running: "basecaller" "hac,5mC_5hmC" "/project/sli68423_1316/users/yang/to_be_delete/guppy_test/pod5_five/" "-x" "auto" "--verbose" "--reference" "/project/sli68423_1316/users/yang/reference/chm13v2.0/chm13v2.0.fa" "--output-dir" "/project/sli68423_1316/users/yang/to_be_delete/guppy_test/pod5_five_dorado_basecall"
[2024-10-27 19:34:58.659] [info] Assuming cert location is /etc/ssl/certs/ca-bundle.crt
[2024-10-27 19:34:58.662] [info] - downloading dna_r10.4.1_e8.2_400bps_hac@v5.0.0 with httplib
[2024-10-27 19:34:59.193] [info] - downloading dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v2 with httplib
[2024-10-27 19:35:00.248] [info] Normalised: chunksize 10000 -> 9996
[2024-10-27 19:35:00.249] [info] Normalised: overlap 500 -> 498
[2024-10-27 19:35:00.249] [info] > Creating basecall pipeline
[2024-10-27 19:35:00.249] [debug] CRFModelConfig { qscale:1.050000 qbias:-0.600000 stride:6 bias:0 clamp:1 out_features:-1 state_len:4 outsize:1024 blank_score:2.000000 scale:1.000000 num_features:1 sample_rate:5000 sample_type:DNA mean_qscore_start_pos:60 SignalNormalisationParams { strategy:pa StandardisationScalingParams { standardise:1 mean:93.692398 stdev:23.506744}} BasecallerParams { chunk_size:9996 overlap:498 batch_size:0} convs: { 0: ConvParams { insize:1 size:16 winlen:5 stride:1 activation:swish} 1: ConvParams { insize:16 size:16 winlen:5 stride:1 activation:swish} 2: ConvParams { insize:16 size:384 winlen:19 stride:6 activation:tanh}} model_type: lstm { bias:0 outsize:1024 blank_score:2.000000 scale:1.000000}}
[2024-10-27 19:35:02.419] [debug] cuda:0 memory available: 33.52GB
[2024-10-27 19:35:02.419] [debug] cuda:0 memory limit 31.75GB
[2024-10-27 19:35:02.419] [debug] cuda:0 maximum safe estimated batch size at chunk size 9996 is 4736
[2024-10-27 19:35:02.419] [debug] cuda:0 maximum safe estimated batch size at chunk size 4998 is 9536
[2024-10-27 19:35:02.419] [debug] Auto batchsize cuda:0: testing up to 9536 in steps of 64
[2024-10-27 19:35:02.420] [info] Calculating optimized batch size for GPU "Tesla V100-PCIE-32GB" and model /project/sli68423_1316/users/yang/to_be_delete/guppy_test/.temp_dorado_model-473ee1b2a5b1658c/dna_r10.4.1_e8.2_400bps_hac@v5.0.0. Full benchmarking will run for this device, which may take some time.
[2024-10-27 19:35:02.838] [debug] Auto batchsize cuda:0: 64, time per chunk 2.297424 ms
[2024-10-27 19:35:03.162] [debug] Auto batchsize cuda:0: 128, time per chunk 1.160064 ms
[2024-10-27 19:35:03.476] [debug] Auto batchsize cuda:0: 192, time per chunk 0.779888 ms
[2024-10-27 19:35:03.811] [debug] Auto batchsize cuda:0: 256, time per chunk 0.641480 ms
[2024-10-27 19:35:04.141] [debug] Auto batchsize cuda:0: 320, time per chunk 0.470227 ms
[2024-10-27 19:35:04.470] [debug] Auto batchsize cuda:0: 384, time per chunk 0.392560 ms
[2024-10-27 19:35:04.801] [debug] Auto batchsize cuda:0: 448, time per chunk 0.336921 ms
[2024-10-27 19:35:05.132] [debug] Auto batchsize cuda:0: 512, time per chunk 0.295740 ms
