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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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0 reads mapped to graph #101

Closed jamesdalg closed 1 year ago

jamesdalg commented 1 year ago

I am using a hifiasm-derived graph to map to chm13 with minigraph. Is there some reason why 0 reads would map to chm13? I am using human sequences and have aligned to reference many, many times.

  mkdir -p /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/minigraph_bubbles/;
        /ceph/project/Wellcome_Discovery/jdalglei/sv_pipeline/minigraph/minigraph -cxggs -t64 /ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.bp.r_utg.gfa > /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/minigraph_bubbles/m64176e_230414_121509.hifi_reads_combined_minigraph_sv_alignment_bubbles_chm13.gfa;
        /ceph/project/Wellcome_Discovery/jdalglei/sv_pipeline/gfatools/gfatools bubble /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/combined/minigraph_bubbles/combined_minigraph_sv_alignment_bubbles_chm13.gfa > /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/m64176e_230414_121509.hifi_reads_minigraph_sv_alignment_bubbles.bed;

[M::main::4.326*1.00] loaded the graph from "/ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa"
[M::mg_index::60.185*2.58] indexed the graph
[M::mg_opt_update::63.714*2.49] occ_max1=100; lc_max_occ=2
[M::ggen_map::94.375*1.86] loaded file "/ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.bp.r_utg.gfa"
[M::ggen_map::94.379*1.86] mapped 0 sequence(s) to the graph
[M::main] Version: 0.20-r559
[M::main] CMD: /ceph/project/Wellcome_Discovery/jdalglei/sv_pipeline/minigraph/minigraph -cxggs -t64 /ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.bp.r_utg.gfa
[M::main] Real time: 96.369 sec; CPU: 177.561 sec; Peak RSS: 16.905 GB
ERROR: failed to read the graph

This is my hifiasm output, and exact commands used:

(sm_pacbio) /ceph/project/Wellcome_Discovery/jdalglei/code/sm/snakemake-pacbio$ cat ../logs/hifiasm.sample=m64176e_230414_121509.hifi_reads-557.out
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 128
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=70149, mem_mib=66900, disk_mb=70149, disk_mib=66900
Select jobs to execute...

[Sun Jun 18 20:57:01 2023]
rule hifiasm:
    input: /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/fastq/m64176e_230414_121509.hifi_reads.fastq.gz
    output: /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.ec.fa.gz, /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.bp.r_utg.gfa
    jobid: 0
    reason: Missing output files: /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.bp.r_utg.gfa, /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.ec.fa.gz
    wildcards: sample=m64176e_230414_121509.hifi_reads
    resources: mem_mb=70149, mem_mib=66900, disk_mb=70149, disk_mib=66900, tmpdir=/var/scratch/jdalglei/557

        #module load samtools;
        rm -rf /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/;
        mkdir -p /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/;
        /ceph/project/Wellcome_Discovery/jdalglei/sv_pipeline/hifiasm/hifiasm -t 128 -o /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm --write-paf --write-ec /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/fastq/m64176e_230414_121509.hifi_reads.fastq.gz ;
        pigz -p 128  /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.ec.fa;

