Aborted on recalculate_window_advance()

[jwalewski]

Hello hifiasm team,

I am trying to use hifiasm on simulated HiFi and Nanopore reads (so both datasets are haploid, since they came from published genome assemblies. As I read in the documentation, I used the -l0 option.)

I got an error on recalculate_window(), which resulted in the program being aborted. For debugging's sake, I've included the rest of the error message.

Let me know if there's anything else you need or any questions you have for me.

(base) rednewt@Enceladus:~$ hifiasm -o /mnt/g/ultimate/Silico_Data/Assembly_Output/HIFI_ASM_ONLY/Test_24_2_22 -t 36 -l0 --ul /mnt/g/ultimate/Silico_Data/Nanopore_input/Athaliana.fa2Xv1.fq.gz /mnt/g/ultimate/Silico_Data/HiFi_input/Athaliana.fa5Xv1.fastq.gz
[M::ha_analyze_count] lowest: count[23] = 10929
[M::ha_analyze_count] highest: count[24] = 12382
[M::ha_hist_line]     2: ****************************************************************************************************> 8294256
[M::ha_hist_line]     3: ****************************************************************************************************> 12575384
[M::ha_hist_line]     4: ****************************************************************************************************> 14715068
[M::ha_hist_line]     5: ****************************************************************************************************> 13659652
[M::ha_hist_line]     6: ****************************************************************************************************> 10762080
[M::ha_hist_line]     7: ****************************************************************************************************> 7336458
[M::ha_hist_line]     8: ****************************************************************************************************> 4378719
[M::ha_hist_line]     9: ****************************************************************************************************> 2284038
[M::ha_hist_line]    10: ****************************************************************************************************> 1131980
[M::ha_hist_line]    11: ****************************************************************************************************> 556115
[M::ha_hist_line]    12: ****************************************************************************************************> 273297
[M::ha_hist_line]    13: ****************************************************************************************************> 137431
[M::ha_hist_line]    14: ****************************************************************************************************> 84970
[M::ha_hist_line]    15: ****************************************************************************************************> 58107
[M::ha_hist_line]    16: ****************************************************************************************************> 42872
[M::ha_hist_line]    17: ****************************************************************************************************> 35748
[M::ha_hist_line]    18: ****************************************************************************************************> 30670
[M::ha_hist_line]    19: ****************************************************************************************************> 25186
[M::ha_hist_line]    20: ****************************************************************************************************> 19032
[M::ha_hist_line]    21: ****************************************************************************************************> 15870
[M::ha_hist_line]    22: **************************************************************************************************** 12414
[M::ha_hist_line]    23: **************************************************************************************** 10929
[M::ha_hist_line]    24: **************************************************************************************************** 12382
[M::ha_hist_line]    25: ******************************************************************************************** 11432
[M::ha_hist_line]    26: ***************************************************************** 8086
[M::ha_hist_line]    27: ************************************************************ 7387
[M::ha_hist_line]    28: *********************************************** 5821
[M::ha_hist_line]    29: ******************************************** 5465
[M::ha_hist_line]    30: ************************************ 4444
[M::ha_hist_line]    31: ************************************ 4435
[M::ha_hist_line]    32: **************************** 3435
[M::ha_hist_line]    33: **************************** 3468
[M::ha_hist_line]    34: ***************************** 3571
[M::ha_hist_line]    35: ************************ 3001
[M::ha_hist_line]    36: ************************* 3117
[M::ha_hist_line]    37: *********************** 2793
[M::ha_hist_line]    38: ******************** 2466
[M::ha_hist_line]    39: ********************** 2773
[M::ha_hist_line]    40: ****************** 2286
[M::ha_hist_line]    41: ******************** 2457
[M::ha_hist_line]    42: ***************** 2140