[2024-10-27 19:35:05.465] [debug] Auto batchsize cuda:0: 576, time per chunk 0.265573 ms
[2024-10-27 19:35:05.797] [debug] Auto batchsize cuda:0: 640, time per chunk 0.237253 ms
[2024-10-27 19:35:06.131] [debug] Auto batchsize cuda:0: 704, time per chunk 0.217567 ms
[2024-10-27 19:35:06.465] [debug] Auto batchsize cuda:0: 768, time per chunk 0.197416 ms
[2024-10-27 19:35:06.798] [debug] Auto batchsize cuda:0: 832, time per chunk 0.183381 ms
[2024-10-27 19:35:07.105] [debug] Auto batchsize cuda:0: 896, time per chunk 0.169938 ms
[2024-10-27 19:35:07.440] [debug] Auto batchsize cuda:0: 960, time per chunk 0.159548 ms
[2024-10-27 19:35:07.776] [debug] Auto batchsize cuda:0: 1024, time per chunk 0.149868 ms
[2024-10-27 19:35:08.114] [debug] Auto batchsize cuda:0: 1088, time per chunk 0.142947 ms
[2024-10-27 19:35:08.451] [debug] Auto batchsize cuda:0: 1152, time per chunk 0.133771 ms
[2024-10-27 19:35:08.789] [debug] Auto batchsize cuda:0: 1216, time per chunk 0.126944 ms
[2024-10-27 19:35:09.128] [debug] Auto batchsize cuda:0: 1280, time per chunk 0.121820 ms
[2024-10-27 19:35:09.468] [debug] Auto batchsize cuda:0: 1344, time per chunk 0.115640 ms
[2024-10-27 19:35:09.809] [debug] Auto batchsize cuda:0: 1408, time per chunk 0.110585 ms
[2024-10-27 19:35:10.150] [debug] Auto batchsize cuda:0: 1472, time per chunk 0.106030 ms
[2024-10-27 19:35:10.492] [debug] Auto batchsize cuda:0: 1536, time per chunk 0.101767 ms
[2024-10-27 19:35:10.807] [debug] Auto batchsize cuda:0: 1600, time per chunk 0.097519 ms
[2024-10-27 19:35:11.150] [debug] Auto batchsize cuda:0: 1664, time per chunk 0.094273 ms
[2024-10-27 19:35:11.493] [debug] Auto batchsize cuda:0: 1728, time per chunk 0.090696 ms
[2024-10-27 19:35:11.836] [debug] Auto batchsize cuda:0: 1792, time per chunk 0.087653 ms
[2024-10-27 19:35:12.181] [debug] Auto batchsize cuda:0: 1856, time per chunk 0.084837 ms
[2024-10-27 19:35:12.527] [debug] Auto batchsize cuda:0: 1920, time per chunk 0.083036 ms
[2024-10-27 19:35:12.876] [debug] Auto batchsize cuda:0: 1984, time per chunk 0.080273 ms
[2024-10-27 19:35:13.225] [debug] Auto batchsize cuda:0: 2048, time per chunk 0.078479 ms
[2024-10-27 19:35:13.578] [debug] Auto batchsize cuda:0: 2112, time per chunk 0.076900 ms
[2024-10-27 19:35:13.932] [debug] Auto batchsize cuda:0: 2176, time per chunk 0.075844 ms
[2024-10-27 19:35:14.291] [debug] Auto batchsize cuda:0: 2240, time per chunk 0.075374 ms
[2024-10-27 19:35:14.652] [debug] Auto batchsize cuda:0: 2304, time per chunk 0.074257 ms
[2024-10-27 19:35:15.020] [debug] Auto batchsize cuda:0: 2368, time per chunk 0.074736 ms
[2024-10-27 19:35:15.396] [debug] Auto batchsize cuda:0: 2432, time per chunk 0.075905 ms
[2024-10-27 19:35:15.775] [debug] Auto batchsize cuda:0: 2496, time per chunk 0.075126 ms
[2024-10-27 19:35:16.155] [debug] Auto batchsize cuda:0: 2560, time per chunk 0.073611 ms
[2024-10-27 19:35:16.533] [debug] Auto batchsize cuda:0: 2624, time per chunk 0.071108 ms
[2024-10-27 19:35:16.913] [debug] Auto batchsize cuda:0: 2688, time per chunk 0.070045 ms
[2024-10-27 19:35:17.294] [debug] Auto batchsize cuda:0: 2752, time per chunk 0.068730 ms
[2024-10-27 19:35:17.678] [debug] Auto batchsize cuda:0: 2816, time per chunk 0.067252 ms
[2024-10-27 19:35:18.064] [debug] Auto batchsize cuda:0: 2880, time per chunk 0.065911 ms
[2024-10-27 19:35:18.454] [debug] Auto batchsize cuda:0: 2944, time per chunk 0.065125 ms
[2024-10-27 19:35:18.845] [debug] Auto batchsize cuda:0: 3008, time per chunk 0.063765 ms
[2024-10-27 19:35:19.239] [debug] Auto batchsize cuda:0: 3072, time per chunk 0.063104 ms
[2024-10-27 19:35:19.634] [debug] Auto batchsize cuda:0: 3136, time per chunk 0.061944 ms
[2024-10-27 19:35:20.033] [debug] Auto batchsize cuda:0: 3200, time per chunk 0.061225 ms
[2024-10-27 19:35:20.434] [debug] Auto batchsize cuda:0: 3264, time per chunk 0.060192 ms
[2024-10-27 19:35:20.837] [debug] Auto batchsize cuda:0: 3328, time per chunk 0.059494 ms
[2024-10-27 19:35:21.259] [debug] Auto batchsize cuda:0: 3392, time per chunk 0.061098 ms
[2024-10-27 19:35:21.768] [debug] Auto batchsize cuda:0: 3456, time per chunk 0.072215 ms
[2024-10-27 19:35:22.278] [debug] Auto batchsize cuda:0: 3520, time per chunk 0.071341 ms
[2024-10-27 19:35:22.792] [debug] Auto batchsize cuda:0: 3584, time per chunk 0.070591 ms
[2024-10-27 19:35:23.311] [debug] Auto batchsize cuda:0: 3648, time per chunk 0.069965 ms
[2024-10-27 19:35:23.835] [debug] Auto batchsize cuda:0: 3712, time per chunk 0.069383 ms
[2024-10-27 19:35:24.369] [debug] Auto batchsize cuda:0: 3776, time per chunk 0.069501 ms
[2024-10-27 19:35:24.914] [debug] Auto batchsize cuda:0: 3840, time per chunk 0.069950 ms
[2024-10-27 19:35:25.463] [debug] Auto batchsize cuda:0: 3904, time per chunk 0.069370 ms
[2024-10-27 19:35:26.022] [debug] Auto batchsize cuda:0: 3968, time per chunk 0.069239 ms
[2024-10-27 19:35:26.590] [debug] Auto batchsize cuda:0: 4032, time per chunk 0.069395 ms
[2024-10-27 19:35:27.165] [debug] Auto batchsize cuda:0: 4096, time per chunk 0.069214 ms
[2024-10-27 19:35:27.743] [debug] Auto batchsize cuda:0: 4160, time per chunk 0.068361 ms
[2024-10-27 19:35:28.323] [debug] Auto batchsize cuda:0: 4224, time per chunk 0.067669 ms
[2024-10-27 19:35:28.897] [debug] Auto batchsize cuda:0: 4288, time per chunk 0.065895 ms
[2024-10-27 19:35:29.475] [debug] Auto batchsize cuda:0: 4352, time per chunk 0.065328 ms
[2024-10-27 19:35:30.054] [debug] Auto batchsize cuda:0: 4416, time per chunk 0.064525 ms
[2024-10-27 19:35:30.642] [debug] Auto batchsize cuda:0: 4480, time per chunk 0.063759 ms
[2024-10-27 19:35:31.227] [debug] Auto batchsize cuda:0: 4544, time per chunk 0.063254 ms
[2024-10-27 19:35:31.816] [debug] Auto batchsize cuda:0: 4608, time per chunk 0.063149 ms
[2024-10-27 19:35:32.420] [debug] Auto batchsize cuda:0: 4672, time per chunk 0.063581 ms
[2024-10-27 19:35:33.029] [debug] Auto batchsize cuda:0: 4736, time per chunk 0.062994 ms
[2024-10-27 19:35:33.641] [debug] Auto batchsize cuda:0: 4800, time per chunk 0.062656 ms
