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View Code? Open in Web Editor NEWEvaluate variant calls and its combination with k-mer multiplicity
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the choice of --peak
I have two fully-phased haploid assembly of a diploid specices ,but I only want to polishing one of the two fully-phased haploid genome,How should I choose the parameter “--peak” ，is haploid peak value （43.3）or double of haploid_peak value（86.6）?
Adjusted QV values are very low and not improved by merfin
I was using the --hist feature, and came across 2 questions. The first is that the adjusted QV looks very low, but may be reasonably as the calculation just involves adding the overcopy kmers to the missing ones.
The bigger question is that the adjusted QV doesn't change after using merfin, although the merqury QV does (yay!). I've included a subrange of the hist output, but it looks like merfin pushes everything down, going past 0. In the extreme case, the lowest pre-polish was -8.4 and -25.6 after, so it does this likely mean under-represented variations are being chosen too often?
asm
K-mers not found in reads (missing) : 22751
K-mers overly represented in assembly: 208843260.00
K-mers found in the assembly: 3170334467
Merqury QV: 64.66
Adjusted QV: 24.89
The [-2,2] range is
-2.0 1309089
-1.8 592517
-1.6 1014281
-1.4 1305191
-1.2 5581550
-1.0 30997025
-0.8 19795362
-0.6 85256699
-0.4 268855226
-0.2 350358386
0.0 2372053119
0.2 14067234
0.4 6891564
0.6 1342089
0.8 783304
1.0 6148793
1.2 365881
1.4 245394
1.6 271201
1.8 149874
2.0 312288
I then did the same on the assembly I had polished with deepvariant+merfin. This was done before some of the new changes, so was called with bcftools consensus -H 2 as in the docs at the time.
K-mers not found in reads (missing) : 4124
K-mers overly represented in assembly: 209126554.00
K-mers found in the assembly: 3170649177
Merqury QV: 72.08
Adjusted QV: 24.89
and the same subrange
-2.0 1401373
-1.8 627265
-1.6 1074023
-1.4 1381121
-1.2 5639493
-1.0 30930969
-0.8 19649484
-0.6 85134989
-0.4 268863845
-0.2 353061409
0.0 2369464081
0.2 14059266
0.4 6922802
0.6 1347577
0.8 788057
1.0 6163117
1.2 384571
1.4 250586
1.6 288123
1.8 145490
2.0 320921
merfin doesnt respect -threads option
Hi!
FYI, I'm running merfin -dump -threads 8 at the moment, and it is currently running the meryl count step on the genome sequence fasta with 16 threads. Is this a bug?
Best,
Jessen
null output in hist and dump due to missing seek operation
This might be something that can be updated in meryl-utility, so tagging @brianwalenz just in case.
The first time running merfin -hist, the output has a bunch of nulls/nans. The number of contigs is correct, but they appear to be uninitialised. Running the exact same command again then works correctly.
This doesn't appear to happen for -vmer, so after some digging, I noticed that the vmer critical block has
sfile->findSequence(seqId);
sfile->loadSequence(seq);
while for hist and dump it is only the loading.
It looks like findSequence from mery-utility is just a seek operation. I don't know too much about seeks, but presumably after generating the index, the loadSequence is just reading from the end of the index and hence the nulls.
After adding in the findSequence commands before the loading in hist and dump made this problem go away.
Generating fasta index.
Number of contigs: 712
0 (null) 0 0 0 nan
1 (null) 0 0 0 nan
2 (null) 0 0 0 nan
3 (null) 0 0 0 nan
Failed with 'Aborted'; backtrace (libbacktrace):
Hi，
I got an error when running merfin (-polish) :
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Failed with 'Aborted'; backtrace (libbacktrace):
Failed with 'Segmentation fault'; backtrace (libbacktrace):
/var/spool/slurm/d/job4944107/slurm_script: line 8: 23698 Segmentation fault merfin -polish -threads 2 -sequence merge.filter.uniq.vcf -readmers union.meryl -peak 46.4 -prob lookup_table.txt -seqmers /public1/home/seq.fa.meryl -output merfin -memory 1000
Could someone help me?
diploid assembly, haploid reads
Questions: 1. In analyzing an assembly made from diploid DNA using Illumina reads from haploid DNA (a meiotic product from the diploid individual), should ploidy be set to one or two for Merfin? 2. If uncollapsed haplotypes seem likely to be present, is it better to try to purge duplicated regions before polishing, or after? 3. Is it possible that Genomescope2 might underestimate genome size if the genome contains large amounts of repetitive sequences?
Details: I am using Merfin to assess the quality of a long-read assembly made by wtdbg2/redbean from about 25x coverage of a mix of ONT PromethION and PacBio RSII reads. The long-read libraries and assembly were made from diploid DNA, but the Illumina reads I'm using for kmer comparisons were made from a haploid meiotic product from the diploid parent. I take this to mean that the Illumina reads should lack kmers found in the assembly, but any kmers present in the reads and not in the assembly should be either sequencing errors or assembly errors. The size of the wtdbg2 assembly is about 40% larger than the expected haploid genome size of 22.5 Gb, but the Genomescope2 analysis of the (haploid) reads and (diploid) assembly using the diploid setting (-p 2) estimated genome size around 6.5 Gb. 
.
Using Merfin -hist with -sequence <diploid.assembly.fa> -readmers <haploid.reads.meryl> -peak 46 -prob <Genomescope2.lookup.table> -output merfin.hist produces output that is skewed toward the negative, and the stderr output confirms that distribution.
K-mers not found in reads (missing) : 13,284,222,107
K-mers overly represented in assembly: 4,018,646,355.17
K-mers found in the assembly: 32,079,612,419
Plotting the merfin.hist table in R, and zooming in on the region from -50 to 50 on the x-axis shows there are three different traces, as though the assembly is a mix of three different fractions with different K* distributions. One hypothesis is that the PromethION and PacBio RSII reads give rise to regions with different properties, or perhaps non-collapsed haplotypes that are redundant. I haven't tried polishing this assembly yet, so I don't know if that might help.
