KeyError: ('C', 1, 'm')

[Wshengquan]

hello，
I got an error when I used mathphaser：
/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/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 of pandas. Pass (name,) instead of name to silence this warning.
phased_df_chr.get_group(chromosome).iterrows()
/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import require
Traceback (most recent call last):
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 1471, in
main(sys.argv[1:])
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 1437, in main
) = get_assignment_max(
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 898, in get_assignment_max
base_modification_list = get_base_modification_dictionary( # build the dictionary with snp phased reads
File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 243, in get_base_modification_dictionary
for i in mm[methylation_identifier]: # Remora only output one type of score: c 1 m/c 0 m, but this part can be improved for other methlyation callers
KeyError: ('C', 1, 'm')
My run command is：meth_phaser_parallel -b sample.whatshap.haplotagged.bam -r ref.fa -g sample.phased.gtf -vc sample.haplotype.phased.VCF -o path/to/output
why this happened？
Any help to overcome this is appreciated!

Best

[Fu-Yilei]

Could you please attach one read from your bam file? I am suspecting there are some bugs with the methylation signal reading. Thanks! Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: Wshengquan ***@***.***> Sent: Monday, July 15, 2024 8:44:03 AM To: treangenlab/methphaser ***@***.***> Cc: Subscribed ***@***.***> Subject: [treangenlab/methphaser] KeyError: ('C', 1, 'm') (Issue #22) hello， I got an error when I used mathphaser： /share/home/yzwl_hanxs/anaconda3/envs/danbeixing/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 of pandas. Pass (name,) instead of name to silence this warning. phased_df_chr.get_group(chromosome).iterrows() /share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import require Traceback (most recent call last): File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 1471, in main(sys.argv[1:]) File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 1437, in main ) = get_assignment_max( File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 898, in get_assignment_max base_modification_list = get_base_modification_dictionary( # build the dictionary with snp phased reads File "/share/home/yzwl_hanxs/anaconda3/envs/danbeixing/bin/methphasing", line 243, in get_base_modification_dictionary for i in mm[methylation_identifier]: # Remora only output one type of score: c 1 m/c 0 m, but this part can be improved for other methlyation callers KeyError: ('C', 1, 'm') My run command is：meth_phaser_parallel -b sample.whatshap.haplotagged.bam -r ref.fa -g sample.phased.gtf -vc sample.haplotype.phased.VCF -o path/to/output why this happened？ Any help to overcome this is appreciated! Best — Reply to this email directly, view it on GitHub<#22>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADDV4HSJUIW34QP42SJNL7DZMPG2HAVCNFSM6AAAAABK4SWL4WVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQYDQNZYGU2TQOA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[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<=<;8((((((///0@IFICB>;788956,&&&&&+,//3333336JSJKNKGGSDDDSINSMKHSKSSSLKJSJQKHG?<<=J;;/////;>.BHEHJLQJJNLGSMNIGKNSSJSISJSSISSQISHPMPSSINJSLSRSLJHISHSSISSKNSSISOSIHSISSISSQGJSSPRSHHNLJKKKSKPSSSIKCSFDEJGHOJIFMSJLJHSLISKSJSSISJSHKILHOLSPKHFFSLHSNSMKSKJJOSLSPS(((((GKKJOSLQHSSHJSISKSOMOKEH;;::;FSINPMLILSMOSSKRJRMSSMKIPSSLSISSSSGHGKJHMOJIMSHNHIHSONSSSMSSOKHSJFLNLSSOMSKHKKSSEEJKSSSSSSSSGJSKJSOSSMKSJMIFHSGSKSLSJNSKJSSHHMLIHRMMHSKHRGIJHSLLSSQHSLIISJB99:?GLEJESIPSMSSH>:;:;JRFOSLIOKFSKKKSSHOSJSIJS>==<:<9;;ACGMF@AEPKFHSKNSNERSSOJGKKSMSJHRKLHHNOHKKSSSPSJKKMIRJHKMLHSNSSSSSISSQS===>===MSQMNJNSPNSHGSGHGLLFGMLSFIILJNKSNRHMKKKKIIKKJKKJSLSJIIGLLIHD410,++)'&&'''%%%&&&&(((&&'(&'($$$%'(()3457@>.,,,,1&&&((-+++@BIRKSISIPSSMKHJISSJLE?@BBAGSKSJSPSKIPHSKSSSSNSSHHMSJGDCCJMSSSLNSSMLHKL
SMSJJMKSSKOMNSSHSSMMLSMJKSSISGSJOJOFIN>>==>SJSKSSKISSISSKNISSLHFSSSSRHGISIIGHGN@@CCBGOKGFHIKHKJISHRHJSSKSHSSKISIHRHKSKSGEJNMSJHSJNNSJNSGJHSJJSSHHSMOSSSHSSJSJHSPSLSGSKSNKNNGGHLGHSNPSJNPKJOSSGJNSSSKKHSLSSSLJSSILKSIGNSSSLISKSRHSILKDHIIPSSHSOSRSSMLMMOKLIHGNKQMJSOFEFLBFEPOFIKHLSHSKNGSSSECLHJJHLSSMSIKSSSSSSSSHHINMSJGEKIKSIJB><<<==:4433/00HSIIGEJHKJGSSSSJSSSISGLJSGIRLNILSMHHJGSLHIJSNINGSSMJJHHHJDDFHLNQIKLSKSMKKSSMOKMLJIMJIJSSHSMSOLSKSNSKSSSGOHIPSSHGISLSJKJSOLOJOGKNSMPKSSFSEQKJKISPJLOSSMHLJJSGIJC>@,,--.HGEGHGB80--,++(&'()((()BFADGR<<;;;<CECDMMSIJSSKSSKKSSHILSSQLSNA@AA@HHSNPIKLJSSSSHSKSLSFNKEGFMF:<20GJSFEHGKSKGNLSLSSLSLIJHQSISHMB76S:9989JSSSKFIJESKMSLHISHKSGS8GEIGSFSSGIEAA55=?@BJIKSQLRLGOHKHJIIHONHSSSNSLLJGSLKLGSSGME<;>100004100000EIELIJGCNIHMMHHMSSJHI?:98,,)((%%%$$%''&),-2367622658EIFCABB?8889ESNSKSLGFIJFDJFEGGJSLSSIQSHSFGHSIQSSJFDDCCESPSKMPSJILJKHLNSHJHMHKJIFHJ
FCDCDOPSIHOJJSMLJSSHKIIKIPGMIKSSM?>>?H;;<<<EFFGSQBCLIKFHLGSISISPJSRLSKSSQIHSSNJDMNLKSGHKFGISKSPSKILSKNSHSDHHSHA@@JSISSSGJOJRSQJHHKHSSISGLSHKSGISSJMSJGKNOSIISSNKSJSLKLIH@NRIENINESIJLJKHSNISSHSISEBFEFNSHMHSLOKHLJSOSIIIS
JSPIJIMSLSKKSILSPSQHKMSHMSKGKLKLIKKSSHHHIKGILIEQMLOSHSNGHFFHHPSDRKEMHLKSSSSSHMRSJGSSSJHQMSSMMSSJJHOKSLKJPSIQKFIJMJLSMKNSLLSIOSKSJSSSJJCF>;;@AASSMPSSJSSNNNSSSKHSHKSJSJRHPHLSKKHKHFCODJHHEGECB)&&&&*((112GOKIKHFGSSLHHKSSNISLI@MJSSFHFLSSLNLMJJSSJNS??>??SSKSQHIKLPSIGJSJBA642222>??AFKFHSIILGQSHILSMLIJKJILJJOSHSSKIHHRGJSPSSFSGIJSL;:981023356AADCCCEHSHHOSJHQISLPKMFHH:4554448=@GNSNJMILHSKJKKMSMSNKIJISKJSKS<<1111364311BEEESNSSJSMLLSNHILSLJSJNJKJMJJHKOSLHIIFFEHEFLLSNG;40()*3767@ADCSSHSGSSPSHMSQJOIAFC?>>>>A33333;@>2?:9:69<?<GH56DBBDEGSLGPJSMSFSHRSJGSIGMSPSSIOJIIGSKSNKSKSHPSKLSSSSJSHIJSS?D-----SSNKLHMSFSILSHOSLSKIIJIIKSSSJISIHKLLSJISKPQISKKSLGAISKGFEB7D@?
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755.)&% qs:i:21 du:f:9.5696 ns:i:47848 ts:i:592 mx:i:3 ch:i:843 st:Z:2024-04-08T11:56:24.693+00:00 rn:i:5741 fn:Z:PAW37422_pass_b74e10a2_68ebe454_253.pod5 sm:f:100.808 sd:f
:28.356 sv:Z:quantile dx:i:0 RG:Z:68ebe454a63ea33cf655142d882767dfb3012d4a_dna_r10.4.1_e8.2_400bps_sup@v4.2.0 MN:i:3722 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;
