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Published 20 hours ago • verified publisher icon chhylp123

hifiasm error 6 when assembling large genome together with Hi-C data and can not obtain hap1 and hap2 contigs

Open wuxiaopei0509 opened this issue 1 year ago • 10 comments

Sorry to disturbing you. I used the Hifiasm-0.19.6-r595 version to assemble a huge genome more than 20Gb. However, when I add Hi-C data to do the phased assembly. I cannot get the haplotype-resolved assembly ,namely hap1.contig.gfa and hap2.contig.gfa. Another, an errcor occured after bin files have been written. That is 1698125033024 Then the program is interrupted. I want to know the possible reason and whether it is related with the machine we use. The RAM of our machine is 2T. Thank you a lot !

wuxiaopei0509 avatar Oct 24 '23 05:10 wuxiaopei0509

Did hifiasm produce bin files? Could you please show me what bin files did hifiasm produced?

chhylp123 avatar Oct 26 '23 12:10 chhylp123

Did hifiasm produce bin files? Could you please show me what bin files did hifiasm produced?

Yes, it produced bin files (.asm.ec.bin,.asm.ovlp.reverse.bin和*.asm.ovlp.source.bin) and some other files like *.hic.p_ctg.gfa and *.asm.hic.p_utg.gfa. The produces files list as below: 1698713976530

wuxiaopei0509 avatar Oct 30 '23 01:10 wuxiaopei0509

It might be no enough memory. Could you please use another machine with larger RAM? We may conside to reduce the memory cost for hifiasm soon.

chhylp123 avatar Nov 01 '23 13:11 chhylp123

You can reuse the existing bin files for the new Hi-C assembly. As such the running time won't be too long.

chhylp123 avatar Nov 01 '23 13:11 chhylp123

Just rerun hifiasm with the exactly the same command line.

chhylp123 avatar Nov 05 '23 02:11 chhylp123

Tnanks very much for your reply, I runed the hifiasm without hi-C reads, and I got the results including *hap1.p_ctg.gfa,*hap2.p_ctg.gfa and *.p_ctg.gfa. However, the size of *hap1.p_ctg.gfa is 36G and *hap2.p_ctg.gfa is 22G. The estimated size of my genome is ~20G. What is the reason for the extraordinary large size of the hap1 ? Another question is there was also Error 6 in the log file, does it have impacts on the final assembly results ? 1699167362067 Thank you very much!

wuxiaopei0509 avatar Nov 05 '23 06:11 wuxiaopei0509

Please see: https://hifiasm.readthedocs.io/en/latest/faq.html#how-can-i-tweak-parameters-to-improve-hi-c-integrated-assembly. ERROR6 is a warning so no need to worry about that.

chhylp123 avatar Nov 05 '23 12:11 chhylp123

Hello, I am also try to use hifiasm to assmeble a genome about 20G, I have inputed ONT, HiFi and Hi-C data all together. I got the bin file on day 23, but now another 32 days have passed and I still don't have the final ctg.gfa file. I am very anxious and I would like to ask you, how much time did it take you to get the final result? Looking forward to your reply. Thank you very much!

hcph avatar May 09 '24 13:05 hcph

Hi @hcph, could you please show me the command line? Is hifiasm still running with all CPUs?

chhylp123 avatar May 13 '24 13:05 chhylp123

Hi @hcph, could you please show me the command line? Is hifiasm still running with all CPUs?