Segfault in VCF loading
Hi,
I was trying to use merfin with a deepvariant vcf to explore polishing a hifi assembly. When loading the variants, there was a segfault. I've posted the stacktrace below, where it seems the issue is a gt variable is empty and causes the segfault.
From what I could tell, it happened immediately, where ii was on its first iteration in L225 of vcf.c. It is probably related, but it appears that most records were rejected, as below
Loaded 43 records with 43 unique contig(s) from 0 contig IDs.
while excluding 460383 invalid records
The first few lines of the variants were
NC_006853.1_RagTag 2226 . GCC G 1.9 RefCall . GT:GQ:DP:AD:VAF:PL ./.:4:11:8,2:0.181818:0,2,30
NC_006853.1_RagTag 2468 . CG C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:32:13:10,3:0.230769:0,31,47
NC_006853.1_RagTag 18569 . GC G 35.7 PASS . GT:GQ:DP:AD:VAF:PL 0/1:7:104:51,39:0.375:34,0,5
stacktrace
0x0000000000414880 in gtAllele::parseGT (this=0x3e71a50, gt=0x0,
ref=0x693080 "\005\331\030\203\276N\251\263\252\373\214?\002@\266J\310+\036\023e\243\070\235$\260\256z\225p5ܐ\235\023o\016\022\032Ā\214\274\241\204",
alts=0x676b60, alleles=0x3e71a70, isValid=@0x6c33f0: true)
at merfin/vcf.C:59
#2 0x0000000000414817 in gtAllele::gtAllele (this=0x3e71a50, record=0x6c3380)
at merfin/vcf.C:43
#3 0x000000000041618d in posGT::posGT (this=0x3d2d000, record=0x6c3380)
at merfin/vcf.H:138
#4 0x000000000041560c in vcfFile::loadFile (this=0x664650,
inName=0x7fffffffcb15 "../../DV_test/output/asm.output.vcf.gz")
at merfin/vcf.C:228
#5 0x00000000004150b6 in vcfFile::vcfFile (this=0x664650,
inName=0x7fffffffcb15 "../../DV_test/output/asm.output.vcf.gz")
at merfin/vcf.C:154
#6 0x0000000000408b05 in main (argc=18, argv=0x7fffffffc418)
at merfin/merfin.C:985
Input for cartesian plot
I haven't run merfin yet for the illumina data I have yet, but wasn't entirely clear on the usage of the cartesian plot scripts. The input for cartesian_plot.R is the output of simplify_dump.sh, and the input for that should be $1=illumina.dump and $2=hifi.dump?
Seg Fault?
I got a seg fault error running merfin:
184493 Segmentation fault (core dumped) merfin -polish -threads 40 -sequence genome.out.fasta -peak
here's the total command output:
Found 1 command tree.
Counting 46 (estimated) billion canonical 21-mers from 1 input file:
sequence-file: m64047_210504_171840.ccs.filt.fastq
SIMPLE MODE
-----------
21-mers
-> 4398046511104 entries for counts up to 65535.
-> 64 Tbits memory used
50359637777 input bases
-> expected max count of 201438551, needing 13 extra bits.
-> 52 Tbits memory used
14 TB memory needed
COMPLEX MODE
------------
prefix # of struct kmers/ segs/ min data total
bits prefix memory prefix prefix memory memory memory
------ ------- ------- ------- ------- ------- ------- -------
1 2 P 240 MB 11 GM 15 MS 8192 B 120 GB 120 GB
2 4 P 234 MB 6003 MM 7506 kS 16 kB 117 GB 117 GB
3 8 P 228 MB 3001 MM 3659 kS 32 kB 114 GB 114 GB
4 16 P 222 MB 1500 MM 1782 kS 64 kB 111 GB 111 GB
5 32 P 217 MB 750 MM 868 kS 128 kB 108 GB 108 GB
6 64 P 211 MB 375 MM 422 kS 256 kB 105 GB 105 GB
7 128 P 205 MB 187 MM 205 kS 512 kB 102 GB 102 GB
8 256 P 200 MB 93 MM 99 kS 1024 kB 99 GB 99 GB
9 512 P 195 MB 46 MM 48 kS 2048 kB 96 GB 97 GB
10 1024 P 190 MB 23 MM 23 kS 4096 kB 93 GB 93 GB
11 2048 P 188 MB 11 MM 11 kS 8192 kB 90 GB 91 GB
12 4096 P 188 MB 6003 kM 5630 S 16 MB 87 GB 88 GB
13 8192 P 195 MB 3001 kM 2723 S 32 MB 85 GB 85 GB
14 16 kP 214 MB 1500 kM 1314 S 64 MB 82 GB 82 GB
15 32 kP 259 MB 750 kM 634 S 128 MB 79 GB 79 GB
16 64 kP 354 MB 375 kM 305 S 256 MB 76 GB 76 GB
17 128 kP 551 MB 187 kM 147 S 512 MB 73 GB 74 GB
18 256 kP 950 MB 93 kM 71 S 1024 MB 71 GB 71 GB
19 512 kP 1752 MB 46 kM 34 S 2048 MB 68 GB 69 GB
20 1024 kP 3368 MB 23 kM 17 S 4096 MB 68 GB 71 GB
21 2048 kP 6592 MB 11 kM 8 S 8192 MB 64 GB 70 GB Best Value!
