Hi, I have a problem using lofreq with human sequencing data and hg19 or GRCh38 reference sequences ( downloaded from NCBI with manually changed file extension .fna -> .fa). I guess it might be a problem with improper file format or index. I get an output as follows:
nils321$ lofreq checkref GRCh38_latest_genomic.fa 1214474-H8.bam [fai_load] build FASTA index. [fai_fetch_seq] The sequence "1" not found
FATAL(samutils.c|checkref:653): Failed to fetch sequence 1 from fasta file
Failed
An fasta index file was created (see bottom for content).
Can anybody help? Would be awesome! Thanks a lot!
Nils
in short: the BAM file was created with a different reference. The checkref
subcommand checks whether the reference fasta given on the command line
matches the one given in the BAM header. In your case the BAM header
contains a sequence named "1", which is not part of the fasta file.
Hi, I have a problem using lofreq with human sequencing data and hg19 or
GRCh38 reference sequences ( downloaded from NCBI with manually changed
file extension .fna -> .fa). I guess it might be a problem with improper
file format or index. I get an output as follows:
nils321$ lofreq checkref GRCh38_latest_genomic.fa 1214474-H8.bam [fai_load] build FASTA index. [fai_fetch_seq] The sequence "1" not found
FATAL(samutils.c|checkref:653): Failed to fetch sequence 1 from fasta file
Failed
An fasta index file was created (see bottom for content).
Can anybody help? Would be awesome! Thanks a lot!
Nils
Hi, I have a problem using lofreq with human sequencing data and hg19 or GRCh38 reference sequences ( downloaded from NCBI with manually changed file extension .fna -> .fa). I guess it might be a problem with improper file format or index. I get an output as follows:
nils321$ lofreq checkref GRCh38_latest_genomic.fa 1214474-H8.bam
[fai_load] build FASTA index.
[fai_fetch_seq] The sequence "1" not found
FATAL(samutils.c|checkref:653): Failed to fetch sequence 1 from fasta file
Failed
An fasta index file was created (see bottom for content).
Can anybody help? Would be awesome! Thanks a lot!
Nils
GRCh38_latest_genomic.fai ->
NC_000001.11 248956422 68 80 81
NT_187361.1 175055 252068566 80 81
NT_187362.1 32032 252245930 80 81
NT_187363.1 127682 252278483 80 81
NT_187364.1 66860 252407882 80 81
NT_187365.1 40176 252475698 80 81
NT_187366.1 42210 252516497 80 81
NT_187367.1 176043 252559355 80 81
NT_187368.1 40745 252737719 80 81
NT_187369.1 41717 252779094 80 81
NC_000002.12 242193529 252821401 80 81
NT_187370.1 161471 498042465 80 81
NT_187371.1 153799 498206070 80 81
NC_000003.12 198295559 498361860 80 81
NT_167215.1 155397 699136224 80 81
NC_000004.12 190214555 699293632 80 81
NT_113793.3 209709 891885984 80 81
NC_000005.10 181538259 892098383 80 81
NT_113948.1 92689 1075905986 80 81
NC_000006.12 170805979 1075999902 80 81
NC_000007.14 159345973 1248941024 80 81
