Wshengquan

Thanks for your reply. Here's one of my reads: 8e9d05a0-9447-4b61-9600-1d9e92384702 0 1 1 60 1513S328M2I1M1I255M2D501M4D2M1I41M1I232M2D841M3S * 0 0 GGGAACTCCTCCTTTTTTTTTCCTAAGAAATTATCTAAATAATAAATTTTGTTGAAGTGTTTGTC TAGGATTTCAAGGTAACGGCCTAGAAGTCACCATCTAACCACTGTGGCAAATCCGTATGAGTGACATTAGAAGAAGTAATCTTTTGTCTATCATTTTTAATTTTATTAAGTTGAATACATAATTTTACAATTTTATAGTCGCTAATGACTAATTGGTTAATTATCCAGCCAATGAAACTAGTAGAGGGAGTTTAGGAAATGCAGAATAATTAGGCATTTCCTAGGACTTGTGTAAATTAGAATATGACGGTAGCATTTTTATGGTTGTAAAATCAGAGGGAAGGCATATATATAGCTGTTGTAGTTTTTGTTTTTGTTTTTGTTTTTTTTTTAATGGCTACACCCACGGCATGTGGAAGTGTCCCTGGTTCCTGGTTTCTGGGCCAGGGATTGAATCCAAGCCACAGCTGCAGCAATACCAGATCCTTTAACCCACCGCACTGGGCTGGTGATTGAACCCTGACCTACACAGCAACCCAAGCTGCTGCAGTTGAAGTCTTAATCCGCTGTGTCGCAGCAGGAATTCCCATATAGCAGTTTTTAAAACAGTTAAAACTATCTATTTTGTCAAACAGTCATTTTGATGAGACATATTTTATGAATTTTTTCGTATGTAACTAAATATCTGATATTAATACTTTAGAGTTGTTTGAAAGTAATTTTTTGCTTTATATCATGTAACCTAGTAACTGAAGCCATTGCATATATATAAATGGCAGTACATTAATATTGTTTCTGAGAGCCCATTGGAAACAGGAGGTCACTTCACTATCTGTTGGTATGCTTGTAATCTGATTTATTAATTCCTTCTGGAGGTTGAAAAGGGTTATCAGTTGATTTGCCTAAAAAAATCATTAATAAAATTTACAGTTAAAGAAAATTTTTGTAACTTCTGTCTTCACTTGTTGGAATGTGTGTGAAAGAACACACAGATCTTGGTCCAGCTGCCCTAGTAGCCACAGTTTACTTGTCGGCTCCCTGTCCAAGAGTACACATGCCACATGGCCATGGAAGGGAATCCTGTATAGAAACAATGACAGGTATCTGGGTGGCTGTCATTGTCTAATTCTCCTGACAGAATCAGCAGTCTGAGTGACTCATTAACCGTTGTCTCTGACTGTTTCAGCGATTTGCTGCTGTAATCATGAGAATAAGAGAAACCCGCAGACACCGCACTAAATATCAGCTCTGGGAAAATGGTGTGCACGGGAGCCAAGAGGTGGGTCTAAAAGGGTTCATTGTCCTAGTCTGTGCGTTAGGAAAGAAAAGGCTGTATGTCGTGGTTTCTAGGTATTAGGTTACTACTGTGATACATTGTCATTGTTGCTTTCTGTTAAGGTGGTTGATTTTCATCACTGCAGACAGCAGTAACTTCATTTTCTTAAAATCAGGCATGAGTAAGGATGTGTGTTATCATCTGATTTCCATATAGTTGAGCGTGATTATGTGCTTAATTTTTGTCATTTCTCACCCCTGCTCTTGAGAGCTTTTGTTGATAATGTTGTTATTGCTTTCATTCTGCTTTTATTTTGTAAGCCCTGCACTCATTCATCGCTGTACCCGAATATGAGGTAAGGAGTGGTAAAGAAAGACTGGACATAAAAGAGGAATTAGCATTTGCACTCTTCAGATATAAATGCCATCAGTATTTTCCTATTAAAATGAAGCTTGTTTTCATCTCAGTGGAAATCTGTGGCTAAAGTACAACAATAGTAATGATAATGGTGAGGCTGTTGTACTTCACATCTATAAAATCTTGCATCAATAATTTGATTAACCAGATTCCTTTGGGTAGGCCTACGTTTTCTGTCAGAGACACAGGAATACTTTATAAATAAAATTGTTAATGTCTGTTGATCTTTTTTCATTGGAAGAGGGTGACCAGTTTACCTTTTGAAAAAAAACTTTCCTAATTTGGGCTTTTTTTTTTTTCTCCTTTTTAGGGCTGTACCCATGGCATATGAAAGTTCCTGTGCTAAGGGTTGATCAGAGCTGCAGCTGCCAGGTTACGCTACAGCAACACCAGATCAGGTTGTCTGTGGCCTTTGCCATAGCTTGGGGCAGCACCGGATCCTTAACCCACTGAGTGAGGCCAGGGATTGAACCTGCATCCTCCTGGATACTAGTTGGGTTCTTAACCTGCTGAGCCACAATGGGAACTCCTGGGCTTTTTATAAGTTATACGTTAAATAATTATTTTAGCTGTCTTTGAGTATGAATATCTCACTTTTTCTTTCCTTAGTGAAGAACAGTCCAGACTAGCAGCAAGAAAATATGCCAGAGTTGTACAGAAGTTGGGTTTTCCAGCTAAATTCTTGGACTTCAAGATTCAGAACATGGTGGGGAGCTGTGATGTGAAGTTCCCTATAAGGTTAGAAGGCCTTGTGCTTACCCACCAACAGTTCAGTAGGTAAGTCTGAAATGGATTGTGATTGCTTTTGGCAACAATTAATTTATAACCTATTTAAACACTGTTCATGATTTTTAAAAAACATGCAAAGTAATTGGTATATGAAATCAAATTATTTTGGTTTTTTCATCTTCAGGACCATAGCAGTGGCATATGGAAGTTTCCGGGCCAGGGGTCAAATCAGAGCTGCAACTGCCAACCTCCACCACGGCCACAGCAGTGCCAGGTCCCAGCTATGTCTGTGATTTACATCGCAGCTCAGGGCGAAACCAGATCCTTAACCCACTGAGCAGGGCCAGGGATCGAACCTGAATCCTCACTGATACAGTTTTGTTACCACTGAGCCACCATAGGAGCTCCCAAATGATTCACATATAGATGTTTTACTATTGAAATTTCTCCCATTCCTACCATTCTCACTGGTCTTCTACTTCTTAATGATACCCCAGACTCCCCTTTACTAGGATGAAATTGGTTCCCCTTCTGTATGTTTCATCGTTTCATTGCTCAATGAATACATTTCAAATGCATGAATTAGAAGTTCCTGTTATGGTGGATATGACATTTCTTTCTCTTTGTTTTCCCTGCTGCTCTCCTGGTGAAGACTTTAAAGGCAGGCTTGCCCATCTCTGCAGACCCTGCTTGCAGCATGCGCCTGGCGTGCTGTGCCCTTAATTGCACCAGGGCCTTTGCACATCCCGCTTTTATGCCTGGTGCTCTTGTTTCACTCTTCACCTAGGAAACTCCCACCGGCATTTCATGTATCCATCCAGGCATCTTTTCTTCAGAGAAGCCTGTCTTGAATTTTTCACTGGGCTAAACACACACACACCTAACTATTTTCAGTCTCTCTAACTAACAAAATGAGATGACTAGGATTAGAAAAAAACATACCAGTAGTGCATTTGGTCTGACAACACAGCGAAAGGTTCATTGTCTAACCAGTATCTTTTCTATCACTTTTGGTTAAGTCGCCTGACCTAGGTTAACACTTTGAGGATATTTCAGTTTAAGGAGATGAGATGTGAATGATTAGAAGGTAAACTGTGTGACTGTCATATCTTAGACATAAGTAATTCATTAGGCTCTTGTAAATCAGTGTACTTCACTTGTCCAGAGTGAAACTTGATGAGGGGCAGAGACTACAGAACATATTTATAAAGCTCTTGTTCTCATGTCTGGAAATTCAGATTCATTAGAAGTAAGAGTTCGTTGGCCTTCAGGTGCCAATTACAAGTCAGCTTGAG ISQKMJSFEB===:;AABFJECHEFHMHJNGQSQMJMMSHISJKMSCKSSSS9557JFJJEJFSFJLLGSSIHLIJHJSKIMSSSLKKSJPIILOSKLKIHNIHIKSQJSHSNOLIGNSLLJSKPJIIIO>LHA@BDNJLKIJKSMJSLLSSMMISMGJIILSOOKHSSLSRNSJHINMSSJSMIPLJSSJJSGJSKSIPIMSISISMKKIPOHKKHSIPJOHNNKKHKIMJLHMOJPJSKMIKQLHIHHSQIJHSNLKKHJNOSJJSMJSSJKKSLEOJIJHISSHPIJLMLSIIMSPQSJSIJSLIJSHJRKKJLIGE@88=;0///GNISJKSLFGISSISJJSNSKKHJKOJIF::9989ABCEKHEISLPSSSIHGKFJRGI@>;AEISSSSHGEESSSKOKIMSISKHJHHSSSKPSLGLISSJEHSQPLGLNKOSJIGECED@A;;:99:44459CEDBFJJHKJSGHFSLSJHSSSOSMJSMHSQSLGGMJJISNIIGLKPJSSSILKICEKIHJJSJHSKNSKKII==2?:9:69