22 4096 kP 12 GB 6004 M 4 S 16 GB 64 GB 76 GB
23 8192 kP 25 GB 3002 M 2 S 32 GB 64 GB 89 GB
24 16 MP 50 GB 1501 M 1 S 64 GB 64 GB 114 GB
25 32 MP 101 GB 751 M 1 S 128 GB 128 GB 229 GB
26 64 MP 202 GB 376 M 1 S 256 GB 256 GB 458 GB
27 128 MP 405 GB 188 M 1 S 512 GB 512 GB 917 GB
28 256 MP 810 GB 94 M 1 S 1024 GB 1024 GB 1834 GB
29 512 MP 1620 GB 47 M 1 S 2048 GB 2048 GB 3668 GB
FINAL CONFIGURATION
-------------------
Estimated to require 134 GB memory out of 376 GB allowed.
Estimated to require 2 batches.
Configured complex mode for 134.562 GB memory per batch, and up to 2 batches.
Start counting with THREADED method.
Used 20.955 GB / 376.238 GB to store 2093707 kmers; need 0.019 GB to sort 32156 kmers
Used 21.085 GB / 376.238 GB to store 12561864 kmers; need 0.020 GB to sort 33711 kmers
Used 21.233 GB / 376.238 GB to store 25124022 kmers; need 0.021 GB to sort 35059 kmers
Used 21.380 GB / 376.238 GB to store 37685928 kmers; need 0.023 GB to sort 38250 kmers
Used 21.528 GB / 376.238 GB to store 50247687 kmers; need 0.023 GB to sort 38250 kmers
Used 21.673 GB / 376.238 GB to store 62809404 kmers; need 0.023 GB to sort 38250 kmers
Used 21.818 GB / 376.238 GB to store 75371079 kmers; need 0.023 GB to sort 38250 kmers
Used 21.917 GB / 376.238 GB to store 161208824 kmers; need 0.058 GB to sort 97311 kmers
Used 22.021 GB / 376.238 GB to store 314041409 kmers; need 0.096 GB to sort 161817 kmers
Used 22.121 GB / 376.238 GB to store 431282031 kmers; need 0.122 GB to sort 203849 kmers
Used 22.233 GB / 376.238 GB to store 542243657 kmers; need 0.137 GB to sort 229598 kmers
Used 22.326 GB / 376.238 GB to store 625988472 kmers; need 0.171 GB to sort 287669 kmers
Used 22.426 GB / 376.238 GB to store 709733615 kmers; need 0.197 GB to sort 330745 kmers
Used 22.534 GB / 376.238 GB to store 795571329 kmers; need 0.217 GB to sort 363991 kmers
Used 22.643 GB / 376.238 GB to store 877222411 kmers; need 0.234 GB to sort 393394 kmers
Used 22.750 GB / 376.238 GB to store 954687104 kmers; need 0.255 GB to sort 427496 kmers
Used 22.854 GB / 376.238 GB to store 1025869759 kmers; need 0.277 GB to sort 464254 kmers
Used 22.966 GB / 376.238 GB to store 1101240830 kmers; need 0.291 GB to sort 488123 kmers
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Used 23.860 GB / 376.238 GB to store 1641406779 kmers; need 0.418 GB to sort 701275 kmers
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Used 24.754 GB / 376.238 GB to store 2120858941 kmers; need 0.545 GB to sort 914800 kmers
Used 24.871 GB / 376.238 GB to store 2181576822 kmers; need 0.555 GB to sort 930648 kmers
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Used 25.089 GB / 376.238 GB to store 2292542156 kmers; need 0.591 GB to sort 990751 kmers
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Used 25.549 GB / 376.238 GB to store 2522848945 kmers; need 0.646 GB to sort 1083450 kmers
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Used 36.255 GB / 376.238 GB to store 7195974696 kmers; need 1.829 GB to sort 3068730 kmers
Used 36.371 GB / 376.238 GB to store 7244130777 kmers; need 1.841 GB to sort 3088371 kmers
Used 36.487 GB / 376.238 GB to store 7292286530 kmers; need 1.854 GB to sort 3110280 kmers
Used 36.603 GB / 376.238 GB to store 7340442466 kmers; need 1.864 GB to sort 3126448 kmers
Used 36.715 GB / 376.238 GB to store 7386504923 kmers; need 1.879 GB to sort 3152128 kmers
Used 36.830 GB / 376.238 GB to store 7434661370 kmers; need 1.890 GB to sort 3170062 kmers
Used 36.942 GB / 376.238 GB to store 7480723596 kmers; need 1.904 GB to sort 3193819 kmers
Used 37.059 GB / 376.238 GB to store 7528879703 kmers; need 1.914 GB to sort 3211978 kmers
Used 37.175 GB / 376.238 GB to store 7577036101 kmers; need 1.926 GB to sort 3230864 kmers
Used 37.286 GB / 376.238 GB to store 7623098684 kmers; need 1.942 GB to sort 3257891 kmers
Used 37.402 GB / 376.238 GB to store 7671255251 kmers; need 1.952 GB to sort 3274160 kmers
Used 37.519 GB / 376.238 GB to store 7719410680 kmers; need 1.961 GB to sort 3289514 kmers
Used 37.632 GB / 376.238 GB to store 7765473620 kmers; need 1.976 GB to sort 3315553 kmers
Used 37.753 GB / 376.238 GB to store 7815723033 kmers; need 1.986 GB to sort 3332158 kmers
Used 37.865 GB / 376.238 GB to store 7861785721 kmers; need 2.003 GB to sort 3359807 kmers
Used 37.982 GB / 376.238 GB to store 7909942536 kmers; need 2.011 GB to sort 3374173 kmers
Used 38.098 GB / 376.238 GB to store 7958098952 kmers; need 2.022 GB to sort 3392254 kmers