NC_000008.11 145138636 1410278890 80 81
NC_000009.12 138394717 1557231827 80 81
NT_187372.1 40062 1697356598 80 81
NT_187373.1 38054 1697397281 80 81
NT_187374.1 176845 1697435931 80 81
NT_187375.1 39050 1697615107 80 81
NC_000010.11 133797422 1697654715 80 81
NC_000011.10 135086622 1833124674 80 81
NT_187376.1 100316 1969900001 80 81
NC_000012.12 133275309 1970001640 80 81
NC_000013.11 114364328 2104942960 80 81
NC_000014.9 107043718 2220736911 80 81
NT_113796.3 201709 2329118798 80 81
NT_167219.1 211173 2329323151 80 81
NT_187377.1 194050 2329537086 80 81
NT_113888.1 191469 2329733684 80 81
NT_187378.1 38115 2329927669 80 81
NT_187379.1 39555 2329966383 80 81
NT_187380.1 172810 2330006555 80 81
NT_187381.1 43739 2330181648 80 81
NC_000015.10 101991189 2330226003 80 81
NT_187382.1 448248 2433492199 80 81
NC_000016.10 90338345 2433946120 80 81
NT_187383.1 1872759 2525413812 80 81
NC_000017.11 83257441 2527310050 80 81
NT_113930.2 185591 2611608327 80 81
NT_187384.1 280839 2611796355 80 81
NT_187385.1 112551 2612080822 80 81
NC_000018.10 80373285 2612194849 80 81
NC_000019.10 58617616 2693572870 80 81
NC_000020.11 64444167 2752923276 80 81
NC_000021.9 46709983 2818173064 80 81
NC_000022.11 50818468 2865466991 80 81
NT_187386.1 150754 2916920812 80 81
NT_187387.1 41543 2917073573 80 81
NT_187388.1 179772 2917115758 80 81
NT_187389.1 165050 2917297900 80 81
NT_187390.1 42811 2917465136 80 81
NT_187391.1 181920 2917508605 80 81
NT_187392.1 103838 2917692921 80 81
NT_187393.1 99375 2917798179 80 81
NT_187394.1 73985 2917898919 80 81
NC_000023.11 156040895 2917973897 80 81
NC_000024.10 57227415 3075965372 80 81
NT_187395.1 37240 3133908245 80 81
NT_187396.1 2274 3133946050 80 81
NT_187397.1 2165 3133948452 80 81
NT_187398.1 1942 3133950744 80 81
NT_187399.1 1472 3133952810 80 81
NT_187400.1 21476 3133954400 80 81
NT_187401.1 4416 3133976244 80 81
NT_187402.1 1201 3133980815 80 81
NT_187403.1 1444 3133982131 80 81
NT_187404.1 2276 3133983693 80 81
NT_187405.1 998 3133986097 80 81
NT_187406.1 12399 3133987207 80 81
NT_187407.1 37690 3133999860 80 81
NT_187408.1 1179 3134038121 80 81
NT_187409.1 2646 3134039414 80 81
NT_187410.1 2489 3134042193 80 81
NT_187411.1 1029 3134044813 80 81
NT_187412.1 2145 3134045954 80 81
NT_187413.1 2321 3134048225 80 81
NT_187414.1 2140 3134050675 80 81
NT_187415.1 2043 3134052941 80 81
NT_187416.1 1445 3134055109 80 81
NT_187417.1 981 3134056672 80 81
NT_187418.1 1884 3134057765 80 81
NT_187419.1 1361 3134059772 80 81
NT_187420.1 392061 3134061250 80 81
NT_187421.1 1233 3134458311 80 81
NT_187422.1 1774 3134459659 80 81
NT_187423.1 3920 3134461555 80 81
NT_187424.1 92983 3134465623 80 81
NT_187425.1 112505 3134559868 80 81
NT_187426.1 4055 3134673879 80 81
NT_187427.1 2415 3134678084 80 81
NT_187428.1 2318 3134680629 80 81
NT_187429.1 2186 3134683075 80 81
NT_187430.1 1951 3134685388 80 81