[2024-10-27 19:35:34.255] [debug] Auto batchsize cuda:0: 4864, time per chunk 0.062111 ms
[2024-10-27 19:35:34.873] [debug] Auto batchsize cuda:0: 4928, time per chunk 0.061821 ms
[2024-10-27 19:35:35.496] [debug] Auto batchsize cuda:0: 4992, time per chunk 0.061505 ms
[2024-10-27 19:35:36.107] [debug] Auto batchsize cuda:0: 5056, time per chunk 0.059114 ms
[2024-10-27 19:35:36.720] [debug] Auto batchsize cuda:0: 5120, time per chunk 0.058786 ms
[2024-10-27 19:35:37.440] [debug] Auto batchsize cuda:0: 5184, time per chunk 0.067836 ms
[2024-10-27 19:35:38.156] [debug] Auto batchsize cuda:0: 5248, time per chunk 0.067001 ms
[2024-10-27 19:35:38.878] [debug] Auto batchsize cuda:0: 5312, time per chunk 0.067148 ms
[2024-10-27 19:35:39.606] [debug] Auto batchsize cuda:0: 5376, time per chunk 0.066893 ms
[2024-10-27 19:35:40.336] [debug] Auto batchsize cuda:0: 5440, time per chunk 0.065901 ms
[2024-10-27 19:35:41.074] [debug] Auto batchsize cuda:0: 5504, time per chunk 0.065914 ms
[2024-10-27 19:35:41.823] [debug] Auto batchsize cuda:0: 5568, time per chunk 0.066344 ms
[2024-10-27 19:35:42.578] [debug] Auto batchsize cuda:0: 5632, time per chunk 0.066077 ms
[2024-10-27 19:35:43.344] [debug] Auto batchsize cuda:0: 5696, time per chunk 0.066490 ms
[2024-10-27 19:35:44.117] [debug] Auto batchsize cuda:0: 5760, time per chunk 0.066478 ms
[2024-10-27 19:35:44.897] [debug] Auto batchsize cuda:0: 5824, time per chunk 0.066013 ms
[2024-10-27 19:35:45.685] [debug] Auto batchsize cuda:0: 5888, time per chunk 0.065431 ms
[2024-10-27 19:35:46.470] [debug] Auto batchsize cuda:0: 5952, time per chunk 0.064813 ms
[2024-10-27 19:35:47.254] [debug] Auto batchsize cuda:0: 6016, time per chunk 0.064097 ms
[2024-10-27 19:35:48.044] [debug] Auto batchsize cuda:0: 6080, time per chunk 0.063895 ms
[2024-10-27 19:35:48.836] [debug] Auto batchsize cuda:0: 6144, time per chunk 0.063595 ms
[2024-10-27 19:35:49.633] [debug] Auto batchsize cuda:0: 6208, time per chunk 0.063137 ms
[2024-10-27 19:35:50.431] [debug] Auto batchsize cuda:0: 6272, time per chunk 0.062600 ms
[2024-10-27 19:35:51.235] [debug] Auto batchsize cuda:0: 6336, time per chunk 0.062624 ms
[2024-10-27 19:35:52.045] [debug] Auto batchsize cuda:0: 6400, time per chunk 0.062327 ms
[2024-10-27 19:35:52.857] [debug] Auto batchsize cuda:0: 6464, time per chunk 0.061893 ms
[2024-10-27 19:35:53.679] [debug] Auto batchsize cuda:0: 6528, time per chunk 0.061618 ms
[2024-10-27 19:35:54.485] [debug] Auto batchsize cuda:0: 6592, time per chunk 0.059492 ms
[2024-10-27 19:35:55.297] [debug] Auto batchsize cuda:0: 6656, time per chunk 0.059199 ms
[2024-10-27 19:35:56.104] [debug] Auto batchsize cuda:0: 6720, time per chunk 0.058794 ms
[2024-10-27 19:35:56.919] [debug] Auto batchsize cuda:0: 6784, time per chunk 0.058868 ms
[2024-10-27 19:35:57.831] [debug] Auto batchsize cuda:0: 6848, time per chunk 0.065547 ms
[2024-10-27 19:35:58.749] [debug] Auto batchsize cuda:0: 6912, time per chunk 0.065309 ms
[2024-10-27 19:35:59.668] [debug] Auto batchsize cuda:0: 6976, time per chunk 0.064794 ms