Used 38.210 GB / 376.238 GB to store 8004161241 kmers; need 2.037 GB to sort 3417892 kmers
Used 38.327 GB / 376.238 GB to store 8052318182 kmers; need 2.048 GB to sort 3436590 kmers
Used 38.439 GB / 376.238 GB to store 8098380697 kmers; need 2.062 GB to sort 3459198 kmers
Used 38.556 GB / 376.238 GB to store 8146536966 kmers; need 2.074 GB to sort 3478776 kmers
Used 38.673 GB / 376.238 GB to store 8194693130 kmers; need 2.087 GB to sort 3501225 kmers
Used 38.790 GB / 376.238 GB to store 8242849132 kmers; need 2.099 GB to sort 3521505 kmers
Used 38.906 GB / 376.238 GB to store 8291005443 kmers; need 2.114 GB to sort 3547064 kmers
Used 39.023 GB / 376.238 GB to store 8339161481 kmers; need 2.124 GB to sort 3563036 kmers
Used 39.135 GB / 376.238 GB to store 8385223893 kmers; need 2.141 GB to sort 3591180 kmers
Used 39.257 GB / 376.238 GB to store 8435473847 kmers; need 2.149 GB to sort 3605984 kmers
Used 39.374 GB / 376.238 GB to store 8483630389 kmers; need 2.165 GB to sort 3632833 kmers
Used 39.491 GB / 376.238 GB to store 8531785880 kmers; need 2.174 GB to sort 3647116 kmers
Used 39.608 GB / 376.238 GB to store 8579941361 kmers; need 2.182 GB to sort 3661617 kmers
Used 39.721 GB / 376.238 GB to store 8626003922 kmers; need 2.199 GB to sort 3688777 kmers
Used 39.844 GB / 376.238 GB to store 8676254182 kmers; need 2.207 GB to sort 3702486 kmers
Used 39.957 GB / 376.238 GB to store 8722316554 kmers; need 2.223 GB to sort 3729626 kmers
Used 40.075 GB / 376.238 GB to store 8770472928 kmers; need 2.233 GB to sort 3746224 kmers
Used 40.192 GB / 376.238 GB to store 8818628781 kmers; need 2.246 GB to sort 3767327 kmers
Used 40.310 GB / 376.238 GB to store 8866784607 kmers; need 2.257 GB to sort 3786285 kmers
Used 40.422 GB / 376.238 GB to store 8912847179 kmers; need 2.271 GB to sort 3810417 kmers
Used 40.539 GB / 376.238 GB to store 8961004099 kmers; need 2.281 GB to sort 3826230 kmers
Used 40.651 GB / 376.238 GB to store 9007066682 kmers; need 2.296 GB to sort 3852408 kmers
Used 40.774 GB / 376.238 GB to store 9057317067 kmers; need 2.303 GB to sort 3863976 kmers
Used 40.882 GB / 376.238 GB to store 9101285224 kmers; need 2.320 GB to sort 3892743 kmers
Used 41.006 GB / 376.238 GB to store 9151535725 kmers; need 2.327 GB to sort 3904093 kmers
Used 41.114 GB / 376.238 GB to store 9195504364 kmers; need 2.345 GB to sort 3934614 kmers
Used 41.232 GB / 376.238 GB to store 9243661053 kmers; need 2.353 GB to sort 3947569 kmers
Used 41.349 GB / 376.238 GB to store 9291816295 kmers; need 2.363 GB to sort 3963736 kmers
Used 41.462 GB / 376.238 GB to store 9337880222 kmers; need 2.376 GB to sort 3986155 kmers
Used 41.579 GB / 376.238 GB to store 9386037061 kmers; need 2.390 GB to sort 4009523 kmers
Used 41.696 GB / 376.238 GB to store 9434193492 kmers; need 2.400 GB to sort 4026193 kmers
Used 41.809 GB / 376.238 GB to store 9480256547 kmers; need 2.413 GB to sort 4048204 kmers
Used 41.923 GB / 376.238 GB to store 9526319355 kmers; need 2.426 GB to sort 4070080 kmers
Used 42.035 GB / 376.238 GB to store 9572382777 kmers; need 2.441 GB to sort 4094968 kmers
Used 42.149 GB / 376.238 GB to store 9618444793 kmers; need 2.454 GB to sort 4117408 kmers
Used 42.272 GB / 376.238 GB to store 9668694622 kmers; need 2.459 GB to sort 4124989 kmers
Used 42.390 GB / 376.238 GB to store 9716851290 kmers; need 2.473 GB to sort 4148656 kmers
Used 42.508 GB / 376.238 GB to store 9765008135 kmers; need 2.481 GB to sort 4162741 kmers
Used 42.620 GB / 376.238 GB to store 9811071407 kmers; need 2.496 GB to sort 4187193 kmers
Used 42.738 GB / 376.238 GB to store 9859227410 kmers; need 2.507 GB to sort 4206005 kmers
Used 42.851 GB / 376.238 GB to store 9905289478 kmers; need 2.521 GB to sort 4229707 kmers
Used 42.968 GB / 376.238 GB to store 9953445430 kmers; need 2.532 GB to sort 4247781 kmers
Used 43.081 GB / 376.238 GB to store 9999508496 kmers; need 2.545 GB to sort 4270544 kmers
Used 43.198 GB / 376.238 GB to store 10047666046 kmers; need 2.557 GB to sort 4290760 kmers
Used 43.311 GB / 376.238 GB to store 10093729012 kmers; need 2.571 GB to sort 4312790 kmers
Used 43.430 GB / 376.238 GB to store 10141884901 kmers; need 2.578 GB to sort 4324366 kmers
Used 43.538 GB / 376.238 GB to store 10185854406 kmers; need 2.597 GB to sort 4356366 kmers
Used 43.656 GB / 376.238 GB to store 10234011305 kmers; need 2.604 GB to sort 4369040 kmers
Used 43.774 GB / 376.238 GB to store 10282167948 kmers; need 2.616 GB to sort 4388153 kmers