[M::ha_analyze_count] lowest: count[5] = 53910416
[M::ha_analyze_count] highest: count[13] = 176216153
[M::ha_hist_line]     2: ******* 13062814
[M::ha_hist_line]     3: ************ 21737419
[M::ha_hist_line]     4: ********************* 36949695
[M::ha_hist_line]     5: ******************************* 53910416
[M::ha_hist_line]     6: **************************************** 70122758
[M::ha_hist_line]     7: ************************************************* 86908589
[M::ha_hist_line]     8: *********************************************************** 104368045
[M::ha_hist_line]     9: ********************************************************************** 123201742
[M::ha_hist_line]    10: ********************************************************************************* 142852858
[M::ha_hist_line]    11: ******************************************************************************************* 160450744
[M::ha_hist_line]    12: ************************************************************************************************** 172776247
[M::ha_hist_line]    13: **************************************************************************************************** 176216153
[M::ha_hist_line]    14: ************************************************************************************************ 169223301
[M::ha_hist_line]    15: **************************************************************************************** 154760534
[M::ha_hist_line]    16: **************************************************************************** 133724383
[M::ha_hist_line]    17: ************************************************************** 109611852
[M::ha_hist_line]    18: ************************************************ 85130180
[M::ha_hist_line]    19: ************************************ 63178472
[M::ha_hist_line]    20: ************************** 45614786
[M::ha_hist_line]    21: ****************** 31591110
[M::ha_hist_line]    22: ************ 21156020
[M::ha_hist_line]    23: ******** 13752104
[M::ha_hist_line]    24: ***** 8934759
[M::ha_hist_line]    25: *** 5913414
[M::ha_hist_line]    26: ** 4018146
[M::ha_hist_line]    27: ** 2864236
[M::ha_hist_line]    28: * 2172513
[M::ha_hist_line]    29: * 1740877
[M::ha_hist_line]    30: * 1487035
[M::ha_hist_line]    31: * 1310932
[M::ha_hist_line]    32: * 1180632
[M::ha_hist_line]    33: * 1070768
[M::ha_hist_line]    34: * 973493
[M::ha_hist_line]  rest: ********** 17330219
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_ft_gen] peak_hom: 13; peak_het: -1
[M::ha_ct_shrink::982.243*13.34] ==> counted 6239030 distinct minimizer k-mers
[M::ha_ft_gen::988.117*13.27@49.199GB] ==> filtered out 6239030 k-mers occurring 65 or more times
[M::ha_opt_update_cov] updated max_n_chain to 100
[M::yak_count] collected 1110567740 minimizers
[M::ha_pt_gen::1868.622*10.51] ==> counted 105848974 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[5] = 2482762
[M::ha_analyze_count] highest: count[13] = 7037927
[M::ha_hist_line]     1: ****************************************************************************************************> 21469485
[M::ha_hist_line]     2: ************ 859001
[M::ha_hist_line]     3: *************** 1090747
[M::ha_hist_line]     4: ************************* 1747121
[M::ha_hist_line]     5: *********************************** 2482762
[M::ha_hist_line]     6: ********************************************* 3157650
[M::ha_hist_line]     7: ****************************************************** 3820069
[M::ha_hist_line]     8: **************************************************************** 4477761
[M::ha_hist_line]     9: ************************************************************************* 5168533
[M::ha_hist_line]    10: ************************************************************************************ 5881384
[M::ha_hist_line]    11: ********************************************************************************************* 6522784
[M::ha_hist_line]    12: *************************************************************************************************** 6952466
[M::ha_hist_line]    13: **************************************************************************************************** 7037927
[M::ha_hist_line]    14: ************************************************************************************************ 6724482
[M::ha_hist_line]    15: *************************************************************************************** 6120115
[M::ha_hist_line]    16: *************************************************************************** 5267394
[M::ha_hist_line]    17: ************************************************************* 4307034
[M::ha_hist_line]    18: *********************************************** 3339596