[2024-10-27 19:36:00.591] [debug] Auto batchsize cuda:0: 7040, time per chunk 0.064532 ms
[2024-10-27 19:36:01.515] [debug] Auto batchsize cuda:0: 7104, time per chunk 0.063972 ms
[2024-10-27 19:36:02.445] [debug] Auto batchsize cuda:0: 7168, time per chunk 0.063910 ms
[2024-10-27 19:36:03.385] [debug] Auto batchsize cuda:0: 7232, time per chunk 0.064019 ms
[2024-10-27 19:36:04.343] [debug] Auto batchsize cuda:0: 7296, time per chunk 0.064010 ms
[2024-10-27 19:36:05.308] [debug] Auto batchsize cuda:0: 7360, time per chunk 0.064038 ms
[2024-10-27 19:36:06.273] [debug] Auto batchsize cuda:0: 7424, time per chunk 0.063857 ms
[2024-10-27 19:36:07.241] [debug] Auto batchsize cuda:0: 7488, time per chunk 0.063741 ms
[2024-10-27 19:36:08.216] [debug] Auto batchsize cuda:0: 7552, time per chunk 0.063754 ms
[2024-10-27 19:36:09.218] [debug] Auto batchsize cuda:0: 7616, time per chunk 0.063768 ms
[2024-10-27 19:36:10.202] [debug] Auto batchsize cuda:0: 7680, time per chunk 0.063149 ms
[2024-10-27 19:36:11.193] [debug] Auto batchsize cuda:0: 7744, time per chunk 0.062954 ms
[2024-10-27 19:36:12.187] [debug] Auto batchsize cuda:0: 7808, time per chunk 0.062194 ms
[2024-10-27 19:36:13.167] [debug] Auto batchsize cuda:0: 7872, time per chunk 0.061556 ms
[2024-10-27 19:36:14.151] [debug] Auto batchsize cuda:0: 7936, time per chunk 0.061223 ms
[2024-10-27 19:36:15.141] [debug] Auto batchsize cuda:0: 8000, time per chunk 0.061048 ms
[2024-10-27 19:36:16.133] [debug] Auto batchsize cuda:0: 8064, time per chunk 0.060844 ms
[2024-10-27 19:36:17.137] [debug] Auto batchsize cuda:0: 8128, time per chunk 0.060486 ms
[2024-10-27 19:36:18.144] [debug] Auto batchsize cuda:0: 8192, time per chunk 0.060653 ms
[2024-10-27 19:36:19.140] [debug] Auto batchsize cuda:0: 8256, time per chunk 0.059257 ms
[2024-10-27 19:36:20.150] [debug] Auto batchsize cuda:0: 8320, time per chunk 0.059418 ms
[2024-10-27 19:36:21.160] [debug] Auto batchsize cuda:0: 8384, time per chunk 0.059405 ms
[2024-10-27 19:36:22.167] [debug] Auto batchsize cuda:0: 8448, time per chunk 0.058754 ms
[2024-10-27 19:36:23.215] [debug] Auto batchsize cuda:0: 8512, time per chunk 0.060786 ms
[2024-10-27 19:36:24.334] [debug] Auto batchsize cuda:0: 8576, time per chunk 0.064380 ms
[2024-10-27 19:36:25.458] [debug] Auto batchsize cuda:0: 8640, time per chunk 0.063734 ms
[2024-10-27 19:36:26.586] [debug] Auto batchsize cuda:0: 8704, time per chunk 0.063495 ms
[2024-10-27 19:36:27.717] [debug] Auto batchsize cuda:0: 8768, time per chunk 0.063582 ms
[2024-10-27 19:36:28.854] [debug] Auto batchsize cuda:0: 8832, time per chunk 0.062819 ms
[2024-10-27 19:36:29.990] [debug] Auto batchsize cuda:0: 8896, time per chunk 0.062924 ms
[2024-10-27 19:36:31.135] [debug] Auto batchsize cuda:0: 8960, time per chunk 0.063036 ms
[2024-10-27 19:36:32.291] [debug] Auto batchsize cuda:0: 9024, time per chunk 0.062755 ms
[2024-10-27 19:36:33.454] [debug] Auto batchsize cuda:0: 9088, time per chunk 0.062941 ms