Used 43.887 GB / 376.238 GB to store 10328230209 kmers; need 2.630 GB to sort 4412715 kmers
Used 44.009 GB / 376.238 GB to store 10378480710 kmers; need 2.637 GB to sort 4423953 kmers
Used 44.118 GB / 376.238 GB to store 10422449460 kmers; need 2.656 GB to sort 4456037 kmers
Used 44.241 GB / 376.238 GB to store 10472698535 kmers; need 2.660 GB to sort 4463297 kmers
Used 44.355 GB / 376.238 GB to store 10518761368 kmers; need 2.674 GB to sort 4486102 kmers
Used 44.473 GB / 376.238 GB to store 10566917119 kmers; need 2.686 GB to sort 4505911 kmers
Used 44.592 GB / 376.238 GB to store 10615073955 kmers; need 2.696 GB to sort 4523145 kmers
Used 44.705 GB / 376.238 GB to store 10661136538 kmers; need 2.710 GB to sort 4546915 kmers
Used 44.818 GB / 376.238 GB to store 10707199070 kmers; need 2.725 GB to sort 4572138 kmers
Used 44.936 GB / 376.238 GB to store 10755355453 kmers; need 2.732 GB to sort 4584316 kmers
Used 45.054 GB / 376.238 GB to store 10803512415 kmers; need 2.749 GB to sort 4612272 kmers
Used 45.172 GB / 376.238 GB to store 10851669139 kmers; need 2.758 GB to sort 4626960 kmers
Used 45.286 GB / 376.238 GB to store 10897731974 kmers; need 2.770 GB to sort 4647932 kmers
Used 45.399 GB / 376.238 GB to store 10943795492 kmers; need 2.785 GB to sort 4672729 kmers
Used 45.517 GB / 376.238 GB to store 10991952181 kmers; need 2.792 GB to sort 4684704 kmers
Used 45.635 GB / 376.238 GB to store 11040108286 kmers; need 2.810 GB to sort 4715084 kmers
Used 45.758 GB / 376.238 GB to store 11090358703 kmers; need 2.817 GB to sort 4725840 kmers
Used 45.870 GB / 376.238 GB to store 11136421853 kmers; need 2.838 GB to sort 4760723 kmers
Used 45.994 GB / 376.238 GB to store 11186672724 kmers; need 2.842 GB to sort 4767812 kmers
Used 46.108 GB / 376.238 GB to store 11232734889 kmers; need 2.856 GB to sort 4792293 kmers
Used 46.221 GB / 376.238 GB to store 11278797367 kmers; need 2.869 GB to sort 4814198 kmers
Used 46.333 GB / 376.238 GB to store 11324860470 kmers; need 2.884 GB to sort 4838399 kmers
Used 46.451 GB / 376.238 GB to store 11373017602 kmers; need 2.892 GB to sort 4852439 kmers
Used 46.571 GB / 376.238 GB to store 11421173775 kmers; need 2.902 GB to sort 4868730 kmers
Used 46.685 GB / 376.238 GB to store 11467237177 kmers; need 2.916 GB to sort 4891905 kmers
Used 46.798 GB / 376.238 GB to store 11513300894 kmers; need 2.936 GB to sort 4924979 kmers
Used 46.921 GB / 376.238 GB to store 11563549904 kmers; need 2.942 GB to sort 4935738 kmers
Used 47.039 GB / 376.238 GB to store 11611706740 kmers; need 2.952 GB to sort 4953354 kmers
Used 47.152 GB / 376.238 GB to store 11657769818 kmers; need 2.968 GB to sort 4978979 kmers
Used 47.275 GB / 376.238 GB to store 11708019919 kmers; need 2.974 GB to sort 4988842 kmers
Used 47.383 GB / 376.238 GB to store 11751989698 kmers; need 2.994 GB to sort 5022513 kmers
Used 47.507 GB / 376.238 GB to store 11802240871 kmers; need 2.997 GB to sort 5027580 kmers
Used 47.620 GB / 376.238 GB to store 11848304316 kmers; need 3.013 GB to sort 5054640 kmers
Used 47.738 GB / 376.238 GB to store 11896461279 kmers; need 3.022 GB to sort 5069976 kmers
Used 47.851 GB / 376.238 GB to store 11942524142 kmers; need 3.038 GB to sort 5096436 kmers
Used 47.969 GB / 376.238 GB to store 11990681356 kmers; need 3.049 GB to sort 5114849 kmers
Used 48.088 GB / 376.238 GB to store 12038838046 kmers; need 3.064 GB to sort 5140797 kmers
Used 48.207 GB / 376.238 GB to store 12086995197 kmers; need 3.071 GB to sort 5152049 kmers
Used 48.325 GB / 376.238 GB to store 12135151718 kmers; need 3.089 GB to sort 5182384 kmers
Used 48.444 GB / 376.238 GB to store 12183307344 kmers; need 3.096 GB to sort 5194399 kmers
Used 48.557 GB / 376.238 GB to store 12229369319 kmers; need 3.108 GB to sort 5214477 kmers
Used 48.671 GB / 376.238 GB to store 12275432345 kmers; need 3.122 GB to sort 5237624 kmers
Used 48.789 GB / 376.238 GB to store 12323588803 kmers; need 3.130 GB to sort 5250963 kmers
Used 48.906 GB / 376.238 GB to store 12371745302 kmers; need 3.147 GB to sort 5279884 kmers
Used 49.030 GB / 376.238 GB to store 12421995787 kmers; need 3.152 GB to sort 5288365 kmers
Used 49.142 GB / 376.238 GB to store 12468058243 kmers; need 3.166 GB to sort 5312329 kmers
Used 49.260 GB / 376.238 GB to store 12516214218 kmers; need 3.176 GB to sort 5328124 kmers
Used 49.373 GB / 376.238 GB to store 12562277389 kmers; need 3.192 GB to sort 5355131 kmers
Used 49.492 GB / 376.238 GB to store 12610433490 kmers; need 3.202 GB to sort 5372444 kmers