Thank you for your reply. My command is [hifiasm -o total_add.asm -t 150 --n-hap 6 --ul ont.sup.pass.fq.gz --ul-cut 500 --h1 hic_R1_clean.fq.gz --h2 hic_R2_clean.fq.gz Hifi_total.fastq.gz 2>hifiasmtotal_new2_nohup.txt &]. And the last lines in the log file including information as following: [M::ha_hist_line] rest: ******************************** 2429102 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: count[226] = 476060 [M::ha_pt_gen] peak_hom: 226; peak_het: 112 [M::ha_ct_shrink::94971.61515.53] ==> counted 445067811 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 49805377384 minimizers [M::ha_pt_gen::104298.46917.36] ==> indexed 49270219638 positions, counted 445067811 distinct minimizer k-mers [M::ha_assemble::552178.013[email protected]] ==> corrected reads for round 1 [M::ha_assemble] # bases: 1644486975154; # corrected bases: 2798408340; # recorrected bases: 2507467 [M::ha_assemble] size of buffer: 25.897GB [M::yak_count] collected 49692381746 minimizers [M::ha_pt_gen::565415.71145.57] ==> counted 427377114 distinct minimizer k-mers [M::ha_pt_gen] count[4095] = 0 (for sanity check) [M::ha_analyze_count] lowest: count[31] = 136458 [M::ha_analyze_count] highest: count[114] = 7543209 [M::ha_hist_line] 1: **************************************************************************************************> 34436789 [M::ha_hist_line] 2: ***************************** 2166961 [M::ha_hist_line] 3: ****************** 1351795 [M::ha_hist_line] 4: ***************** 1288839 [M::ha_hist_line] 5: ***************** 1271541 [M::ha_hist_line] 6: **************** 1235380 [M::ha_hist_line] 7: **************** 1174218 [M::ha_hist_line] 8: *************** 1103019 [M::ha_hist_line] 9: ************** 1029189 [M::ha_hist_line] 10: ************* 952454 [M::ha_hist_line] 11: ************ 875003 [M::ha_hist_line] 12: ********** 785980 [M::ha_hist_line] 13: ********* 682236 [M::ha_hist_line] 14: ******** 589351 [M::ha_hist_line] 15: ******* 493058 [M::ha_hist_line] 16: ***** 397075 [M::ha_hist_line] 17: **** 330230 [M::ha_hist_line] 18: **** 274066 [M::ha_hist_line] 19: *** 231258 [M::ha_hist_line] 20: *** 203936 [M::ha_hist_line] 21: ** 183505 [M::ha_hist_line] 22: ** 171044 [M::ha_hist_line] 23: ** 159437 [M::ha_hist_line] 24: ** 153525 [M::ha_hist_line] 25: ** 148852 [M::ha_hist_line] 26: ** 146181 [M::ha_hist_line] 27: ** 141819 [M::ha_hist_line] 28: ** 140209 [M::ha_hist_line] 29: ** 139420 [M::ha_hist_line] 30: ** 137997 [M::ha_hist_line] 31: ** 136458 [M::ha_hist_line] 32: ** 136632 [M::ha_hist_line] 33: ** 137343 [M::ha_hist_line] 34: ** 137692 [M::ha_hist_line] 35: ** 139017 [M::ha_hist_line] 36: ** 140818 [M::ha_hist_line] 37: ** 143094 [M::ha_hist_line] 38: ** 146478 [M::ha_hist_line] 39: ** 151012 [M::ha_hist_line] 40: ** 155064 [M::ha_hist_line] 41: ** 159866 [M::ha_hist_line] 42: ** 165792 [M::ha_hist_line] 43: ** 171526 [M::ha_hist_line] 44: ** 178434 [M::ha_hist_line] 45: ** 185338 [M::ha_hist_line] 46: *** 191443 [M::ha_hist_line] 47: *** 202387 [M::ha_hist_line] 48: *** 208603 [M::ha_hist_line] 49: *** 217717 [M::ha_hist_line] 50: *** 226533 [M::ha_hist_line] 51: *** 236835 [M::ha_hist_line] 52: *** 247048 [M::ha_hist_line] 53: *** 258938 [M::ha_hist_line] 54: **** 269152 [M::ha_hist_line] 55: **** 282868 [M::ha_hist_line] 56: **** 296782 [M::ha_hist_line] 57: **** 303839 [M::ha_hist_line] 58: **** 320800 [M::ha_hist_line] 59: **** 338310 [M::ha_hist_line] 60: ***** 352382 [M::ha_hist_line] 61: ***** 366138 [M::ha_hist_line] 62: ***** 387120 [M::ha_hist_line] 63: ***** 406859 [M::ha_hist_line] 64: ****** 428876 [M::ha_hist_line] 65: ****** 