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fiberseq / fibertools-rs

Tools for fiberseq data written in rust.
https://fiberseq.github.io/fibertools/fibertools.html
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Can't run predict-m6a on ONT data #51

Closed connorhorton closed 5 months ago

connorhorton commented 5 months ago

I'm running predict-m6a and getting the following error:

(base) connor@Connors-MacBook-Pro fiberseq % ft predict-m6a -m 225 -vvv sample.bam m6a.out
[2024-05-27T19:12:57Z DEBUG ft] DEBUG logging enabled
[2024-05-27T19:12:57Z TRACE ft] TRACE logging enabled
[2024-05-27T19:12:57Z DEBUG ft] Using 8 threads.
[2024-05-27T19:12:57Z INFO  ft] Starting ft-predict-m6a
[2024-05-27T19:12:57Z TRACE bio_io] last program samtools
[2024-05-27T19:12:57Z TRACE bio_io] "@HD\tVN:1.6\tSO:unknown\n@PG\tID:basecaller\tPN:dorado\tVN:0.3.1+bb8c5ee\tCL:dorado basecaller /private/groups/migalab/iviolich/dorado_runs/models/dna_r10.4.1_e8.2_400bps_sup@v4.2.0 /data/scratch/iviolich//07_05_23_R1041_FiberSeq/input/07_05_23_R1041_FiberSeq/pod5_dir --modified-bases 6mA\n@PG\tID:samtools\tPN:samtools\tPP:basecaller\tVN:1.19.2\tCL:samtools view -h 07_05_23_R1041_FiberSeq_dorado_v0.3.0_R1041_sup4.2.0_6mA.bam\n@RG\tID:4d2d92f7d540c50a0a45341f561cac836e1eaaaf_dna_r10.4.1_e8.2_400bps_sup@v4.2.0\tPU:PAO26846\tPM:PC48B200\tDT:2023-07-05T23:08:51.339+00:00\tPL:ONT\tDS:basecall_model=dna_r10.4.1_e8.2_400bps_sup@v4.2.0 runid=4d2d92f7d540c50a0a45341f561cac836e1eaaaf\tLB:07_05_23_R1041_FiberSeq\tSM:07_05_23_R1041_FiberSeq\n@PG\tID:ft.1\tPN:fibertools-rs\tPP:samtools\tVN:0.3.2\tCL:ft predict-m6a -m 225 -vvv sample.bam m6a.out"
thread 'main' panicked at 'assertion failed: `(left == right)`
  left: `""`,
 right: `"CCS"`', bio-io/src/lib.rs:291:5
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

It seems like fibertools is expecting CCS data? However I can run add-nucleosomes and I don't get any errors.

sam file to reproduce error below:

@HD VN:1.6  SO:unknown
@PG ID:basecaller   PN:dorado   VN:0.3.1+bb8c5ee    CL:dorado basecaller /private/groups/migalab/iviolich/dorado_runs/models/dna_r10.4.1_e8.2_400bps_sup@v4.2.0 /data/scratch/iviolich//07_05_23_R1041_FiberSeq/input/07_05_23_R1041_FiberSeq/pod5_dir --modified-bases 6mA
@PG ID:samtools PN:samtools PP:basecaller   VN:1.19.2   CL:samtools view -h 07_05_23_R1041_FiberSeq_dorado_v0.3.0_R1041_sup4.2.0_6mA.bam
@RG ID:4d2d92f7d540c50a0a45341f561cac836e1eaaaf_dna_r10.4.1_e8.2_400bps_sup@v4.2.0  PU:PAO26846 PM:PC48B200 DT:2023-07-05T23:08:51.339+00:00    PL:ONT  DS:basecall_model=dna_r10.4.1_e8.2_400bps_sup@v4.2.0 runid=4d2d92f7d540c50a0a45341f561cac836e1eaaaf LB:07_05_23_R1041_FiberSeq  SM:07_05_23_R1041_FiberSeq
0e059548-4cd3-418d-9e74-90fe88ee06bf    4   *   0   0   *   *   0   0   TTTCTGTAACACTGGTTTTGGATTCAATTTAACCATTTCACATTTATAATGAAAAGTGTTTCACGTTTTCGTGCGCCGCTCACGCAAAGTTCTCATCAAAGAGCCATCACAGACTCTATGAACTACAGCCTAGGAGTCATCGACCAAATGATATACCTTTATGATTCCCTAATTATCATCTATTATTATCACAGCAGAAACAAACAAAGCACACACTGATGGGAATATAATAAAAAGAAAGAAAAAATTCTTATAATCAAAAAGTTATCAAAAATAGAATAATAGATTAACATTGACTGAACTTGCAAAAAGACTATCAGATTCTTATAGAGAGTTAAAAGGCTAGCTGAAAGATCAGGTAAGTCTAGCCCTGTGTTGGGCATTGGATCGTCCACCACTCACTCATGAGCTCCAAAAGGTGGAGCTAATAGATTATTTCGAAGGGCTGAGACATTGGATTCGTTCAGCAAGAGAACAATTTTCTACGAGGTTCGACTGTGTGCTGTGGTGGAACGACGAGGTCCCCAAAGAGCCTTAGGTTTCATGATTCCGGTTGAGTGTTTCCTTGAATTCAGATTTGATAGTAATAGGAATGCGTAATGAAAATACACTCAAACTTCAACAATTCCGACCTAAACTTACAAGTTCTTGAAAAAAGATCTCGTTGAATACACAGGACATGAATTTTATCACTTTAACCATTCATGTGTCCAGTTAAGATGGCGTCGAGTATATTCACAATGTTGTGGACCATTACCACCATCCATCTTCCAACTTTTCATCATTTTGCAGGCCCTTGATTGCCCGATGACGATCGCTTCCCATTTCCCCCTCTACCCGGCCCTCAACACCTTTGTTTCCATTTCTGTGCATTGACTGCTTCATGTGCTGTAAGTGGAATCATGTGTGCCTTTTGTGGGTTTGGCTGTTTCCTTTGGTGCTGTGTTTAAGTCCATCCAGTCTGTCACATGTGAGAATTTCGTTCCTTTAGGGTTTTGAAGTAGCTCCATTGTGGGTGTGGATGTCCACATTTGTTTGTTCCTTTGGTCGATGGATGGTTCATCTTTTGCACCATTTGGCAAAGACTGCTTGAACCAATCCCCACAGCGAGATTCGGCTCAGTTTCAAACTCAGCACCCTGCCAGCTGTAAGAAGGATGGATGTAAGCACTCATCATCTTCTAGATGCCCTGGGAGTTGGAGTGAACCATGCATATGTTTTCAGGCTGGATAGGACCATGAATCTATAAGCCTCCAGGCCCAGGCCATGTCCTGATGCCTTGGAGGTGGGTAGAGAAAAAGCACACTTATCAATCTCAAAACAATGTTCCACCGACCATCATCCACCACCACAGCAGACTGTGCTCTTCTGTTGTATTTTTTTCCTATCGATTCTTTCAGCAGAGGCTTTCTTCACTGAAAAATACATTAATTCTTTAAAAATAGCCTCAAGGACAATAACTTCTTAGAAGTTAGGATACATAGCGGCTCATTGACTTCTCCTGTTGTATTTTTGGATCCTATCCATCCTTTCCTGGTGTGGTCACACAGTCCAGAAAGGACATAACAAAAGCCCCCACGCTCCAGGCACAATGAGACATAGCATCCCCTTTCCTCTGCTAACACCTGTTTGATTTTTTGAAAAATGACTATAAATCCTCTCACTTCCTTCTTATAGAAGGAGAAAATAGATTTTTTTCACTTGGTTTCCAAAAATATGTTGGTTCTGACATATTTTTTCTTGATTATGGCTTCACCATCATGGCACCATGATGACTTGCTTCAAGAGCCCAAGACATAGTGAGATACTAAGGCATATGATCCCCAAGGCTTCTCTACAACTTCCTAAGTGTATCATTACCTCTACATGTAGAGTGCTTGTCTTCTGTTCCAGTGTTCTTACTCCACTGCATCTGCTTCTCTTTTCACCTGTTTCTGTGCTAAGGTTTAGACTTGCTGCCTCCTGGTGCCCTCAGCTTGCCATGGGATCCACATCCCCAGCAGCCAGCTAGGAGTTGACAAGGATTGTGCAAACTAACACCCTGCAAATTATCATTTCATTCTTACCATTTTGTACAGATCTAGAATATAAATCTGACCCTATGATTACTCCACAGAAACCCTCACACCCTTCCCATCTGGGGGAGCAGTAATTTCTGCCTCACTGCCTGCTTGTGTGAGGGTGTAGATGGCAGTAGGTGGGAGAAAGGTTGCACGGTTGGTCAGAATAAGCTTAGCAATAATGTGTATTCTATCTTCTGTAGACTCATTAGCTAGTGTTTGTGGCTGGTTTTTAGAGATGAAGCAGAGGGTCACATTATTTTTAAAAACCTGTTCTCTCTCTTAATATTGTAGTGAGAGTGTAACTTACCCTTCCAAGGTCTCAACTGGCAGCCTCCACACTCCTAATGTTTCTGACCTTCATACTGTTCCAAGTAGGTTTCTAAATAAGTAGAGTAGATGATAAATATTATAGCTATTATTTGTTTCATGTCTTGGAGAGAGTTTTGAATAATCAAGAGACATGGAGGGAGGGTTCAGAGAAAGAGAGTAAGAATATTCTGTCTCCATTTCCCCCAGTCCTACTGAAGACACAATCATTAAGTTCTCTGAACTACATTGCTTCATTTTAAAAAATGTGATAATTTTCTAAGATGATGGTCTAGCAACTCTAAGTAGTTTCTATGTCTTCTAGGCATCAGCAGTGGAGGTCTGTTAAAATGCGGTGAAAGTATGCTGGTTTGTTTTCATGCTGCTGATAAGAACACCTACTGAACTCAGAACAAAGAGCAGCTTGATTGGTTTAATTTGCACATGGCTCAGAGAAGGCCTCAGAAATAATGATAGAGATGAAAGACACTTCTTACATAGCAGAATGGCAGAAGAAGTAGAAGAAGCAAAGCAGGAGCCCCTGATGTGACCATGAGATCTCATGGACTCCTACAGCTGTCACAAGAAGGAGCATGGGAGGAACAGCACCATGAATTAATGCCTCCCCTGGACCCCTCCCACGACATGGAGGTTACAATGATAGATGAGACTCAATGAGACACAGCAGACATATTGGGAAGGATTTGTGTAGTAAGAGATTATGATATAGAGGAAGAGAGAGAGAGACTCAGATGAACCTGTGCAGTCTTTGGATTAGATATGAAGTATAAATGGTTCACAGATTTTTTTTTGAGATATGGTCTCACTCTATTGCTGGTCTGGTGCAATGGCCATGGCTAACTGCAGCCTCAAACTCCTGGGCTCAAGCAATCCTCCCACTTCAGCCTTCCAAGTAGCTGGGACTACAGGTATCTGCCACCACACCTGGCTAATTTAAAAAATTTTTAGAAATGAGTTTTGTTATCTTGCCCAGGCTGGTCTTGAACTTTGTGGCCTCAAGCAGTCCTCCTACCTCAGCGTGGTTCATGAGATTTTTTTATAGGGT 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qs:i:6  du:f:6.8944 ns:i:34472  ts:i:10 mx:i:1  ch:i:811    st:Z:2023-07-06T00:51:02.766+00:00  rn:i:5460   fn:Z:output.pod5    sm:f:103.536    sd:f:29.7441    sv:Z:quantile   dx:i:0  RG:Z:4d2d92f7d540c50a0a45341f561cac836e1eaaaf_dna_r10.4.1_e8.2_400bps_sup@v4.2.0    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ML:B:C,69,194,132,44,45,75,99,22,40,23,68,40,231,80,73,45,34,44,35,170,110,16,104,196,177,159,51,61,54,25,86,38,124,32,196,118,23,29,169,171,138,252,13,13,12,161,45,148,23,13,17,70,115,200,33,52,18,16,178,109,74,58,33,71,12,13,51,24,81,51,84,25,47,87,100,17,25,19,14,23,43,12,18,12,59,46,31,35,52,121,21,26,161,101,132,57,13,34,17,59,120,69,201,20,17,28,13,140,157,185,81,177,15,24,28,103,117,129,230,215,228,230,178,40,22,22,29,130,221,160,31,42,43,235,50,35,20,12,24,47,238,172,113,120,160,148,196,43,36