[2024-10-27 19:36:34.638] [debug] Auto batchsize cuda:0: 9152, time per chunk 0.063390 ms
[2024-10-27 19:36:35.820] [debug] Auto batchsize cuda:0: 9216, time per chunk 0.062932 ms
[2024-10-27 19:36:37.006] [debug] Auto batchsize cuda:0: 9280, time per chunk 0.062997 ms
[2024-10-27 19:36:38.198] [debug] Auto batchsize cuda:0: 9344, time per chunk 0.062921 ms
[2024-10-27 19:36:39.375] [debug] Auto batchsize cuda:0: 9408, time per chunk 0.062015 ms
[2024-10-27 19:36:40.566] [debug] Auto batchsize cuda:0: 9472, time per chunk 0.061333 ms
[2024-10-27 19:36:41.753] [debug] Auto batchsize cuda:0: 9536, time per chunk 0.061180 ms
[2024-10-27 19:36:41.753] [debug] Adding chunk timings to internal cache for GPU Tesla V100-PCIE-32GB, model /project/sli68423_1316/users/yang/to_be_delete/guppy_test/.temp_dorado_model-473ee1b2a5b1658c/dna_r10.4.1_e8.2_400bps_hac@v5.0.0 (52 entries)
[2024-10-27 19:36:41.753] [debug] Largest batch size for cuda:0: 8448, time per chunk 0.058754 ms
[2024-10-27 19:36:41.753] [debug] Final batch size for cuda:0[0]: 3328
[2024-10-27 19:36:41.753] [debug] Final batch size for cuda:0[1]: 8448
[2024-10-27 19:36:41.753] [info] cuda:0 using chunk size 9996, batch size 3328
[2024-10-27 19:36:41.753] [debug] cuda:0 Model memory 15.61GB
[2024-10-27 19:36:41.753] [debug] cuda:0 Decode memory 6.44GB
[2024-10-27 19:36:43.138] [info] cuda:0 using chunk size 4998, batch size 8448
[2024-10-27 19:36:43.138] [debug] cuda:0 Model memory 19.82GB
[2024-10-27 19:36:43.138] [debug] cuda:0 Decode memory 8.18GB
[2024-10-27 19:38:45.747] [debug] Loaded index with 25 target seqs
[2024-10-27 19:38:52.492] [debug] BasecallerNode chunk size 9996
[2024-10-27 19:38:52.492] [debug] BasecallerNode chunk size 4998
[2024-10-27 19:38:52.546] [debug] Load reads from file /project/sli68423_1316/users/yang/to_be_delete/guppy_test/pod5_five/PAO20051_pass_f9438981_ac3ed4cb_1000.pod5
[2024-10-27 19:38:55.413] [debug] Load reads from file /project/sli68423_1316/users/yang/to_be_delete/guppy_test/pod5_five/PAO20051_pass_f9438981_ac3ed4cb_1001.pod5
[2024-10-27 19:39:22.526] [debug] Load reads from file /project/sli68423_1316/users/yang/to_be_delete/guppy_test/pod5_five/PAO20051_pass_f9438981_ac3ed4cb_1003.pod5
[2024-10-27 19:40:03.012] [debug] Load reads from file /project/sli68423_1316/users/yang/to_be_delete/guppy_test/pod5_five/PAO20051_pass_f9438981_ac3ed4cb_0.pod5
[2024-10-27 19:40:31.885] [debug] Load reads from file /project/sli68423_1316/users/yang/to_be_delete/guppy_test/pod5_five/PAO20051_pass_f9438981_ac3ed4cb_1002.pod5
[2024-10-27 19:49:35.184] [info] > Simplex reads basecalled: 19999
[2024-10-27 19:49:35.184] [info] > Simplex reads filtered: 1
[2024-10-27 19:49:35.184] [info] > Basecalled @ Samples/s: 2.296586e+06
[2024-10-27 19:49:35.185] [debug] > Including Padding @ Samples/s: 2.693e+06 (85.27%)
[2024-10-27 19:49:35.880] [info] > Finished
HalfPhoton commented
Hi @liuyang2006,
Use the CG context model - hac,5mC_5hmC
-> hac,5mCG_5hmCG
liuyang2006 commented
Thank you!