ML:B:C,14,13,53,12,35,21,16,14,112,191,38,66,13,12,12,39,111,24,13,22,80,72,66,148,40,35,28,14,28,35,40,29,16,13,26,251,29,241,106,70,12,171,107,16,21,12,12,16,18,12,12,17,15,12,17,22,13,14,22,25,46,18,71,17,24,17,23,17,48,20,25,15,20,15,78,20,139,100,80,74,146,146,112,125,167,117,108,87,25,51,12,38,46,12,15,13,12,111,18,21,20,19,14,12,31,26,30,41,59,39,17,12,13,56,77,45,31,14,53,29,222,132,113,74,21,97,14,14,18,17,22,25,34,16,68,14,210,38,14,25,16,159,12,13,102,13,15,17,18,34,126,38,22,33,25,19,39,93,47,76,15,21,15,39,14,15,14,32,21,35,43,62,49,51,64,36,36,15,21,62,45,255,255,29,42,38,40,17,227,32,37,29,15,226,91,21,156,42,85,112,128,14,132,14,88,206,12,14,13,16,15,15,40,38,53,51,53,63,30,26,87,12,159,14,14,13,90,21,12,14,24,63,22,13,14,12,20,112,133,55,43,108,31,138,13,16,17,59,29,182,18,15,8,0,3,8,3,1,1,3,4,2,5,5,16,8,2,9,28,40,33,25,33,18,30,125,7,51,6,2,2,2,2,1,4,5,4,4,3,2,4,8,15,100,9,8,12,12,147,19,13,30,6,7,5,2,9,16,15,12,9,6,5,4,2,3,3,11,5,6,6,3,14,255,30,10,7,22,5,8,11,6,6,4,6,8,10,6,7,6,5,5,5,3,4,0,0,7,11,9,7,0,5,2,29,27,71,47,3,7,2,2,1,37,78,28,7,8,17,18,1,11,9,4,11,7,9,5,2,1,2,3,3,2,2,2,6,3,44,9,23,39,1,3,9,7,18,6,7,8,7,4,21,8,13,7,6,6,4,47,6,7,5,9,15,19,34,22,11,11,0,5,4,6,13,130,57,230,22,11,11,21,9,12,21,27,86,5,5,7,8,10,10,14,16,5,7,5,4,7,7,9,7,8,3,3,4,11,5,7,1,24,5,4,8,7,7,9,49,7,6,6,4,3,4,2,8,2,5,5,8,11,12,3,10,6,17,11,2,12,3,2,2,5,5,2,6,4,20,24,9,16,13,10,11,13,12,14,4,12,4,2,2,25,28,3,4,6,3,4,2,6,11,10,13,11,10,10,3,3,7,7,3,4,2,0,1,3,12,1,3,2,15,6,4,10,13,8,14,11,9,4,4,9,15,14,8,10,7,3,4,4,5,20,15,16,4,18,1,8,8,11,12,5,4,6,3,3,20,8,7,8,13,4,3,11,7,3,5,13,66,13,2,3,3,7,7,9,12,4,3,1,3,2,106,92,5,5,17,10,2,39,21,8,10,9,5,63,7,16,255,13,24,12,37,254,252,22,12,13,13,240,13,254,16,36,40,40,39,52,50,24,24,20,79,19,13,14,12,12,254,16,12,13,14,15,13,14,22,9,7,18,17,14,240,36,235,17,225,12,16,18,12,22,38,16,22,17,13,16,16,13,17,16,22,22,18,28,12,14,0,6,12,23,46,18,22,20,18,19,12,21,16,18,15,20,31,13,18,15,13,18,13,255,16,17,18,200,255,19,18,43,65,137,90,25,37,253,12,254,55,38,37,18,12,15,26,254,244,12,12,21,17,20,14,42,254,12,14,14,14,12,12,14,12,27,246,13,11,254,12,15,19,100,18,16,247,22,13,26,12,13,14,13,12,13,14,16,17,13,14,27,36,42,44,29,33,255,14,25,232,85,94,110,8,70,26,29,59,31,4,234,51,44,18,18,21,28,27,28,26,27,17,20,15,14,17,19,17,14,20,13,15,15,24,14,16,254,12,15,12,16,18,16,19,50,13,22,21,15,13,14,12,12,45,18,16,20,27,13,252,20,19,41,29,14,12,14,13,16,21,21,12,24,19,224,55,35,26,30,34,26,31,24,28,13,212,251,22,31,229,76,246,28,23,19,20,12,24,36,23,23,244,23,25,17,17,21,20,18,16,13,17,14,16,47,254,14,16,11,12,12,21,24,16,24,26,23,16,15,58,26,23,20,28,26,16,14,13,17,31,29,29,251,79,254,21,16,20,28,20,19,22,23,28,11,12,248,15,25,12,12,12,21,14,20,14,189,10,14,13,24,28,14,16,21,15,13,254,22,253,15,2,13,16,30,19,12,29,234,16,24,29,22,22,30 NM:i:25 ms:i:4282 AS:i:4276 nn:i:0 de:f:0.00860507 tp:A:P cm:i:350 s1:i:1968 s2:i:0 MD:Z:169G154G1G154T72C23C0A4^TA501^TTGG3T77A55A38A98^TG119T721 rl:i:400 SA:Z:1,5438,-,2207S1514M1I,60,15;
Is there an error because the label of methylation recorded in my bam file is MM instead of mm