,63,186,183,171,206,13,13,154,25,253,88,38,83,16,109,211,49,40,47,65,80,73,91,35,25,61,155,123,41,36,41,54,23,15,104,23,68,121,120,60,12,26,86,16,217,194,75,254,181,56,27,66,28,44,116,188,55,99,42,134,48,94,17,64,64,254,13,116,12,44,85,20,33,189,13,23,76,73,64,19,19,62,56,35,161,55,38,92,146,87,208,206,72,97,42,26,107,110,21,44,110,47,165,224,16,54,166,97,24,227,123,148,72,20,196,62,20,219,80,46,110,46,94,110,84,107,162,36,29,20,100,195,13,175,113,75,250,21,22,13,122,131,242,214,109,40,153,27,125,79,150,20,75,110,225,69,126,187,113,62,89,72,95,159,21,35,35,118,119,152,75,99,54,30,24,18,15,19,16,50,73,149,12,28,13,14,239,66,50,15,17,34,95,252,57,108,137,212,42,67,23,15,226,14,250,216,12,16,67,30,245,41,105,99,33,20,18,12,20,25,56,46,42,41,35,194,31,62,15,13,43,31,91,136,26,31,38,60,41,171,56,12,16,34,156,245,111,18,34,26,147,104,83,87,207,216,157,129,196,85,219,252,15,95,25,45,229,17,37,178,111,50,91,97,23,185,51,137,246,77,177,251,15,70,195,37,18,66,194,231,124,127,254,57,77,28,252,163,251,37,54,102,107,215,117,38,14,43,247,86,19,177,56,35,30,18,13,203,63,51,22,28,213,160,61,156,64,84,184,63,210,223,202,122,249,184,89,236,97,194,192,240,218,24,61,235,69,50,28,32,237,24,46,114,142,91,46,45,38,155,33,23,31,92,17,34,49,132,184,26,227,97,239,239,66,40,149,40,78,101,51,14,28,111,65,217,86,34,31,14,15,185,53,22,137,14,173,27,228,35,24,105,213,13,15,31,153,65,148,51,89,83,95,217,137,29,46,226,21,40,81,187,83,26,156,237,58,16,27,60,141,119,111,229,147,45,249,28,31,13,15,58,122,96,29,91,206,162,13,20,33,188,128,52,71,140,169,41,57,22,26,79,45,28,70,239,90,137,95,122,253,162,191,120,91,120,158,15,18,22,22,43,53,63,161,94,247,46,35,147,77,96,190,238,16,34,35,13,251,182,18,41,253,247,237,160,30,146,39,218,12,62,34,38,249,18,35,65,59,32,110,238,131,159,234,229,119,210,50,123,189,254,118,45,223,15,14,16,58,201,131,28,64,234,252,174,154,151,249,36,50,60,96,88,253,17,250,55,239,125,54,131,80,61,60,36,205,132,95,40,64,188,25,35,94,18,116,207,46,31,39,19,251,22,107,73,78,107,164,105,121,176,153,156,40,255,16,249,25,117,141,251,61,53,85,13,52,75,56,34,121,125,115,102,69,33,25,107,47,149,219,69,125,59,56,185,86,44,173,201,42,245,226,249,14,68,119,41,41,92,35,64,117,38,210,162,91,142,240,167,87,190,62,82,172,37,106,104,61,49,28,75
StephanieBohaczuk commented 5 months ago

m6A prediction isn't available for ONT data. First run your data through an ONT m6A caller (like Dorado) and then you should be able to use add-nucleosomes after that. I'm guessing right now add-nucleosomes is running but isn't adding anything meaningful to your files.