NT_187431.1 1300 3134687463 80 81
NT_187432.1 22689 3134688879 80 81
NT_187433.1 138126 3134711951 80 81
NT_187434.1 5674 3134851903 80 81
NT_187435.1 8127 3134857747 80 81
NT_187436.1 6361 3134866075 80 81
NT_187437.1 5353 3134872615 80 81
NT_187438.1 3253 3134878134 80 81
NT_187439.1 1899 3134881527 80 81
NT_187440.1 2983 3134883549 80 81
NT_187441.1 2168 3134886669 80 81
NT_187442.1 993 3134888964 80 81
NT_187443.1 91309 3134890069 80 81
NT_187444.1 1202 3134982619 80 81
NT_187445.1 1599 3134983936 80 81
NT_187446.1 1400 3134985654 80 81
NT_187447.1 2969 3134987171 80 81
NT_187448.1 1553 3134990277 80 81
NT_187449.1 7046 3134991949 80 81
NT_187450.1 31033 3134999183 80 81
NT_187451.1 44474 3135030703 80 81
NT_187452.1 4685 3135075832 80 81
NT_187453.1 4513 3135080675 80 81
NT_187454.1 6504 3135085344 80 81
NT_187455.1 6158 3135092029 80 81
NT_187456.1 3041 3135098363 80 81
NT_187457.1 5796 3135101542 80 81
NT_187458.1 1652 3135107510 80 81
NT_187459.1 1040 3135109282 80 81
NT_187460.1 1368 3135110434 80 81
NT_187461.1 2699 3135111919 80 81
NT_187462.1 1048 3135114751 80 81
NT_187463.1 1428 3135115912 80 81
NT_187464.1 1428 3135117457 80 81
NT_187465.1 1026 3135119002 80 81
NT_187466.1 1121 3135120140 80 81
NT_187467.1 1803 3135121375 80 81
NT_187468.1 2855 3135123300 80 81
NT_187469.1 3530 3135126290 80 81
NT_187470.1 8320 3135129964 80 81
NT_187471.1 1048 3135138487 80 81
NT_187472.1 1045 3135139648 80 81
NT_187473.1 1298 3135140806 80 81
NT_187474.1 2387 3135142220 80 81
NT_187475.1 1537 3135144736 80 81
NT_187476.1 1143 3135146392 80 81
NT_187477.1 1880 3135147649 80 81
NT_187478.1 1216 3135149652 80 81
NT_187479.1 970 3135150983 80 81
NT_187480.1 1788 3135152065 80 81
NT_187481.1 1484 3135153975 80 81
NT_187482.1 1750 3135155577 80 81
NT_187483.1 1308 3135157448 80 81
NT_187484.1 1658 3135158872 80 81
NT_187485.1 971 3135160650 80 81
NT_187486.1 1930 3135161733 80 81
NT_187487.1 990 3135163787 80 81
NT_187488.1 4215 3135164889 80 81
NT_187489.1 1136 3135169256 80 81
NT_187490.1 2656 3135170506 80 81
NT_187491.1 1650 3135173295 80 81
NT_187492.1 1451 3135175065 80 81
NT_187493.1 2378 3135176634 80 81
NT_187494.1 2805 3135179141 80 81
NT_187495.1 7992 3135182081 80 81
NT_187496.1 7642 3135190272 80 81
NT_113901.1 182896 3135198110 80 81
NT_167213.1 179198 3135383394 80 81
NT_167214.1 161802 3135564933 80 81
NT_167218.1 179693 3135728859 80 81
NT_187497.1 157432 3135910900 80 81
NT_167220.1 15008 3136070401 80 81
NT_167208.1 164239 3136085697 80 81
NT_187498.1 210658 3136252090 80 81
NT_187499.1 168472 3136465483 80 81
NT_187500.1 41891 3136636162 80 81
NT_187501.1 66486 3136678678 80 81
NT_187502.1 198735 3136746097 80 81
NT_187503.1 93321 3136947418 80 81
NT_187504.1 158759 3137042007 80 81
NT_187505.1 148850 3137202852 80 81
NT_187506.1 150742 3137353664 80 81
NT_187507.1 27745 3137506392 80 81