MM:Z:A+a.,0,17,2,6,3,0,0,3,12,0,12,2,13,1,9,5,0,3,12,8,0,0,0,0,0,0,0,0,2,7,0,0,0,2,0,0,3,0,0,0,2,9,63,0,0,0,3,0,0,47,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,13,0,0,0,1,0,0,6,2,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0,0,4,0,3,1,1,0,17,0,0,0,50,0,1,23,39,0,0,43,1,3,0,0,0,0,4,0,0,0,0,0,0,0,0,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,1,12,1,14,0,0,0,3,4,0,0,0,0,0,0,0,3,2,0,3,6,0,39,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,2,1,0,0,1,0,0,2,2,8,0,17,4,0,0,0,12,14,0,1,0,0,0,4,0,0,0,1,0,0,0,1,2,5,0,0,1,33,12,0,0,12,0,1,41,1,0,6,1,1,4,8,0,0,0,0,0,0,0,0,0,0,0;C+h.,9,0,2,3,0,2,0,6,3,2,2,0,1,1,7,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,5,3,1,0,0,0,0,0,3,0,0,0,0,0,1,1,0,0,1,11,14,0,0,1,0,0,0,13,0,0,0,0,0,0,0,0,0,1,0,0,2,0,0,0,2,0,0,0,0,0,0,0,0,4,0,0,0,0,1,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,3,0,0,0,0,0,0,0,0,1,0,2,2,0,0,0,5,6,4,0,0,0,0,0,0,8,1,0,1,0,0,16,4,6,0,1,0,1,0,0,1,2,0,0,0,9,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,8,0,0,5,2,3,0,0,4,1,0,0,0,0,0,1,12,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0,22,0,8,3,0,0,3,1,0,4,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0,5,1,0,0,1,2,2,8,16,0,0,0,0,0,0,7,1,1,4,9,2,0,0,0,8,1,0,0,0,0,0;**_C+m_**.,9,0,2,3,0,2,0,6,3,2,2,0,1,1,7,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,5,3,1,0,0,0,0,0,3,0,0,0,0,0,1,1,0,0,1,11,14,0,0,1,0,0,0,13,0,0,0,0,0,0,0,0,0,1,0,0,2,0,0,0,2,0,0,0,0,0,0,0,0,4,0,0,0,0,1,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,3,0,0,0,0,0,0,0,0,1,0,2,2,0,0,0,5,6,4,0,0,0,0,0,0,8,1,0,1,0,0,16,4,6,0,1,0,1,0,0,1,2,0,0,0,9,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,8,0,0,5,2,3,0,0,4,1,0,0,0,0,0,1,12,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0,22,0,8,3,0,0,3,1,0,4,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0,5,1,0,0,1,2,2,8,16,0,0,0,0,0,0,7,1,1,4,9,2,0,0,0,8,1,0,0,0,0,0; MM has not only A+a but also C+m

[subset.zip](https://github.com/user-attachments/files/16243097/subset.zip) This is a subset of my data. Do I need to reinstall mathphaser

Thank you very much for your help, waiting for your test success using the subset file

I used the new version you changed yesterday, but the error is still reported, but it seems to be different： /share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/meth_phaser_parallel:235: FutureWarning: When grouping with a length-1 list-like, you will...

I tried again, but I got a mistake： /share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/meth_phaser_parallel:235: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version...

I did reinstall it from here : https://github.com/treangenlab/methphaser/tree/Fu-Yilei-patch-1 My input file takes up too much memory and cannot be uploaded to you via github, even after compression. How should I...

“you could limit your vcf, gtf and bam to the first 3 phaseblock on chr1. I think those could be sufficient.” I'm sorry, how do I do this? This is...

Thank you very much for your help [train.gz](https://github.com/user-attachments/files/16303957/train.gz) I made specific operations in the files according to the suggestions you gave me but I kept the first chromosome in the...

Long time no see. I have been testing other processes recently, so I am very sorry for not communicating with you in time.May I ask whether this process has been...