[M::ha_hist_line]    43: ******************** 2440
[M::ha_hist_line]    44: **************** 2018
[M::ha_hist_line]    45: ************ 1522
[M::ha_hist_line]    46: ************ 1451
[M::ha_hist_line]    47: *********** 1351
[M::ha_hist_line]    48: ********** 1270
[M::ha_hist_line]    49: *********** 1360
[M::ha_hist_line]    50: *********** 1360
[M::ha_hist_line]    51: ********** 1189
[M::ha_hist_line]    52: ********* 1159
[M::ha_hist_line]    53: ******** 968
[M::ha_hist_line]    54: ******* 902
[M::ha_hist_line]    55: ******** 968
[M::ha_hist_line]    56: ********* 1053
[M::ha_hist_line]    57: ******** 959
[M::ha_hist_line]    58: ****** 758
[M::ha_hist_line]    59: ****** 696
[M::ha_hist_line]    60: ***** 679
[M::ha_hist_line]    61: ****** 715
[M::ha_hist_line]    62: ***** 588
[M::ha_hist_line]    63: **** 532
[M::ha_hist_line]    64: **** 506
[M::ha_hist_line]    65: **** 555
[M::ha_hist_line]    66: **** 522
[M::ha_hist_line]    67: **** 500
[M::ha_hist_line]    68: ***** 648
[M::ha_hist_line]    69: **** 521
[M::ha_hist_line]    70: *** 397
[M::ha_hist_line]    71: *** 361
[M::ha_hist_line]    72: *** 315
[M::ha_hist_line]    73: *** 373
[M::ha_hist_line]    74: *** 424
[M::ha_hist_line]    75: *** 320
[M::ha_hist_line]    76: *** 328
[M::ha_hist_line]    77: ** 271
[M::ha_hist_line]    78: *** 344
[M::ha_hist_line]    79: ** 299
[M::ha_hist_line]    80: ** 245
[M::ha_hist_line]    81: ** 235
[M::ha_hist_line]    82: ** 235
[M::ha_hist_line]    83: ** 218
[M::ha_hist_line]    84: ** 239
[M::ha_hist_line]    85: ** 229
[M::ha_hist_line]    86: * 157
[M::ha_hist_line]    87: * 170
[M::ha_hist_line]    88: * 174
[M::ha_hist_line]    89: * 175
[M::ha_hist_line]    90: * 173
[M::ha_hist_line]    91: ** 270
[M::ha_hist_line]    92: ** 227
[M::ha_hist_line]    93: ** 205
[M::ha_hist_line]    94: * 182
[M::ha_hist_line]    95: *** 395
[M::ha_hist_line]    96: ** 261
[M::ha_hist_line]    97: **** 476
[M::ha_hist_line]    98: **** 471
[M::ha_hist_line]    99: ***** 665
[M::ha_hist_line]   100: *** 406
[M::ha_hist_line]   101: ** 224
[M::ha_hist_line]   102: * 114
[M::ha_hist_line]   103: * 97
[M::ha_hist_line]   104: * 85
[M::ha_hist_line]   105: * 97
[M::ha_hist_line]   106: * 72
[M::ha_hist_line]   107: * 87
[M::ha_hist_line]   108: * 68
[M::ha_hist_line]   109: * 76
[M::ha_hist_line]  rest: ************************ 3004
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_ft_gen] peak_hom: 24; peak_het: -1
[M::ha_ct_shrink::78.417*1.54] ==> counted 2424 distinct minimizer k-mers
[M::ha_ft_gen::78.548*[email protected]] ==> filtered out 2424 k-mers occurring 120 or more times
[M::ha_opt_update_cov] updated max_n_chain to 120
[M::yak_count] collected 15273539 minimizers
[M::ha_pt_gen::83.269*1.75] ==> counted 3372969 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[23] = 407
[M::ha_analyze_count] highest: count[24] = 453
[M::ha_hist_line]     1: ****************************************************************************************************> 406688
[M::ha_hist_line]     2: ****************************************************************************************************> 327496
[M::ha_hist_line]     3: ****************************************************************************************************> 492446
[M::ha_hist_line]     4: ****************************************************************************************************> 572802
[M::ha_hist_line]     5: ****************************************************************************************************> 528964
[M::ha_hist_line]     6: ****************************************************************************************************> 415039
[M::ha_hist_line]     7: ****************************************************************************************************> 281046
[M::ha_hist_line]     8: ****************************************************************************************************> 166698
[M::ha_hist_line]     9: ****************************************************************************************************> 86356
[M::ha_hist_line]    10: ****************************************************************************************************> 42658
[M::ha_hist_line]    11: ****************************************************************************************************> 20750
[M::ha_hist_line]    12: ****************************************************************************************************> 10057
[M::ha_hist_line]    13: ****************************************************************************************************> 5029
[M::ha_hist_line]    14: ****************************************************************************************************> 3085
[M::ha_hist_line]    15: ****************************************************************************************************> 2138
[M::ha_hist_line]    16: ****************************************************************************************************> 1574