[M::ha_hist_line]    19: *********************************** 2481858
[M::ha_hist_line]    20: ************************** 1799729
[M::ha_hist_line]    21: ****************** 1253256
[M::ha_hist_line]    22: ************ 850985
[M::ha_hist_line]    23: ******** 566690
[M::ha_hist_line]    24: ***** 382766
[M::ha_hist_line]    25: **** 267642
[M::ha_hist_line]    26: *** 192912
[M::ha_hist_line]    27: ** 148607
[M::ha_hist_line]    28: ** 120585
[M::ha_hist_line]    29: * 102602
[M::ha_hist_line]    30: * 91303
[M::ha_hist_line]    31: * 82875
[M::ha_hist_line]    32: * 76063
[M::ha_hist_line]    33: * 69793
[M::ha_hist_line]    34: * 64531
[M::ha_hist_line]    35: * 59464
[M::ha_hist_line]    36: * 55095
[M::ha_hist_line]    37: * 50072
[M::ha_hist_line]    38: * 47021
[M::ha_hist_line]    39: * 43508
[M::ha_hist_line]    40: * 40612
[M::ha_hist_line]    41: * 37978
[M::ha_hist_line]    42: * 35496
[M::ha_hist_line]  rest: ******* 501220
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_pt_gen] peak_hom: 13; peak_het: -1
[M::ha_ct_shrink::1868.803*10.52] ==> counted 84379489 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 1110567740 minimizers
[M::ha_pt_gen::1979.366*12.49] ==> indexed 1089098255 positions, counted 84379489 distinct minimizer k-mers
[M::ha_assemble::2333.293*29.65@49.199GB] ==> corrected reads for round 1
[M::ha_assemble] # bases: 41414255663; # corrected bases: 100941312; # recorrected bases: 53021
[M::ha_assemble] size of buffer: 7.890GB
[M::yak_count] collected 1108217270 minimizers
[M::ha_pt_gen::2429.101*30.37] ==> counted 85544291 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[5] = 2361428
[M::ha_analyze_count] highest: count[13] = 6976891
[M::ha_hist_line]     1: ************************* 1709481
[M::ha_hist_line]     2: ******* 466657
[M::ha_hist_line]     3: ************* 910963
[M::ha_hist_line]     4: *********************** 1617654
[M::ha_hist_line]     5: ********************************** 2361428
[M::ha_hist_line]     6: ******************************************* 3019981
[M::ha_hist_line]     7: ***************************************************** 3665177
[M::ha_hist_line]     8: ************************************************************* 4285853
[M::ha_hist_line]     9: *********************************************************************** 4949103
[M::ha_hist_line]    10: ********************************************************************************* 5650260
[M::ha_hist_line]    11: ****************************************************************************************** 6298535
[M::ha_hist_line]    12: ************************************************************************************************* 6796461
[M::ha_hist_line]    13: **************************************************************************************************** 6976891
[M::ha_hist_line]    14: ************************************************************************************************* 6760685
[M::ha_hist_line]    15: ***************************************************************************************** 6240503
[M::ha_hist_line]    16: ****************************************************************************** 5458114
[M::ha_hist_line]    17: ***************************************************************** 4533348
[M::ha_hist_line]    18: *************************************************** 3572698
[M::ha_hist_line]    19: ************************************** 2683056
[M::ha_hist_line]    20: **************************** 1969357
[M::ha_hist_line]    21: ******************** 1394115
[M::ha_hist_line]    22: ************** 952914
[M::ha_hist_line]    23: ********* 639507
[M::ha_hist_line]    24: ****** 429786
[M::ha_hist_line]    25: **** 295513
[M::ha_hist_line]    26: *** 213338
[M::ha_hist_line]    27: ** 160205
[M::ha_hist_line]    28: ** 128620
[M::ha_hist_line]    29: ** 106844
[M::ha_hist_line]    30: * 94167
[M::ha_hist_line]    31: * 84084
[M::ha_hist_line]    32: * 78086
[M::ha_hist_line]    33: * 70954
[M::ha_hist_line]    34: * 66747
[M::ha_hist_line]    35: * 60667
[M::ha_hist_line]    36: * 56895
[M::ha_hist_line]    37: * 51342
[M::ha_hist_line]    38: * 49221
[M::ha_hist_line]    39: * 44354
[M::ha_hist_line]    40: * 41869
[M::ha_hist_line]    41: * 38741
[M::ha_hist_line]    42: * 36146
[M::ha_hist_line]  rest: ******** 523971
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_pt_gen] peak_hom: 13; peak_het: -1
[M::ha_ct_shrink::2429.342*30.37] ==> counted 83834810 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 1108217270 minimizers
[M::ha_pt_gen::2541.409*31.03] ==> indexed 1106507789 positions, counted 83834810 distinct minimizer k-mers
[M::ha_assemble::2846.798*41.28@49.199GB] ==> corrected reads for round 2
