Open baozg opened 2 years ago
I have try FASTK and MERQURY.FK
, but the MERQURY.FK
throw the Segmentation fault
.
Here is the code I use :
FASTK and MERQURY.FK were installed today.
# FASTK for PE250 reads
pigz -p 32 -dc WGS.R1.clean.fastq.gz > WGS.R1.clean.fastq
pigz -p 32 -dc WGS.R2.clean.fastq.gz > WGS.R2.clean.fastq
## FASTK
~/software/FASTK/bin/FastK -v -PWGS -T64 -M200 -k31 -t1 WGS.R1.clean.fastq WGS.R2.clean.fastq
## MERQURY.FK
~/software/MERQURY.FK/bin/MerquryFK -v -T64 -pdf WGS.R1.clean.ktab ./HiFi.V1.fa test
Two log
# FASTK
Partitioning 2 .fastq files into 64 parts
Determining minimizer scheme & partition for WGS.R1.clean
Estimate 214.125G 31-mers
Dividing data into 11 blocks
Using 7-minimizers with 1048 core prefixes
Phase 1: Partitioning K-mers into 704 Super-mer Files
There are 977,698,548 reads totalling 244,424,637,000 bps
Part: 31-mer super-mers ave. length
0: 19,682,823,520 1,663,529,566 11.8
1: 19,674,612,623 1,769,086,703 11.1
2: 19,587,575,233 1,943,187,015 10.1
3: 19,495,814,725 1,840,956,781 10.6
4: 19,544,818,789 1,815,438,713 10.8
5: 19,525,732,179 1,915,986,018 10.2
6: 19,433,353,106 1,797,203,569 10.8
7: 19,506,601,185 1,674,358,484 11.7
8: 19,393,772,868 1,889,521,351 10.3
9: 19,759,183,095 1,588,962,080 12.4
10: 19,475,000,660 1,851,361,455 10.5
Sum: 215,079,287,983 19,749,591,735 10.9
Range 19,393,772,868 - 19,759,183,095 (1.87%)
Resources for phase: 68:10.064u 27:05.233s 5:07.933w 1856.0%
Phase 2: Sorting & Counting K-mers in 11 blocks
Part: wgt'd k-mers savings
0: 2,162,467,906 9.1
1: 2,056,330,156 9.6
2: 1,964,553,110 10.0
3: 2,033,779,444 9.6
4: 2,531,557,027 7.7
5: 2,008,534,812 9.7
6: 1,918,481,344 10.1
7: 1,965,740,025 9.9
8: 1,941,849,517 10.0
9: 2,200,607,424 9.0
10: 1,895,100,055 10.3
All: 22,679,000,820 9.5
Resources for phase: 69:39.686u 11:23.827s 8:13.343w 985.8%
Phase 3 (-t option): Merging K-mer Table Parts
There are 9,391,432,901 31-mers that occur 1-or-more times
The table occupies 65.87 GB
Resources for phase: 7:21.941u 2:38.527s 1:55.494w 519.9%
Total Resources: 145:11.693u 41:07.587s 15:16.770w 1219.4% 107MB
## MERQURY.FK
Single diploid assembly, no trio data
Kmer size is 31
Solid k-mer cutoff is 22
Making CN-spectra plots for ./HiFi.V1
Making .qv and .bed files for assembly ./HiFi.V1
/var/spool/slurm/d/job3906010/slurm_script: line 4: 33521 Segmentation fault ~/software/MERQURY.FK/bin/MerquryFK -v -T64 -pdf WGS.R1.clean.ktab ./HiFi.V1.fa test
Hi, @thegenemyers
Does the
Merqury
have diploid assumption ? We have a phased chromosome-level autotetraploidy plant genome. Can I use theMerqury
for QV estimation ? Do I need any other modification ?Thanks, Zhigui Bao