[M::ha_hist_line]    17: ****************************************************************************************************> 1353
[M::ha_hist_line]    18: ****************************************************************************************************> 1103
[M::ha_hist_line]    19: ****************************************************************************************************> 919
[M::ha_hist_line]    20: ****************************************************************************************************> 671
[M::ha_hist_line]    21: ****************************************************************************************************> 590
[M::ha_hist_line]    22: ****************************************************************************************************> 465
[M::ha_hist_line]    23: ****************************************************************************************** 407
[M::ha_hist_line]    24: **************************************************************************************************** 453
[M::ha_hist_line]    25: **************************************************************************************** 399
[M::ha_hist_line]    26: ******************************************************************** 306
[M::ha_hist_line]    27: ******************************************************* 247
[M::ha_hist_line]    28: ************************************************ 219
[M::ha_hist_line]    29: ********************************************** 207
[M::ha_hist_line]    30: ********************************** 155
[M::ha_hist_line]    31: ********************************* 148
[M::ha_hist_line]    32: ****************************** 136
[M::ha_hist_line]    33: ********************************* 150
[M::ha_hist_line]    34: ************************ 110
[M::ha_hist_line]    35: ************************* 115
[M::ha_hist_line]    36: ************************** 118
[M::ha_hist_line]    37: ******************** 92
[M::ha_hist_line]    38: *********************** 103
[M::ha_hist_line]    39: *********************** 103
[M::ha_hist_line]    40: ****************** 81
[M::ha_hist_line]    41: ***************** 76
[M::ha_hist_line]    42: **************** 72
[M::ha_hist_line]    43: ***************** 75
[M::ha_hist_line]    44: *************** 66
[M::ha_hist_line]    45: ************* 61
[M::ha_hist_line]    46: *********** 50
[M::ha_hist_line]    47: ************ 55
[M::ha_hist_line]    48: ********** 46
[M::ha_hist_line]    49: ********** 46
[M::ha_hist_line]    50: ********** 45
[M::ha_hist_line]    51: ********* 43
[M::ha_hist_line]    52: ******** 37
[M::ha_hist_line]    53: ********* 40
[M::ha_hist_line]    54: ******* 31
[M::ha_hist_line]    55: ******** 36
[M::ha_hist_line]    56: *********** 51
[M::ha_hist_line]    57: ******** 36
[M::ha_hist_line]    58: **** 18
[M::ha_hist_line]    59: ****** 28
[M::ha_hist_line]    60: *** 13
[M::ha_hist_line]    61: ******* 31
[M::ha_hist_line]    62: **** 16
[M::ha_hist_line]    63: **** 20
[M::ha_hist_line]    64: ****** 29
[M::ha_hist_line]    65: *** 15
[M::ha_hist_line]    66: ***** 23
[M::ha_hist_line]    67: ***** 21
[M::ha_hist_line]    68: ***** 22
[M::ha_hist_line]    69: *** 14
[M::ha_hist_line]    70: **** 16
[M::ha_hist_line]    71: ** 11
[M::ha_hist_line]    72: ** 10
[M::ha_hist_line]    73: ****** 25
[M::ha_hist_line]    74: **** 18
[M::ha_hist_line]    75: ** 9
[M::ha_hist_line]    76: *** 12
[M::ha_hist_line]    77: ** 10
[M::ha_hist_line]    78: *** 13
[M::ha_hist_line]    79: ** 8
[M::ha_hist_line]    80: ** 11
[M::ha_hist_line]    81: * 5
[M::ha_hist_line]    82: * 6
[M::ha_hist_line]    83: ** 7
[M::ha_hist_line]    84: ** 8
[M::ha_hist_line]    85: ** 9
[M::ha_hist_line]    86: * 5
[M::ha_hist_line]    87: * 6
[M::ha_hist_line]    88: ** 7
[M::ha_hist_line]    89: * 4
[M::ha_hist_line]    90: * 3
[M::ha_hist_line]    91: ** 11
[M::ha_hist_line]    92: ** 11
[M::ha_hist_line]    93: ** 7
[M::ha_hist_line]    94: *** 12
[M::ha_hist_line]    95: *** 12
[M::ha_hist_line]    96: ** 7
[M::ha_hist_line]    97: *** 13
[M::ha_hist_line]    98: **** 16
[M::ha_hist_line]    99: ***** 23
[M::ha_hist_line]   100: *** 13
[M::ha_hist_line]   101: ** 10
[M::ha_hist_line]   102: * 4
[M::ha_hist_line]   103: * 5
[M::ha_hist_line]  rest: ******* 30
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: count[33] = 150
[M::ha_pt_gen] peak_hom: 33; peak_het: 24
[M::ha_ct_shrink::83.294*1.75] ==> counted 2966281 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 15273539 minimizers
[M::ha_pt_gen::84.696*1.98] ==> indexed 14866851 positions, counted 2966281 distinct minimizer k-mers
hifiasm: Correct.cpp:3511: void recalcate_window_advance(overlap_region_alloc*, All_reads*, const ul_idx_t*, UC_Read*, Correct_dumy*, UC_Read*, kvec_t_u64_warp*, int64_t, double, double): Assertion `error != (unsigned int)-1' failed.
Aborted (core dumped)

[chhylp123]

Would you mind to share the data with me? Thanks so much!

[jwalewski]

Hello, I would be more than happy to share them with you. However, the maximum file size I can upload through this comment is 25MB, and Gzipped the data is still 285 MB.

How would you like the data sent?