[M::ha_assemble] # bases: 41413906223; # corrected bases: 3490358; # recorrected bases: 52437
[M::ha_assemble] size of buffer: 8.123GB
[M::yak_count] collected 1108102080 minimizers
[M::ha_pt_gen::2940.420*41.51] ==> counted 84748634 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[5] = 2356003
[M::ha_analyze_count] highest: count[13] = 6978851
[M::ha_hist_line]     1: ************* 936656
[M::ha_hist_line]     2: ****** 447479
[M::ha_hist_line]     3: ************* 900159
[M::ha_hist_line]     4: *********************** 1614150
[M::ha_hist_line]     5: ********************************** 2356003
[M::ha_hist_line]     6: ******************************************* 3013224
[M::ha_hist_line]     7: **************************************************** 3660047
[M::ha_hist_line]     8: ************************************************************* 4277717
[M::ha_hist_line]     9: *********************************************************************** 4941289
[M::ha_hist_line]    10: ********************************************************************************* 5643372
[M::ha_hist_line]    11: ****************************************************************************************** 6292857
[M::ha_hist_line]    12: ************************************************************************************************* 6793771
[M::ha_hist_line]    13: **************************************************************************************************** 6978851
[M::ha_hist_line]    14: ************************************************************************************************* 6764084
[M::ha_hist_line]    15: ****************************************************************************************** 6246876
[M::ha_hist_line]    16: ****************************************************************************** 5466019
[M::ha_hist_line]    17: ***************************************************************** 4540813
[M::ha_hist_line]    18: *************************************************** 3580192
[M::ha_hist_line]    19: *************************************** 2689507
[M::ha_hist_line]    20: **************************** 1974210
[M::ha_hist_line]    21: ******************** 1398145
[M::ha_hist_line]    22: ************** 955875
[M::ha_hist_line]    23: ********* 641373
[M::ha_hist_line]    24: ****** 431026
[M::ha_hist_line]    25: **** 296250
[M::ha_hist_line]    26: *** 213673
[M::ha_hist_line]    27: ** 160092
[M::ha_hist_line]    28: ** 128874
[M::ha_hist_line]    29: ** 106493
[M::ha_hist_line]    30: * 94647
[M::ha_hist_line]    31: * 84505
[M::ha_hist_line]    32: * 77997
[M::ha_hist_line]    33: * 70947
[M::ha_hist_line]    34: * 66825
[M::ha_hist_line]    35: * 60694
[M::ha_hist_line]    36: * 56942
[M::ha_hist_line]    37: * 51375
[M::ha_hist_line]    38: * 49183
[M::ha_hist_line]    39: * 44400
[M::ha_hist_line]    40: * 41999
[M::ha_hist_line]    41: * 38667
[M::ha_hist_line]    42: * 36269
[M::ha_hist_line]  rest: ******** 525107
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_pt_gen] peak_hom: 13; peak_het: -1
[M::ha_ct_shrink::2940.562*41.51] ==> counted 83811978 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 1108102080 minimizers
[M::ha_pt_gen::3045.754*41.67] ==> indexed 1107165424 positions, counted 83811978 distinct minimizer k-mers
[M::ha_assemble::3347.584*49.38@49.199GB] ==> corrected reads for round 3
[M::ha_assemble] # bases: 41413593517; # corrected bases: 323650; # recorrected bases: 34358
[M::ha_assemble] size of buffer: 7.933GB
[M::yak_count] collected 1108087273 minimizers
[M::ha_pt_gen::3466.719*48.99] ==> counted 84687398 distinct minimizer k-mers
[M::ha_pt_gen] count[4095] = 0 (for sanity check)
[M::ha_analyze_count] lowest: count[5] = 2355039
[M::ha_analyze_count] highest: count[13] = 6979157
[M::ha_hist_line]     1: ************* 879507
[M::ha_hist_line]     2: ****** 444679
[M::ha_hist_line]     3: ************* 898631
[M::ha_hist_line]     4: *********************** 1613695
[M::ha_hist_line]     5: ********************************** 2355039
[M::ha_hist_line]     6: ******************************************* 3012532
[M::ha_hist_line]     7: **************************************************** 3659605
[M::ha_hist_line]     8: ************************************************************* 4277200
[M::ha_hist_line]     9: *********************************************************************** 4940863
[M::ha_hist_line]    10: ********************************************************************************* 5642940
[M::ha_hist_line]    11: ****************************************************************************************** 6292896
[M::ha_hist_line]    12: ************************************************************************************************* 6793840