Used 49.611 GB / 376.238 GB to store 12658590095 kmers; need 3.213 GB to sort 5389759 kmers
Used 49.725 GB / 376.238 GB to store 12704653810 kmers; need 3.225 GB to sort 5410366 kmers
Used 49.838 GB / 376.238 GB to store 12750717015 kmers; need 3.238 GB to sort 5432218 kmers
Used 49.957 GB / 376.238 GB to store 12798873568 kmers; need 3.249 GB to sort 5450546 kmers
Used 50.071 GB / 376.238 GB to store 12844935799 kmers; need 3.261 GB to sort 5471658 kmers
Used 50.184 GB / 376.238 GB to store 12890997983 kmers; need 3.275 GB to sort 5495020 kmers
Used 50.303 GB / 376.238 GB to store 12939154945 kmers; need 3.286 GB to sort 5513500 kmers
Used 50.422 GB / 376.238 GB to store 12987311594 kmers; need 3.295 GB to sort 5527533 kmers
Used 50.540 GB / 376.238 GB to store 13035467547 kmers; need 3.307 GB to sort 5547578 kmers
Used 50.652 GB / 376.238 GB to store 13081531012 kmers; need 3.320 GB to sort 5569221 kmers
Used 50.765 GB / 376.238 GB to store 13127594036 kmers; need 3.332 GB to sort 5590533 kmers
Used 50.884 GB / 376.238 GB to store 13175751082 kmers; need 3.343 GB to sort 5608403 kmers
Used 51.003 GB / 376.238 GB to store 13223907459 kmers; need 3.356 GB to sort 5630060 kmers
Used 51.117 GB / 376.238 GB to store 13269970966 kmers; need 3.369 GB to sort 5652354 kmers
Used 51.236 GB / 376.238 GB to store 13318127456 kmers; need 3.379 GB to sort 5669822 kmers
Used 51.348 GB / 376.238 GB to store 13364190501 kmers; need 3.395 GB to sort 5695130 kmers
Used 51.468 GB / 376.238 GB to store 13412346130 kmers; need 3.404 GB to sort 5710568 kmers
Used 51.582 GB / 376.238 GB to store 13458409660 kmers; need 3.421 GB to sort 5739410 kmers
Used 51.705 GB / 376.238 GB to store 13508660022 kmers; need 3.427 GB to sort 5749095 kmers
Used 51.820 GB / 376.238 GB to store 13554722924 kmers; need 3.441 GB to sort 5772990 kmers
Used 51.937 GB / 376.238 GB to store 13602878785 kmers; need 3.453 GB to sort 5792336 kmers
Used 52.051 GB / 376.238 GB to store 13648941970 kmers; need 3.466 GB to sort 5815233 kmers
Used 52.169 GB / 376.238 GB to store 13697098785 kmers; need 3.474 GB to sort 5829174 kmers
Used 52.282 GB / 376.238 GB to store 13743161770 kmers; need 3.491 GB to sort 5857597 kmers
Used 52.402 GB / 376.238 GB to store 13791318408 kmers; need 3.500 GB to sort 5872409 kmers
Used 52.520 GB / 376.238 GB to store 13839474839 kmers; need 3.518 GB to sort 5901848 kmers
Used 52.639 GB / 376.238 GB to store 13887631696 kmers; need 3.524 GB to sort 5913127 kmers
Used 52.753 GB / 376.238 GB to store 13933694510 kmers; need 3.536 GB to sort 5932870 kmers
Used 52.867 GB / 376.238 GB to store 13979758220 kmers; need 3.549 GB to sort 5953581 kmers
Used 52.981 GB / 376.238 GB to store 14025821160 kmers; need 3.561 GB to sort 5974992 kmers
Used 53.094 GB / 376.238 GB to store 14071884247 kmers; need 3.573 GB to sort 5994965 kmers
Used 53.213 GB / 376.238 GB to store 14120041209 kmers; need 3.583 GB to sort 6011469 kmers
Used 53.326 GB / 376.238 GB to store 14166104905 kmers; need 3.599 GB to sort 6038373 kmers
Used 53.449 GB / 376.238 GB to store 14216355922 kmers; need 3.607 GB to sort 6051708 kmers
Used 53.562 GB / 376.238 GB to store 14262419898 kmers; need 3.624 GB to sort 6079377 kmers
Used 53.686 GB / 376.238 GB to store 14312671575 kmers; need 3.630 GB to sort 6090699 kmers
Used 53.799 GB / 376.238 GB to store 14358734925 kmers; need 3.647 GB to sort 6118616 kmers
Used 53.919 GB / 376.238 GB to store 14406892475 kmers; need 3.655 GB to sort 6131842 kmers
Used 54.027 GB / 376.238 GB to store 14450862002 kmers; need 3.673 GB to sort 6161668 kmers
Used 54.147 GB / 376.238 GB to store 14499018390 kmers; need 3.682 GB to sort 6178148 kmers
Used 54.265 GB / 376.238 GB to store 14547175791 kmers; need 3.692 GB to sort 6193846 kmers
Used 54.379 GB / 376.238 GB to store 14593239739 kmers; need 3.704 GB to sort 6214962 kmers
Used 54.492 GB / 376.238 GB to store 14639303440 kmers; need 3.717 GB to sort 6235331 kmers
Used 54.611 GB / 376.238 GB to store 14687461641 kmers; need 3.728 GB to sort 6254171 kmers
Used 54.725 GB / 376.238 GB to store 14733524623 kmers; need 3.741 GB to sort 6276710 kmers
Used 54.839 GB / 376.238 GB to store 14779587653 kmers; need 3.753 GB to sort 6295877 kmers
Used 54.957 GB / 376.238 GB to store 14827744846 kmers; need 3.763 GB to sort 6312994 kmers
Used 55.070 GB / 376.238 GB to store 14873808143 kmers; need 3.778 GB to sort 6338171 kmers