[Fu-Yilei]

I see. The read you are showing here only has 6mA calls, but MethPhaser can only phase with 5mC calls.

[Fu-Yilei]

MM:Z:A+a? is for 6mA calls. C+m? is for 5mC.

[Wshengquan]

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

[Fu-Yilei]

I see, yes indeed this is a bug of MethPhaser. I would suspect that there are some reads that only have 6mA calls but do not have 5mC calls. I will try to apply a filter to skip those reads.

[Fu-Yilei]

I've made the changes, could you please check the MethPhaser version of (https://github.com/treangenlab/methphaser/tree/Fu-Yilei-patch-1)? Or if you could provide an example BAM file I can do the test.

[Wshengquan]

subset.zip
This is a subset of my data.
Do I need to reinstall mathphaser

[Fu-Yilei]

yeah you need to clone the version in the branch I provided

[Wshengquan]

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

[Wshengquan]

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 need to pass a length-1 tuple to get_group in a future version of pandas
phased_df_chr.get_group(chromosome).iterrows()
/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import require
Traceback (most recent call last):
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 1477, in
main(sys.argv[1:])
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 1443, in main
) = get_assignment_max(
^^^^^^^^^^^^^^^^^^^
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 910, in get_assignment_max
assignment_df = get_base_modification_list_snp_block(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 605, in get_base_modification_list_snp_block
for i in mm[methylation_identifier]:
~~^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: ('C', 1, 'm')

[Fu-Yilei]

sorry forgot to change one spot in the code, now should be fine :)

[Wshengquan]

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 of pandas. Pass (name,) instead of name to silence this warning.
phased_df_chr.get_group(chromosome).iterrows()
/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import require
Traceback (most recent call last):
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 1471, in
main(sys.argv[1:])
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 1437, in main
) = get_assignment_max(
^^^^^^^^^^^^^^^^^^^
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 898, in get_assignment_max
base_modification_list = get_base_modification_dictionary( # build the dictionary with snp phased reads
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/home/yzwl_hanxs/app/dorado-0.7.2-linux-x64/bin/methphasing", line 243, in get_base_modification_dictionary
for i in mm[methylation_identifier]: # Remora only output one type of score: c 1 m/c 0 m, but this part can be improved for other methlyation callers
~~^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: ('C', 1, 'm')

[Fu-Yilei]

Sorry about the back and forth. Was this the program from this patch? https://github.com/treangenlab/methphaser/tree/Fu-Yilei-patch-1 Based on the line number of the bug, it seems like you are using the main branch. Or you can send me the input you are using for this program, it is hard to debug with only subsampled reads.

[Wshengquan]

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 give you my input file