NT_187508.1 62944 3137534585 80 81
NT_187509.1 40191 3137598417 80 81
NT_187510.1 36723 3137639212 80 81
NT_187511.1 79590 3137676496 80 81
NT_187512.1 71251 3137757182 80 81
NT_167209.1 137718 3137829424 80 81
NT_187513.1 186739 3137968965 80 81
NT_167211.2 176608 3138158139 80 81
NT_113889.1 161147 3138337055 80 81
NW_012132914.1 467143 3138500324 80 81
NW_015495298.1 278659 3138973410 80 81
NW_011332688.1 305542 3139255653 80 81
NW_014040926.1 349938 3139565118 80 81
NW_009646195.1 166200 3139919531 80 81
NW_009646194.1 186494 3140087908 80 81
NW_014040925.1 141019 3140276837 80 81
NW_017852928.1 551020 3140419723 80 81
NW_009646196.1 122022 3140977731 80 81
NW_011332687.1 460100 3141101379 80 81
NW_014040927.1 212205 3141567337 80 81
NW_012132915.1 481245 3141782295 80 81
NW_015495299.1 535088 3142269661 80 81
NW_011332690.1 365499 3142811538 80 81
NW_011332689.1 208149 3143181706 80 81
NW_017363813.1 411654 3143392558 80 81
NW_009646197.1 451168 3143809458 80 81
NW_012132916.1 373699 3144266366 80 81
NW_011332691.1 415308 3144644836 80 81
NW_012132917.1 165718 3145065436 80 81
NW_009646198.1 305979 3145233326 80 81
NW_013171799.1 90922 3145543233 80 81
NW_013171800.1 163749 3145635396 80 81
NW_013171801.1 236512 3145801296 80 81
NW_017363814.1 420675 3146040871 80 81
NW_015495300.1 230434 3146466905 80 81
NW_015495301.1 205407 3146700325 80 81
NW_009646199.1 139087 3146908403 80 81
NW_016107297.1 362221 3147049333 80 81
NW_016107298.1 673059 3147416181 80 81
NW_013171803.1 82315 3148097758 80 81
NW_012132918.1 320750 3148181202 80 81
NW_009646200.1 268330 3148506062 80 81
NW_013171802.1 245716 3148777847 80 81
NW_017363815.1 139427 3149026736 80 81
NW_017852929.1 142129 3149168007 80 81
NW_017852930.1 468267 3149312014 80 81
NW_012132919.1 179932 3149786235 80 81
NW_017852932.1 265876 3149968518 80 81
NW_017852931.1 156998 3150237819 80 81
NW_013171804.1 163882 3150396883 80 81
NW_013171805.1 134099 3150562917 80 81
NW_009646201.1 330164 3150698793 80 81
NW_011332694.1 420164 3151033193 80 81
NW_013171806.1 185507 3151458715 80 81
NW_009646202.1 277797 3151646642 80 81
NW_013171807.1 264545 3151928013 80 81
NW_011332693.1 85284 3152195973 80 81
NW_011332692.1 14347 3152282425 80 81
NW_015148966.1 196940 3152297052 80 81
NW_011332695.1 203552 3152496561 80 81
NW_017363816.1 140877 3152702760 80 81
NW_013171808.1 181958 3152845499 80 81
NW_009646203.1 108875 3153029833 80 81
NW_013171809.1 109323 3153140174 80 81
NW_011332696.1 541038 3153250965 80 81
NW_009646204.1 211377 3153798865 80 81
NW_015148967.1 315610 3154012986 80 81
NW_011332697.1 86533 3154332643 80 81
NW_011332699.1 356766 3154420359 80 81
NW_013171810.1 168146 3154781690 80 81
NW_009646205.1 35455 3154952039 80 81
NW_011332700.1 148762 3154988039 80 81
NW_013171811.1 123480 3155138766 80 81
NW_011332698.1 206320 3155263898 80 81
NW_011332701.1 4998962 3155472898 80 81