Used 55.189 GB / 376.238 GB to store 14921965113 kmers; need 3.786 GB to sort 6352158 kmers
Used 55.298 GB / 376.238 GB to store 14965934514 kmers; need 3.803 GB to sort 6379761 kmers
Used 55.421 GB / 376.238 GB to store 15016185703 kmers; need 3.808 GB to sort 6388468 kmers
Used 55.534 GB / 376.238 GB to store 15062248748 kmers; need 3.825 GB to sort 6417420 kmers
Used 55.653 GB / 376.238 GB to store 15110405815 kmers; need 3.834 GB to sort 6431927 kmers
Used 55.767 GB / 376.238 GB to store 15156469574 kmers; need 3.846 GB to sort 6452569 kmers
Used 55.884 GB / 376.238 GB to store 15204625975 kmers; need 3.858 GB to sort 6473240 kmers
Used 55.998 GB / 376.238 GB to store 15250690007 kmers; need 3.874 GB to sort 6499628 kmers
Used 56.117 GB / 376.238 GB to store 15298846992 kmers; need 3.883 GB to sort 6514688 kmers
Used 56.226 GB / 376.238 GB to store 15342816624 kmers; need 3.902 GB to sort 6545991 kmers
Used 56.345 GB / 376.238 GB to store 15390973763 kmers; need 3.908 GB to sort 6557268 kmers
Used 56.460 GB / 376.238 GB to store 15437036971 kmers; need 3.920 GB to sort 6577065 kmers
Used 56.573 GB / 376.238 GB to store 15483100226 kmers; need 3.935 GB to sort 6601791 kmers
Used 56.691 GB / 376.238 GB to store 15531256582 kmers; need 3.945 GB to sort 6618746 kmers
Used 56.806 GB / 376.238 GB to store 15577319687 kmers; need 3.960 GB to sort 6643341 kmers
Used 56.925 GB / 376.238 GB to store 15625477149 kmers; need 3.967 GB to sort 6654723 kmers
Used 57.039 GB / 376.238 GB to store 15671540068 kmers; need 3.981 GB to sort 6678256 kmers
Used 57.158 GB / 376.238 GB to store 15719698038 kmers; need 3.990 GB to sort 6694412 kmers
Used 57.267 GB / 376.238 GB to store 15763668335 kmers; need 4.007 GB to sort 6723266 kmers
Used 57.386 GB / 376.238 GB to store 15811825331 kmers; need 4.017 GB to sort 6739817 kmers
Used 57.505 GB / 376.238 GB to store 15859982339 kmers; need 4.029 GB to sort 6758711 kmers
Used 57.618 GB / 376.238 GB to store 15906045474 kmers; need 4.041 GB to sort 6779213 kmers
Used 57.732 GB / 376.238 GB to store 15952108497 kmers; need 4.053 GB to sort 6799408 kmers
Used 57.845 GB / 376.238 GB to store 15998172067 kmers; need 4.065 GB to sort 6819858 kmers
Used 57.959 GB / 376.238 GB to store 16044235779 kmers; need 4.078 GB to sort 6842123 kmers
Used 58.077 GB / 376.238 GB to store 16092392295 kmers; need 4.087 GB to sort 6856115 kmers
Used 58.190 GB / 376.238 GB to store 16138455487 kmers; need 4.103 GB to sort 6883182 kmers
Used 58.311 GB / 376.238 GB to store 16186611825 kmers; need 4.110 GB to sort 6895782 kmers
Used 58.424 GB / 376.238 GB to store 16232674794 kmers; need 4.127 GB to sort 6924427 kmers
Used 58.542 GB / 376.238 GB to store 16280832113 kmers; need 4.136 GB to sort 6939725 kmers
Used 58.656 GB / 376.238 GB to store 16326894972 kmers; need 4.152 GB to sort 6966110 kmers
Used 58.775 GB / 376.238 GB to store 16375052053 kmers; need 4.162 GB to sort 6982551 kmers
Used 58.895 GB / 376.238 GB to store 16423208955 kmers; need 4.170 GB to sort 6996394 kmers
Used 59.004 GB / 376.238 GB to store 16467177758 kmers; need 4.190 GB to sort 7029287 kmers
Used 59.122 GB / 376.238 GB to store 16515335119 kmers; need 4.201 GB to sort 7048885 kmers
Used 59.245 GB / 376.238 GB to store 16565585788 kmers; need 4.207 GB to sort 7057545 kmers
Used 59.355 GB / 376.238 GB to store 16609555168 kmers; need 4.224 GB to sort 7087455 kmers
Used 59.479 GB / 376.238 GB to store 16659805604 kmers; need 4.229 GB to sort 7094331 kmers
Used 59.592 GB / 376.238 GB to store 16705868057 kmers; need 4.242 GB to sort 7117356 kmers
Used 59.705 GB / 376.238 GB to store 16751930917 kmers; need 4.255 GB to sort 7137867 kmers
Used 59.824 GB / 376.238 GB to store 16800087546 kmers; need 4.265 GB to sort 7155320 kmers
Used 59.936 GB / 376.238 GB to store 16846150969 kmers; need 4.281 GB to sort 7181803 kmers
Used 60.051 GB / 376.238 GB to store 16892213377 kmers; need 4.292 GB to sort 7200384 kmers
Used 60.163 GB / 376.238 GB to store 16938276128 kmers; need 4.307 GB to sort 7225807 kmers
Used 60.283 GB / 376.238 GB to store 16986433069 kmers; need 4.318 GB to sort 7244114 kmers
Used 60.402 GB / 376.238 GB to store 17034589729 kmers; need 4.325 GB to sort 7255878 kmers
Used 60.510 GB / 376.238 GB to store 17078559256 kmers; need 4.343 GB to sort 7286905 kmers
Used 60.634 GB / 376.238 GB to store 17128810317 kmers; need 4.347 GB to sort 7292330 kmers
Used 60.748 GB / 376.238 GB to store 17174873688 kmers; need 4.362 GB to sort 7318066 kmers
