./dorado-0.9.1-linux-x64/bin/dorado basecaller sup,4mC_5mC,6mA /mnt/d/SCRACH/pod5/FAX50596_f8847863_ffa87fb4_0.pod5 > calls_0.bam
we ignore 5hmC like this seems either that or 4mc 5mc to try later TODO
[2025-01-29 21:41:05.187] [info] cuda:0 using chunk size 12288, batch size 32
[2025-01-29 21:41:06.016] [info] cuda:0 using chunk size 6144, batch size 32
[2025-01-29 22:35:45.017] [info] > Finished in (ms): 3277831
[2025-01-29 22:35:45.020] [info] > Simplex reads basecalled: 27888
[2025-01-29 22:35:45.020] [info] > Simplex reads filtered: 47
[2025-01-29 22:35:45.020] [info] > Basecalled @ Samples/s: 3.543277e+05
[2025-01-29 22:35:45.218] [info] > Finished
samtools fastq -T "*" calls_0.bam > calls_0.fq
okidoki
seqtk seq -L 1000 calls_0.fq > calls_0_lt_1000.fq
seqkit seq calls_0.fq -m 100 -Q 10 > calls_0_m1000_q10.fq
hifiasm --ont calls_0_lt_1000.fq -t 4 -o TP1
AHHH FCKKKKK
./dorado-0.9.1-linux-x64/bin/dorado basecaller sup,4mC_5mC,6mA /mnt/d/SCRACH/pod5/FAX50596_f8847863_ffa87fb4_1.pod5 > calls_1.bam
[2025-01-30 10:46:04.046] [info] cuda:0 using chunk size 12288, batch size 32
[2025-01-30 10:46:04.227] [info] cuda:0 using chunk size 6144, batch size 32
[2025-01-30 11:44:54.389] [info] > Finished in (ms): 3529976
[2025-01-30 11:44:54.390] [info] > Simplex reads basecalled: 28654
[2025-01-30 11:44:54.390] [info] > Simplex reads filtered: 26
[2025-01-30 11:44:54.390] [info] > Basecalled @ Samples/s: 7.162525e+05
[2025-01-30 11:44:54.471] [info] > Finished
samtools fastq -T "*" calls_1.bam > calls_1.fq
seqkit seq calls_1.fq -m 100 -Q 14 > calls_1_m100_q14.fq
./dorado-0.9.1-linux-x64/bin/dorado basecaller sup,4mC_5mC,6mA /mnt/d/SCRACH/pod5/FAX50596_f8847863_ffa87fb4_2.pod5 > calls_2.bam
[2025-01-30 11:55:41.027] [info] cuda:0 using chunk size 12288, batch size 32
[2025-01-30 11:55:41.207] [info] cuda:0 using chunk size 6144, batch size 32
[2025-01-30 12:31:59.371] [info] > Finished in (ms): 2177985
[2025-01-30 12:31:59.372] [info] > Simplex reads basecalled: 29075
[2025-01-30 12:31:59.372] [info] > Simplex reads filtered: 27
[2025-01-30 12:31:59.373] [info] > Basecalled @ Samples/s: 8.801333e+05
[2025-01-30 12:31:59.489] [info] > Finished
some broken pods ./dorado-0.9.1-linux-x64/bin/dorado basecaller sup,4mC_5mC,6mA /mnt/d/SCRACH/Alderaan/20241001_1934_MN19744_FAX48832_c7793116/pod5/FAX48832_c7793116_9c6879b9_9.pod5 > calls_ALDERAAN_9.bam