NW_012132920.1 2365364 3160534453 80 81
NW_013171812.1 59016 3162929490 80 81
NW_017852933.1 1927115 3162989345 80 81
NW_013171813.1 267463 3164940656 80 81
NW_012132921.1 169136 3165211570 80 81
NW_017363817.1 281919 3165382936 80 81
NW_016107299.1 154723 3165668481 80 81
NW_017363819.1 276292 3165825245 80 81
NW_017363818.1 246895 3166105098 80 81
NW_014040928.1 205101 3166355187 80 81
NW_013171814.1 407387 3166562953 80 81
NW_014040929.1 405389 3166975532 80 81
NW_009646206.1 370917 3167386090 80 81
NW_016107300.1 163926 3167761765 80 81
NW_016107301.1 170206 3167927862 80 81
NW_016107302.1 168131 3168100317 80 81
NW_016107303.1 293522 3168270669 80 81
NW_016107304.1 241058 3168567980 80 81
NW_016107305.1 159285 3168812168 80 81
NW_016107306.1 178197 3168973566 80 81
NW_016107307.1 166713 3169154112 80 81
NW_016107308.1 99845 3169323031 80 81
NW_016107309.1 161095 3169424244 80 81
NW_016107310.1 223118 3169587474 80 81
NW_016107311.1 100553 3169813495 80 81
NW_016107313.1 171263 3169915424 80 81
NW_016107314.1 145691 3170088944 80 81
NW_016107312.1 156965 3170236573 80 81
NW_009646207.1 156562 3170395606 80 81
NW_014040930.1 155930 3170554231 80 81
NW_014040931.1 174749 3170712216 80 81
NW_009646208.1 153027 3170889255 80 81
NW_015148968.1 145162 3171044300 80 81
NW_015148969.1 101037 3171191378 80 81
NW_017363820.1 188004 3171293782 80 81
NW_009646209.1 101150 3171484237 80 81
NT_187515.1 354444 3171586770 80 81
NT_187517.1 256271 3171945763 80 81
NT_187514.1 109528 3172205357 80 81
NT_187520.1 185285 3172316374 80 81
NW_003315905.1 182439 3172504098 80 81
NW_003315906.1 110268 3172688940 80 81
NW_003315907.2 366580 3172800709 80 81
NT_187521.1 50258 3173171993 80 81
NT_187519.1 911658 3173223001 80 81
NT_187516.1 425601 3174146176 80 81
NT_187518.1 165834 3174577219 80 81
NT_187525.1 136240 3174745244 80 81
NT_187526.1 70887 3174883305 80 81
NT_187529.1 223625 3174955197 80 81
NT_187522.1 120616 3175181736 80 81
NW_003315908.1 143390 3175303981 80 81
NT_187524.1 133041 3175449282 80 81
NT_187531.1 138019 3175584107 80 81
NT_187530.1 110395 3175723972 80 81
NT_187528.1 110099 3175835867 80 81
NW_003571033.2 96131 3175947466 80 81
NW_003315909.1 123821 3176044922 80 81
NT_187527.1 174166 3176170410 80 81
NT_187523.1 161578 3176346873 80 81
NW_003871060.2 173151 3176510592 80 81
NT_187535.1 109187 3176686026 80 81
NT_187537.1 224108 3176796698 80 81
NW_003315913.1 180671 3177023731 80 81
NT_187533.1 173649 3177206781 80 81
NT_187536.1 248252 3177382721 80 81
NT_187538.1 113034 3177634197 80 81
NT_187532.1 205312 3177748762 80 81
NT_187534.1 162429 3177956759 80 81
NT_187539.1 184404 3178121337 80 81
NT_187540.1 220246 3178308165 80 81
NW_003315915.1 376187 3178531286 80 81
NT_187541.1 111943 3178912296 80 81
NT_167250.2 586476 3179025757 80 81
NT_187544.1 158965 3179619683 80 81
NW_003315914.1 164536 3179780758 80 81