Used 60.863 GB / 376.238 GB to store 17220936922 kmers; need 4.373 GB to sort 7337025 kmers
Used 60.982 GB / 376.238 GB to store 17269093619 kmers; need 4.383 GB to sort 7354209 kmers
Used 61.097 GB / 376.238 GB to store 17315156265 kmers; need 4.399 GB to sort 7379702 kmers
Used 61.215 GB / 376.238 GB to store 17363311573 kmers; need 4.410 GB to sort 7398082 kmers
Used 61.328 GB / 376.238 GB to store 17409374114 kmers; need 4.421 GB to sort 7417713 kmers
Used 61.442 GB / 376.238 GB to store 17455436508 kmers; need 4.437 GB to sort 7443387 kmers
Used 61.561 GB / 376.238 GB to store 17503592441 kmers; need 4.448 GB to sort 7462137 kmers
Used 61.675 GB / 376.238 GB to store 17549654790 kmers; need 4.463 GB to sort 7487319 kmers
Used 61.794 GB / 376.238 GB to store 17597811479 kmers; need 4.469 GB to sort 7498335 kmers
Used 61.912 GB / 376.238 GB to store 17645968203 kmers; need 4.481 GB to sort 7518228 kmers
Used 62.026 GB / 376.238 GB to store 17692030180 kmers; need 4.495 GB to sort 7540531 kmers
Used 62.145 GB / 376.238 GB to store 17740185474 kmers; need 4.504 GB to sort 7556530 kmers
Used 62.259 GB / 376.238 GB to store 17786248162 kmers; need 4.520 GB to sort 7583189 kmers
Used 62.378 GB / 376.238 GB to store 17834404196 kmers; need 4.529 GB to sort 7598784 kmers
Used 62.492 GB / 376.238 GB to store 17880465991 kmers; need 4.545 GB to sort 7624408 kmers
Used 62.611 GB / 376.238 GB to store 17928621902 kmers; need 4.555 GB to sort 7642654 kmers
Used 62.725 GB / 376.238 GB to store 17974684632 kmers; need 4.570 GB to sort 7666350 kmers
Used 62.840 GB / 376.238 GB to store 18020747215 kmers; need 4.580 GB to sort 7684252 kmers
Used 62.954 GB / 376.238 GB to store 18066809630 kmers; need 4.596 GB to sort 7710491 kmers
Used 63.068 GB / 376.238 GB to store 18112871898 kmers; need 4.607 GB to sort 7728813 kmers
Used 63.181 GB / 376.238 GB to store 18158934260 kmers; need 4.619 GB to sort 7749283 kmers
Used 63.300 GB / 376.238 GB to store 18207089888 kmers; need 4.625 GB to sort 7759442 kmers
Used 63.410 GB / 376.238 GB to store 18251057139 kmers; need 4.643 GB to sort 7789370 kmers
Used 63.533 GB / 376.238 GB to store 18301306116 kmers; need 4.648 GB to sort 7798871 kmers
Used 63.647 GB / 376.238 GB to store 18347368951 kmers; need 4.661 GB to sort 7819992 kmers
Used 63.762 GB / 376.238 GB to store 18393430742 kmers; need 4.674 GB to sort 7841908 kmers
Used 63.881 GB / 376.238 GB to store 18441587484 kmers; need 4.684 GB to sort 7858950 kmers
Used 63.995 GB / 376.238 GB to store 18487649836 kmers; need 4.700 GB to sort 7884707 kmers
Used 64.110 GB / 376.238 GB to store 18533713028 kmers; need 4.710 GB to sort 7902443 kmers
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Input complete. Writing results to 'reads.meryl', using 40 threads.
finishIteration()--
Finished counting.
Cleaning up.
Bye.
Found 1 command tree.
PROCESSING TREE #1 using 40 threads.
opGreaterThan
threshold=1
reads.meryl
output to reads.gt1.meryl
Cleaning up.
Bye.
Here's the bash script I'm using to process:
#!/bin/bash -ue
echo "warning merfin is experimental"
touch merfin.flag.txt
meryl count k=21 m64047_210504_171840.ccs.filt.fastq output reads.meryl
meryl greater-than 1 reads.meryl output reads.gt1.meryl
merfin -polish -threads 40 -sequence genome.out.fasta -peak
cat kcov.txt
-prob lookup_table.txt -readmers reads.gt1.meryl -vcf final.reshaped.vcf.gz -output merfin
echo "finished merfin"
sleep 120;
exit 0;the usage and meaning of the plot in complele human genome article
in your article,I am very interested in this plot,but i dont know how to draw the plot,and what's means of the shape of the point and the color of point ? could you help me?thanks
Using gff file with merfin ?
Hello,
I polished my assembly using arrow and I have a .gff file, but no .vcf.
Is it possible to run Merfin using a .gff file ?
Otherwise do you know a way to cenvert .ggf to .vcf ?
Thanks
Polish_genome
Hi, author:
I want to polish the assembled genome and then get consensus FASTA, using Merfin. I now have FastA files and Illumina Reads FastQ files; How do I get a VCF file？Is it possible to use GATK to map FASTQ reads to the self-assembled genome FASTA?
Look forward to hearing from you, thanks！
With best wishes.
-peak is haploid or diploid?
At the top of the README, it mentions -peak is used to supply the diploid peak estimate, but in the helper message it says this is the haploid peak?
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