450555 [M::ha_hist_line] 66: ****** 486883 [M::ha_hist_line] 67: ******* 515686 [M::ha_hist_line] 68: ******* 548009 [M::ha_hist_line] 69: ******** 586080 [M::ha_hist_line] 70: ******** 625255 [M::ha_hist_line] 71: ********* 666917 [M::ha_hist_line] 72: ********* 715263 [M::ha_hist_line] 73: ********** 764406 [M::ha_hist_line] 74: *********** 824993 [M::ha_hist_line] 75: ************ 890854 [M::ha_hist_line] 76: ************* 964600 [M::ha_hist_line] 77: ************** 1043648 [M::ha_hist_line] 78: *************** 1128279 [M::ha_hist_line] 79: **************** 1233753 [M::ha_hist_line] 80: ****************** 1344300 [M::ha_hist_line] 81: ******************* 1454562 [M::ha_hist_line] 82: ********************* 1583428 [M::ha_hist_line] 83: *********************** 1710421 [M::ha_hist_line] 84: ************************* 1850440 [M::ha_hist_line] 85: *************************** 1999762 [M::ha_hist_line] 86: ***************************** 2161506 [M::ha_hist_line] 87: ******************************* 2344903 [M::ha_hist_line] 88: ********************************** 2528851 [M::ha_hist_line] 89: ************************************ 2725500 [M::ha_hist_line] 90: *************************************** 2932480 [M::ha_hist_line] 91: ****************************************** 3145359 [M::ha_hist_line] 92: ********************************************* 3378917 [M::ha_hist_line] 93: ************************************************ 3609479 [M::ha_hist_line] 94: *************************************************** 3849507 [M::ha_hist_line] 95: ****************************************************** 4093012 [M::ha_hist_line] 96: ********************************************************** 4361564 [M::ha_hist_line] 97: ************************************************************* 4614456 [M::ha_hist_line] 98: ***************************************************************** 4871296 [M::ha_hist_line] 99: ******************************************************************** 5136430 [M::ha_hist_line] 100: *********************************************************************** 5384714 [M::ha_hist_line] 101: *************************************************************************** 5639188 [M::ha_hist_line] 102: ****************************************************************************** 5877478 [M::ha_hist_line] 103: ********************************************************************************* 6125956 [M::ha_hist_line] 104: ************************************************************************************ 6345576 [M::ha_hist_line] 105: *************************************************************************************** 6564540 [M::ha_hist_line] 106: ****************************************************************************************** 6767583 [M::ha_hist_line] 107: ******************************************************************************************** 6947983 [M::ha_hist_line] 108: ********************************************************************************************** 7107312 [M::ha_hist_line] 109: ************************************************************************************************ 7241539 [M::ha_hist_line] 110: ************************************************************************************************** 7357618 [M::ha_hist_line] 111: *************************************************************************************************** 7436673 [M::ha_hist_line] 112: *************************************************************************************************** 7505181 [M::ha_hist_line] 113: **************************************************************************************************** 7534967 [M::ha_hist_line] 114: **************************************************************************************************** 7543209 [M::ha_hist_line] 115: **************************************************************************************************** 7514589 [M::ha_hist_line] 116: *************************************************************************************************** 7471555 [M::ha_hist_line] 117: ************************************************************************************************** 7405304 [M::ha_hist_line] 118: ************************************************************************************************* 7294797 [M::ha_hist_line] 119: *********************************************************************************************** 7168797 [M::ha_hist_line] 120: ********************************************************************************************* 7010221 [M::ha_hist_line] 121: ****************************************************************************************** 6816232 [M::ha_hist_line] 122: **************************************************************************************** 6624479 [M::ha_hist_line] 123: ************************************************************************************* 6396697 [M::ha_hist_line] 124: ********************************************************************************** 6165756 [M::ha_hist_line] 125: ****************************************************************************** 5912684 [M::ha_hist_line] 126: *************************************************************************** 5649225 [M::ha_hist_line] 127: *********************************************************************** 5377850 [M::ha_hist_line] 128: ******************************************************************** 5098314 [M::ha_hist_line] 129: **************************************************************** 4804264 [M::ha_hist_line] 130: ************************************************************ 4516651 [M::ha_hist_line] 131: ******************************************************** 4229638 [M::ha_hist_line] 132: ***************************************************** 3961721 [M::ha_hist_line] 133: ************************************************* 3676784 [M::ha_hist_line] 134: ********************************************* 3401782 [M::ha_hist_line] 135: ****************************************** 3132456 [M::ha_hist_line] 136: ************************************** 2877942 [M::ha_hist_line] 137: *********************************** 2627878 [M::ha_hist_line] 138: ******************************** 2399299 [M::ha_hist_line] 139: 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163: ** 136007 [M::ha_hist_line] 164: ** 128462 [M::ha_hist_line] 165: ** 121088 [M::ha_hist_line] 166: ** 116292 [M::ha_hist_line] 167: * 111360 [M::ha_hist_line] 168: * 109143 [M::ha_hist_line] 169: * 107381 [M::ha_hist_line] 170: * 107072 [M::ha_hist_line] 171: * 107054 [M::ha_hist_line] 172: * 107834 [M::ha_hist_line] 173: * 109357 [M::ha_hist_line] 174: * 111675 [M::ha_hist_line] 175: ** 114664 [M::ha_hist_line] 176: ** 118195 [M::ha_hist_line] 177: ** 121339 [M::ha_hist_line] 178: ** 125777 [M::ha_hist_line] 179: ** 130216 [M::ha_hist_line] 180: ** 134927 [M::ha_hist_line] 181: ** 140057 [M::ha_hist_line] 182: ** 145928 [M::ha_hist_line] 183: ** 152280 [M::ha_hist_line] 184: ** 158653 [M::ha_hist_line] 185: ** 164422 [M::ha_hist_line] 186: ** 171896 [M::ha_hist_line] 187: ** 178213 [M::ha_hist_line] 188: ** 184668 [M::ha_hist_line] 189: *** 194160 [M::ha_hist_line] 190: *** 202763 [M::ha_hist_line] 191: *** 210821 [M::ha_hist_line] 192: *** 218155 [M::ha_hist_line] 193: *** 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[M::ha_hist_line] 373: * 77649 [M::ha_hist_line] 374: * 76142 [M::ha_hist_line] 375: * 74078 [M::ha_hist_line] 376: * 72839 [M::ha_hist_line] 377: * 70643 [M::ha_hist_line] 378: * 68774 [M::ha_hist_line] 379: * 67169 [M::ha_hist_line] 380: * 65496 [M::ha_hist_line] 381: * 63763 [M::ha_hist_line] 382: * 62472 [M::ha_hist_line] 383: * 60529 [M::ha_hist_line] 384: * 59640 [M::ha_hist_line] 385: * 57816 [M::ha_hist_line] 386: * 56513 [M::ha_hist_line] 387: * 55150 [M::ha_hist_line] 388: * 54173 [M::ha_hist_line] 389: * 52869 [M::ha_hist_line] 390: * 51784 [M::ha_hist_line] 391: * 50748 [M::ha_hist_line] 392: * 49580 [M::ha_hist_line] 393: * 48682 [M::ha_hist_line] 394: * 47835 [M::ha_hist_line] 395: * 46834 [M::ha_hist_line] 396: * 46183 [M::ha_hist_line] 397: * 44974 [M::ha_hist_line] 398: * 44679 [M::ha_hist_line] 399: * 44110 [M::ha_hist_line] 400: * 43818 [M::ha_hist_line] 401: * 42560 [M::ha_hist_line] 402: * 42664 [M::ha_hist_line] 403: * 42157 [M::ha_hist_line] 404: * 42092 [M::ha_hist_line] 405: * 41577 [M::ha_hist_line] 406: * 40913 [M::ha_hist_line] 407: * 40849 [M::ha_hist_line] 408: * 40668 [M::ha_hist_line] 409: * 40346 [M::ha_hist_line] 410: * 40328 [M::ha_hist_line] 411: * 40197 [M::ha_hist_line] 412: * 40248 [M::ha_hist_line] 413: * 40416 [M::ha_hist_line] 414: * 40577 [M::ha_hist_line] 415: * 40093 [M::ha_hist_line] 416: * 40792 [M::ha_hist_line] 417: * 40414 [M::ha_hist_line] 418: * 41084 [M::ha_hist_line] 419: * 41011 [M::ha_hist_line] 420: * 41108 [M::ha_hist_line] 421: * 41570 [M::ha_hist_line] 422: * 41413 [M::ha_hist_line] 423: * 41448 [M::ha_hist_line] 424: * 41776 [M::ha_hist_line] 425: * 41726 [M::ha_hist_line] 426: * 42103 [M::ha_hist_line] 427: * 42275 [M::ha_hist_line] 428: * 42555 [M::ha_hist_line] 429: * 42963 [M::ha_hist_line] 430: * 42916 [M::ha_hist_line] 431: * 43393 [M::ha_hist_line] 432: * 43777 [M::ha_hist_line] 433: * 43989 [M::ha_hist_line] 434: * 44164 [M::ha_hist_line] 435: * 44164 [M::ha_hist_line] 436: * 44413 [M::ha_hist_line] 437: * 44558 [M::ha_hist_line] 438: * 44585 [M::ha_hist_line] 439: * 44525 [M::ha_hist_line] 440: * 44774 [M::ha_hist_line] 441: * 44214 [M::ha_hist_line] 442: * 44683 [M::ha_hist_line] 443: * 44701 [M::ha_hist_line] 444: * 44095 [M::ha_hist_line] 445: * 44160 [M::ha_hist_line] 446: * 44462 [M::ha_hist_line] 447: * 44077 [M::ha_hist_line] 448: * 44425 [M::ha_hist_line] 449: * 43152 [M::ha_hist_line] 450: * 43292 [M::ha_hist_line] 451: * 43464 [M::ha_hist_line] 452: * 43362 [M::ha_hist_line] 453: * 42573 [M::ha_hist_line] 454: * 42244 [M::ha_hist_line] 455: * 42464 [M::ha_hist_line] 456: * 41840 [M::ha_hist_line] 457: * 41740 [M::ha_hist_line] 458: * 41009 [M::ha_hist_line] 459: * 40974 [M::ha_hist_line] 460: * 40346 [M::ha_hist_line] 461: * 39931 [M::ha_hist_line] 462: * 39720 [M::ha_hist_line] 463: * 38950 [M::ha_hist_line] 464: * 38642 [M::ha_hist_line] 465: * 38568 [M::ha_hist_line] rest: ******************************** 2435193 [M::ha_analyze_count] left: none [M::ha_analyze_count] right: count[227] = 475181 [M::ha_pt_gen] peak_hom: 227; peak_het: 114 [M::ha_ct_shrink::565419.29245.57] ==> counted 392940325 distinct minimizer k-mers [M::ha_pt_gen::] counting in normal mode [M::yak_count] collected 49692381746 minimizers [M::ha_pt_gen::579951.18144.99] ==> indexed 49657944957 positions, counted 392940325 distinct minimizer k-mers

The hifiasm is still running with all CPUs.

hcph avatar May 14 '24 13:05 hcph