NT_187542.1 119912 3179947470 80 81
NT_187545.1 205944 3180069000 80 81
NT_187543.1 244096 3180277638 80 81
NT_187550.1 126136 3180524904 80 81
NT_187548.1 179043 3180652735 80 81
NT_187547.1 195710 3180834135 80 81
NW_003315920.1 82728 3181032413 80 81
NW_003571036.1 226852 3181116297 80 81
NT_187551.1 164558 3181346103 80 81
NW_003315917.2 1612928 3181512841 80 81
NW_003315918.1 101241 3183146054 80 81
NT_187549.1 172708 3183248681 80 81
NW_003315919.1 173459 3183423669 80 81
NT_187546.1 131892 3183599415 80 81
NT_167244.2 4672374 3183733080 80 81
NT_187555.1 175808 3188463977 80 81
NT_187554.1 152148 3188642101 80 81
NW_003315921.1 124736 3188796272 80 81
NT_187556.1 870480 3188922686 80 81
NT_187557.1 75005 3189804165 80 81
NW_004166862.2 185823 3189880229 80 81
NT_187552.1 197536 3190068493 80 81
NT_187553.1 271782 3190268617 80 81
NT_187558.1 157952 3190543915 80 81
NT_187561.1 209586 3190703962 80 81
NT_187559.1 158166 3190916288 80 81
NW_003315922.2 119183 3191076553 80 81
NT_187562.1 1111570 3191197344 80 81
NT_187564.1 271455 3192322927 80 81
NT_187563.1 126434 3192597894 80 81
NT_187560.1 209988 3192726027 80 81
NT_187572.1 145606 3192938758 80 81
NT_187568.1 282736 3193086303 80 81
NT_187565.1 292436 3193372692 80 81
NT_187576.1 985506 3193668902 80 81
NT_187570.1 300230 3194666845 80 81
NT_187577.1 624492 3194970946 80 81
NT_187566.1 141812 3195603363 80 81
NT_187567.1 374415 3195747066 80 81
NT_187574.1 133535 3196126280 80 81
NT_187575.1 36640 3196261603 80 81
NT_187573.1 158983 3196298819 80 81
NT_187571.1 305841 3196459908 80 81
NT_187569.1 132244 3196769691 80 81
NW_003315928.1 162988 3196903710 80 81
NW_003315929.1 71551 3197068857 80 81
NW_003315930.1 171286 3197141424 80 81
NW_003315931.1 60032 3197314973 80 81
NT_187578.1 439082 3197375874 80 81
NW_003315934.1 179254 3197820568 80 81
NT_187579.1 181496 3198002183 80 81
NW_003315935.1 309802 3198186071 80 81
NT_187580.1 188315 3198499866 80 81
NT_187586.1 210133 3198690655 80 81
NT_187584.1 177092 3198903535 80 81
NT_187585.1 296895 3199082961 80 81
NT_187583.1 204059 3199383688 80 81
NW_003315936.1 154407 3199590423 80 81
NW_003871073.1 200998 3199746892 80 81
NW_003871074.1 191409 3199950528 80 81
NT_187582.1 67707 3200144450 80 81
NT_187581.1 186169 3200213124 80 81
NW_003571049.1 167313 3200401744 80 81
NW_003571050.1 408271 3200571272 80 81
NT_187588.1 40090 3200984767 80 81
NW_003315938.1 120804 3201025482 80 81
NT_187587.1 238139 3201147917 80 81
NW_003315939.2 169178 3201389158 80 81
NW_003315941.1 138655 3201560576 80 81
NW_003315942.2 152874 3201701090 80 81
NT_187590.1 119498 3201855997 80 81
NW_003315940.1 184319 3201977114 80 81
NT_187589.1 76061 3202163859 80 81
NT_187591.1 56134 3202240993 80 81
NT_187594.1 191684 3202297949 80 81
NT_187593.1 180306 3202492150 80 81
NT_187597.1 103832 3202674830 80 81
NT_187595.1 169134 3202780080 80 81