[M::ha_hist_line]    13: **************************************************************************************************** 6979157
[M::ha_hist_line]    14: ************************************************************************************************* 6764603
[M::ha_hist_line]    15: ****************************************************************************************** 6247477
[M::ha_hist_line]    16: ****************************************************************************** 5466396
[M::ha_hist_line]    17: ***************************************************************** 4541278
[M::ha_hist_line]    18: *************************************************** 3580717
[M::ha_hist_line]    19: *************************************** 2689860
[M::ha_hist_line]    20: **************************** 1974309
[M::ha_hist_line]    21: ******************** 1398419
[M::ha_hist_line]    22: ************** 955974
[M::ha_hist_line]    23: ********* 641473
[M::ha_hist_line]    24: ****** 431158
[M::ha_hist_line]    25: **** 296320
[M::ha_hist_line]    26: *** 213670
[M::ha_hist_line]    27: ** 160161
[M::ha_hist_line]    28: ** 128837
[M::ha_hist_line]    29: ** 106482
[M::ha_hist_line]    30: * 94731
[M::ha_hist_line]    31: * 84479
[M::ha_hist_line]    32: * 77971
[M::ha_hist_line]    33: * 71001
[M::ha_hist_line]    34: * 66791
[M::ha_hist_line]    35: * 60701
[M::ha_hist_line]    36: * 56920
[M::ha_hist_line]    37: * 51364
[M::ha_hist_line]    38: * 49130
[M::ha_hist_line]    39: * 44450
[M::ha_hist_line]    40: * 41972
[M::ha_hist_line]    41: * 38763
[M::ha_hist_line]    42: * 36227
[M::ha_hist_line]  rest: ******** 525180
[M::ha_analyze_count] left: none
[M::ha_analyze_count] right: none
[M::ha_pt_gen] peak_hom: 13; peak_het: -1
[M::ha_ct_shrink::3466.884*48.99] ==> counted 83807891 distinct minimizer k-mers
[M::ha_pt_gen::] counting in normal mode
[M::yak_count] collected 1108087273 minimizers
[M::ha_pt_gen::3567.563*48.96] ==> indexed 1107207766 positions, counted 83807891 distinct minimizer k-mers
[M::ha_assemble::3645.307*50.61@49.199GB] ==> found overlaps for the final round
[M::ha_print_ovlp_stat] # overlaps: 38037299
[M::ha_print_ovlp_stat] # strong overlaps: 22897525
[M::ha_print_ovlp_stat] # weak overlaps: 15139774
[M::ha_print_ovlp_stat] # exact overlaps: 35007981
[M::ha_print_ovlp_stat] # inexact overlaps: 3029318
[M::ha_print_ovlp_stat] # overlaps without large indels: 37890185
[M::ha_print_ovlp_stat] # reverse overlaps: 33549445
Writing PAF to disk ...... 
PAF has been written.
[M::ha_opt_update_cov_min] updated max_n_chain to 100
Writing reads to disk... 
Reads has been written.
Writing ma_hit_ts to disk... 
ma_hit_ts has been written.
Writing ma_hit_ts to disk... 
ma_hit_ts has been written.
bin files have been written.
[M::purge_dups] homozygous read coverage threshold: 12
[M::purge_dups] purge duplication coverage threshold: 16
[M::ug_ext_gfa::] # tips::952
Writing raw unitig GFA to disk... 
Writing processed unitig GFA to disk... 
[M::purge_dups] homozygous read coverage threshold: 12
[M::purge_dups] purge duplication coverage threshold: 16
[M::mc_solve:: # edges: 18802]
[M::mc_solve_core_adv::2.241] ==> Partition
[M::adjust_utg_by_primary] primary contig coverage range: [10, infinity]
Writing /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.bp.p_ctg.gfa to disk... 
[M::reduce_hamming_error_adv::1.056] # inserted edges: 9162, # fixed bubbles: 332
[M::adjust_utg_by_trio] primary contig coverage range: [10, infinity]
[M::recall_arcs] # transitive arcs::80
[M::recall_arcs] # new arcs::135760, # old arcs::91448
[M::clean_trio_untig_graph] # adjusted arcs::0
[M::adjust_utg_by_trio] primary contig coverage range: [10, infinity]
[M::recall_arcs] # transitive arcs::62
[M::recall_arcs] # new arcs::129978, # old arcs::93192
[M::clean_trio_untig_graph] # adjusted arcs::2
[M::output_trio_graph_joint] dedup_base::209516488, miss_base::0
Writing /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.bp.hap1.p_ctg.gfa to disk... 
Writing /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm.bp.hap2.p_ctg.gfa to disk... 
Inconsistency threshold for low-quality regions in BED files: 70%
[M::main] Version: 0.19.5-r592
[M::main] CMD: /ceph/project/Wellcome_Discovery/jdalglei/sv_pipeline/hifiasm/hifiasm -t 128 -o /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230414_121509.hifi_reads/hifiasm/m64176e_230414_121509.hifi_reads_hifiasm.asm --write-paf --write-ec /ceph/project/Wellcome_Discovery/jdalglei/data/pacbio/fastq/m64176e_230414_121509.hifi_reads.fastq.gz
[M::main] Real time: 3983.639 sec; CPU: 185024.211 sec; Peak RSS: 49.199 GB
[Sun Jun 18 22:05:00 2023]
Finished job 0.
1 of 1 steps (100%) done
jamesdalg commented 1 year ago

Given all of this... what can I look at to determine why exactly nothing is mapping to the graph?

jamesdalg commented 1 year ago

I also tried calling them from a gfa from hifiasm, but ran into another error:

       mkdir -p /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230423_000358.hifi_reads/minigraph_bubbles/;
        #/ceph/project/Wellcome_Discovery/jdalglei/sv_pipeline/minigraph/minigraph -cxggs -t64 /ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230423_000358.hifi_reads/hifiasm/m64176e_230423_000358.hifi_reads_hifiasm.asm.bp.r_utg.gfa > /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230423_000358.hifi_reads/minigraph_bubbles/m64176e_230423_000358.hifi_reads_combined_minigraph_sv_alignment_bubbles_chm13.gfa;
        /ceph/project/Wellcome_Discovery/jdalglei/sv_pipeline/minigraph/minigraph -cxasm --call /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230423_000358.hifi_reads/hifiasm/m64176e_230423_000358.hifi_reads_hifiasm.asm.bp.r_utg.gfa /ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa > /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230423_000358.hifi_reads/m64176e_230423_000358.hifi_reads_minigraph_sv_alignment_bubbles.bed
        #/ceph/project/Wellcome_Discovery/jdalglei/sv_pipeline/gfatools/gfatools bubble /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/combined/minigraph_bubbles/combined_minigraph_sv_alignment_bubbles_chm13.gfa > /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230423_000358.hifi_reads/m64176e_230423_000358.hifi_reads_minigraph_sv_alignment_bubbles.bed;

[M::main::29.858*0.57] loaded the graph from "/ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230423_000358.hifi_reads/hifiasm/m64176e_230423_000358.hifi_reads_hifiasm.asm.bp.r_utg.gfa"
[E::mg_index_core] minigraph doesn't work with graphs containing overlapping segments
[M::main] Version: 0.20-r559
[M::main] CMD: /ceph/project/Wellcome_Discovery/jdalglei/sv_pipeline/minigraph/minigraph -cxasm --call /ceph/project/Wellcome_Discovery/jdalglei/results/sm_pacbio/m64176e_230423_000358.hifi_reads/hifiasm/m64176e_230423_000358.hifi_reads_hifiasm.asm.bp.r_utg.gfa /ceph/project/davieslab/jdalglei/reference/chm13v2.0.fa
[M::main] Real time: 34.361 sec; CPU: 21.502 sec; Peak RSS: 6.022 GB
lh3 commented 1 year ago

Minigraph doesn't work with overlap graphs unfortunately.