KmerGenie on Biowulf
KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number.
References:
- Rayan Chikhi, Paul Medvedev; Informed and automated k-mer size selection for genome assembly, Bioinformatics, Volume 30, Issue 1, 1 January 2014, Pages 31–37, doi:10.1093/bioinformatics/btt310
Documentation
Important Notes
- Module Name: kmergenie (see the modules page for more information)
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[teacher@biowulf ~]$ sinteractive --gres lscratch:1 salloc.exe: Pending job allocation 63311518 salloc.exe: job 63311518 queued and waiting for resources salloc.exe: job 63311518 has been allocated resources salloc.exe: Granted job allocation 63311518 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3128 are ready for job srun: error: x11: no local DISPLAY defined, skipping [teacher@cn3128 ~]$ cd /lscratch/$SLURM_JOB_ID [teacher@cn3128 63311518]$ # Use GAGE data (http://gage.cbcb.umd.edu/data/index.html) as an example. [teacher@cn3128 63311518]$ wget \ > http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_{1,2}.fastq.gz \ > http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_{1,2}.fastq.gz --2018-03-07 17:39:23-- http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_1.fastq.gz Resolving dtn07-e0... 10.1.200.243 Connecting to dtn07-e0|10.1.200.243|:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 64204080 (61M) [application/x-gzip] Saving to: “frag_1.fastq.gz” 100%[===================================================================================>] 64,204,080 45.5M/s in 1.3s 2018-03-07 17:39:24 (45.5 MB/s) - “frag_1.fastq.gz” saved [64204080/64204080] --2018-03-07 17:39:24-- http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/frag_2.fastq.gz Connecting to dtn07-e0|10.1.200.243|:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 68386818 (65M) [application/x-gzip] Saving to: “frag_2.fastq.gz” 100%[===================================================================================>] 68,386,818 51.5M/s in 1.3s 2018-03-07 17:39:25 (51.5 MB/s) - “frag_2.fastq.gz” saved [68386818/68386818] --2018-03-07 17:39:25-- http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_1.fastq.gz Connecting to dtn07-e0|10.1.200.243|:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 74810444 (71M) [application/x-gzip] Saving to: “shortjump_1.fastq.gz” 100%[===================================================================================>] 74,810,444 84.5M/s in 0.8s 2018-03-07 17:39:26 (84.5 MB/s) - “shortjump_1.fastq.gz” saved [74810444/74810444] --2018-03-07 17:39:26-- http://gage.cbcb.umd.edu/data/Staphylococcus_aureus/Data.original/shortjump_2.fastq.gz Connecting to dtn07-e0|10.1.200.243|:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 74594473 (71M) [application/x-gzip] Saving to: “shortjump_2.fastq.gz” 100%[===================================================================================>] 74,594,473 85.2M/s in 0.8s 2018-03-07 17:39:27 (85.2 MB/s) - “shortjump_2.fastq.gz” saved [74594473/74594473] FINISHED --2018-03-07 17:39:27-- Downloaded: 4 files, 269M in 4.3s (62.7 MB/s) [teacher@cn3128 63311518]$ ls *.fastq.gz > inputs [teacher@cn3128 63311518]$ module load kmergenie [+] Loading GSL 2.2.1 ... [+] Loading Graphviz v2.38.0 ... [+] Loading gdal 2.0 ... [+] Loading proj 4.9.2 ... [+] Loading gcc 4.9.1 ... [+] Loading openmpi 1.10.0 for GCC 4.9.1 [+] Loading tcl_tk 8.6.3 [+] Loading Zlib 1.2.8 ... [+] Loading Bzip2 1.0.6 ... [+] Loading pcre 8.38 ... [+] Loading liblzma 5.2.2 ... [-] Unloading Zlib 1.2.8 ... [+] Loading Zlib 1.2.8 ... [-] Unloading liblzma 5.2.2 ... [+] Loading liblzma 5.2.2 ... [+] Loading libjpeg-turbo 1.5.1 ... [+] Loading tiff 4.0.7 ... [+] Loading curl 7.46.0 ... [+] Loading boost libraries v1.65 ... [+] Loading R 3.4.0 on cn3128 [-] Unloading Zlib 1.2.8 ... [+] Loading Zlib 1.2.8 ... [+] Loading kmergenie, version 1.7044... [teacher@cn3128 63311518]$ kmergenie inputs -t2 running histogram estimation list of reads: frag_1.fastq.gz frag_2.fastq.gz shortjump_1.fastq.gz shortjump_2.fastq.gz Setting maximum kmer length to: 101 bp computing histograms (from k=21 to k=101): 41 21 51 31 61 81 71 91 101 ntCard wall-clock time over all k values: 88 seconds fitting model to histograms to estimate best k could not fit histograms-k71.histo could not fit histograms-k81.histo estimation of the best k so far: 21 refining estimation around [15; 27], with a step of 2 running histogram estimation list of reads: frag_1.fastq.gz frag_2.fastq.gz shortjump_1.fastq.gz shortjump_2.fastq.gz Setting maximum kmer length to: 101 bp computing histograms (from k=17 to k=27): 19 17 23 21 27 25 ntCard wall-clock time over all k values: 66 seconds fitting model to histograms to estimate best k could not fit histograms-k71.histo could not fit histograms-k81.histo table of predicted num. of genomic k-mers: histograms.dat recommended coverage cut-off for best k: 3 best k: 19 [teacher@cn3128 63311518]$ exit salloc.exe: Relinquishing job allocation 63311518 [teacher@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. kmergenie.sh). For example:
#!/bin/sh set -e module load kmergenie test -n "$SLURM_CPUS_PER_TASK" || SLURM_CPUS_PER_TASK=2 kmergenie inputs.fofn -t $SLURM_CPUS_PER_TASK
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] kmergenie.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. kmergenie.swarm). For example:
kmergenie input1.fofn -t $SLURM_CPUS_PER_TASK kmergenie input2.fofn -t $SLURM_CPUS_PER_TASK kmergenie input3.fofn -t $SLURM_CPUS_PER_TASK kmergenie input4.fofn -t $SLURM_CPUS_PER_TASK
Submit this job using the swarm command.
swarm -f kmergenie.swarm -t 2 [-g #] --module kmergeniewhere
-g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
-t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
--module kmergenie | Loads the kmergenie module for each subjob in the swarm |