NT_187592.1 306913 3202951449 80 81
NT_187596.1 37287 3203262319 80 81
NT_187598.1 322166 3203300193 80 81
NT_187601.1 1511111 3203626507 80 81
NT_187599.1 180703 3205156627 80 81
NT_187600.1 1351393 3205339709 80 81
NT_187602.1 478999 3206708115 80 81
NT_187604.1 263054 3207193222 80 81
NT_187603.1 327382 3207459685 80 81
NW_003315943.1 296527 3207791283 80 81
NT_187605.1 244917 3208091637 80 81
NW_003315944.2 388773 3208339739 80 81
NT_187606.1 430880 3208733492 80 81
NT_187610.1 134193 3209169876 80 81
NT_187609.1 63982 3209305867 80 81
NT_187608.1 232857 3209370769 80 81
NT_187607.1 2659700 3209606657 80 81
NW_003315945.1 192462 3212299729 80 81
NW_003315946.1 89672 3212494722 80 81
NW_003315952.3 375691 3212585638 80 81
NT_187613.1 391357 3212966146 80 81
NT_187611.1 196688 3213362515 80 81
NT_187614.1 2877074 3213561782 80 81
NW_003871091.1 278131 3216474943 80 81
NW_003871092.1 70345 3216756674 80 81
NW_003315953.2 133151 3216828022 80 81
NT_167251.2 1821992 3216962958 80 81
NW_003315954.1 223995 3218807848 80 81
NT_187615.1 235827 3219034763 80 81
NT_187616.1 108763 3219273658 80 81
NW_003315955.1 90219 3219383904 80 81
NT_187612.1 178921 3219475371 80 81
NT_187618.1 111737 3219656651 80 81
NW_003315956.1 289831 3219769910 80 81
NW_003315959.1 164789 3220063489 80 81
NW_003315960.1 198278 3220230461 80 81
NW_003315957.1 104552 3220431341 80 81
NW_003315958.1 167950 3220537325 80 81
NW_003315961.1 159547 3220707500 80 81
NT_187617.1 167999 3220869164 80 81
NT_187622.1 61734 3221039383 80 81
NT_187621.1 52969 3221102009 80 81
NW_003315962.1 385657 3221155764 80 81
NW_003315964.2 170222 3221546365 80 81
NW_003315965.1 188024 3221718838 80 81
NW_003315963.1 155864 3221909338 80 81
NT_187619.1 43156 3222067273 80 81
NT_187620.1 233762 3222111091 80 81
NW_003571054.1 987716 3222347907 80 81
NW_003315966.2 128386 3223348093 80 81
NT_187623.1 118774 3223478204 80 81
NT_187625.1 58661 3223598583 80 81
NT_187624.1 183433 3223658098 80 81
NW_003315967.2 63917 3223843949 80 81
NT_187628.1 166743 3223908787 80 81
NT_187627.1 143900 3224077737 80 81
NW_003315968.2 201197 3224223561 80 81
NW_003315969.2 74653 3224427398 80 81
NW_003315970.2 116689 3224503110 80 81
NT_187626.1 82692 3224621378 80 81
NT_187629.1 259914 3224705224 80 81
NT_187632.1 186262 3224968507 80 81
NT_187633.1 304135 3225157218 80 81
NT_187630.1 263666 3225465275 80 81
NT_187631.1 101331 3225732357 80 81
NW_003315972.2 96924 3225835078 80 81
NW_003315971.2 162811 3225933337 80 81
NT_187634.1 284869 3226098302 80 81
NT_187635.1 144206 3226386851 80 81
NT_187646.1 162212 3226532986 80 81
NT_187648.1 214158 3226697344 80 81
NT_187647.1 161218 3226914298 80 81
NT_187649.1 162896 3227077650 80 81
NT_187650.1 378547 3227242702 80 81
NT_187651.1 1144418 3227626101 80 81
NT_187652.1 130957 3228784943 80 81
NT_113891.3 4795265 3228917661 80 81
NT_187653.1 190869 3233772985 80 81
NT_187655.1 136959 3233966358 80 81
NT_187654.1 318687 3234105147 80 81
NT_187656.1 106711 3234427938 80 81
NT_187657.1 214625 3234536105 80 81
NT_187658.1 572349 3234753533 80 81
NT_187659.1 196384 3235333157 80 81
NT_187660.1 5161414 3235532116 80 81
NT_187662.1 137721 3240758168 80 81
NT_187664.1 157099 3240897731 80 81
NT_187661.1 325800 3241056915 80 81
NW_003871093.1 88070 3241386911 80 81
NT_187663.1 1423190 3241476202 80 81
NT_187665.1 174061 3242917308 80 81
NT_187666.1 157710 3243093670 80 81
NW_003571055.2 729520 3243253483 80 81
NW_004504305.1 74013 3243992245 80 81
NT_187667.1 274009 3244067302 80 81
NT_187678.1 166540 3244344855 80 81
NT_187679.1 555799 3244513596 80 81
NT_167245.2 4604811 3245076467 80 81
NT_187680.1 229282 3249738957 80 81
NT_187681.1 218612 3249971226 80 81
NW_003571056.2 1064304 3250192703 80 81
NT_187682.1 176103 3251270431 80 81
NT_187688.1 163458 3251448854 80 81
NT_167246.2 4677643 3251614481 80 81
NW_003571057.2 1091841 3256350727 80 81
NT_187689.1 197351 3257456335 80 81
NT_167247.2 4827813 3257656277 80 81
NW_003571058.2 1066390 3262544570 80 81
NT_187690.1 164170 3263624408 80 81
NT_167248.2 4606388 3263790755 80 81
NW_003571059.2 1002683 3268454855 80 81
NT_187691.1 165607 3269470190 80 81
NT_167249.2 4929269 3269637993 80 81
NW_003571060.1 987100 3274629009 80 81
NT_187692.1 76752 3275628566 80 81
NW_003571061.2 796479 3275706409 80 81
NT_187693.1 1066800 3276512966 80 81
NT_187636.1 248807 3277593236 80 81
NT_187637.1 170399 3277845289 80 81
NT_187638.1 157053 3278017955 80 81
NT_187639.1 171027 3278177107 80 81
NT_187640.1 204239 3278350409 80 81
NT_187641.1 209512 3278557339 80 81
NT_187642.1 155532 3278769609 80 81
NT_187643.1 170698 3278927221 80 81
NT_187644.1 184499 3279100191 80 81
NT_187645.1 170680 3279287131 80 81
NT_187668.1 205194 3279460081 80 81
NT_187669.1 170665 3279667976 80 81
NT_187670.1 184516 3279840914 80 81
NT_187671.1 190932 3280027874 80 81
NT_187672.1 123111 3280221334 80 81
NT_187673.1 170701 3280346125 80 81
NT_187674.1 198005 3280519095 80 81
NT_187675.1 282224 3280719711 80 81
NT_187676.1 187935 3281005598 80 81
NT_187677.1 189352 3281196020 80 81
NT_187683.1 186203 3281387874 80 81
NT_187684.1 200773 3281576542 80 81
NT_187685.1 170148 3281779960 80 81
NT_187686.1 215732 3281952372 80 81
NT_187687.1 170537 3282170936 80 81
NT_113949.2 177381 3282343739 80 81
NC_012920.1 16569 3282523395 80 81
Hi Nils,
in short: the BAM file was created with a different reference. The checkref
subcommand checks whether the reference fasta given on the command line
matches the one given in the BAM header. In your case the BAM header
contains a sequence named "1", which is not part of the fasta file.
Hope this helps,
Andreas
On 13 November 2017 at 06:05, Nils Engel nils321@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC