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A language and runtime for distributed, incremental data processing in the cloud
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Reflow is a system for incremental data processing in the cloud.Reflow enables scientists and engineers to compose existing tools(packaged in Docker images) using ordinary programming constructs.Reflow then evaluates these programs in a cloud environment,transparently parallelizing work and memoizing results. Reflow wascreated atGRAIL to manage our NGS (nextgeneration sequencing) bioinformatics workloads onAWS, but has also been used for many otherapplications, including model training and ad-hoc data analyses.
Reflow comprises:
- a functional, lazy, type-safe domain specific language for writing workflow programs;
- a runtime for evaluating Reflow programsincrementally, coordinating cluster execution, and transparent memoization;
- a cluster scheduler to dynamically provision and tear down resources from a cloud provider (AWS currently supported).
Reflow thus allows scientists and engineers to write straightforwardprograms and then have them transparently executed in a cloudenvironment. Programs are automatically parallelized and distributedacross multiple machines, and redundant computations (even acrossruns and users) are eliminated by its memoization cache. Reflowevaluates its programsincrementally:whenever the input data or program changes, only those outputs thatdepend on the changed data or code are recomputed.
In addition to the default cluster computing mode, Reflow programscan also be run locally, making use of the local machine's Dockerdaemon (including Docker for Mac).
Reflow was designed to support sophisticated, large-scalebioinformatics workflows, but should be widely applicable toscientific and engineering computing workloads. It was builtusingGo.
Reflow joins alonglist of systemsdesigned to tackle bioinformatics workloads, but differ from these inimportant ways:
- it is a vertically integrated system with a minimal set of external dependencies; this allows Reflow to be "plug-and-play": bring your cloud credentials, and you're off to the races;
- it defines a strict data model which is used for transparent memoization and other optimizations;
- it takes workflow software seriously: the Reflow DSL provides type checking, modularity, and other constructors that are commonplace in general purpose programming languages;
- because of its high level data model and use of caching, Reflow computesincrementally: it is always able to compute the smallest set of operations given what has been computed previously.
- Quickstart - AWS
- Simple bioinformatics workflow
- 1000align
- Documentation
- Developing and building Reflow
- Debugging Reflow runs
- A note on Reflow's EC2 cluster manager
- Setting up a TaskDB
- Support and community
You can get binaries (macOS/amd64, Linux/amd64) for the latestrelease at theGitHub releasepage.
If you are developing Reflow,or would like to build it yourself,please follow the instructions in the section"Developing and building Reflow."
Reflow is distributed with an EC2 cluster manager, and a memoizationcache implementation based on S3. These must be configured beforeuse. Reflow maintains a configuration file in$HOME/.reflow/config.yamlby default (this can be overridden with the-config option). Reflow'ssetup commands modify this file directly. After each step, the currentconfiguration can be examined by runningreflow config.
Note Reflow must have access to AWS credentials and configuration in theenvironment (AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY,AWS_REGION) whilerunning these commands.
% reflow setup-ec2% reflow configcluster: ec2clusterec2cluster: securitygroup: <a newly created security group here> maxpendinginstances: 5 maxhourlycostusd: 10 disktype: gp3 instancesizetodiskspace: 2xlarge: 300 3xlarge: 300 ... diskslices: 0 ami: "" sshkey: [] keyname: "" cloudconfig: {} instancetypes: - c3.2xlarge - c3.4xlarge ...reflow: reflowversion,version=<hash>tls: tls,file=$HOME/.reflow/reflow.pemAfter runningreflow setup-ec2, we see that Reflow created a newsecurity group (associated with the account's default VPC), andconfigured the cluster to use some default settings. Feel free toedit the configuration file ($HOME/.reflow/config.yaml) to yourtaste. If you want to use spot instances, add a new key underec2cluster:spot: true.
Reflow only configures one security group per account: Reflow will reusea previously created security group ifreflow setup-ec2 is run anew.Seereflow setup-ec2 -help for more details.
Next, we'll set up a cache. This isn't strictly necessary, but we'llneed it in order to use many of Reflow's sophisticated caching andincremental computation features. On AWS, Reflow implements a cachebased on S3 and DynamoDB. A new S3-based cache is provisioned byreflow setup-s3-repository andreflow setup-dynamodb-assoc, eachof which takes one argument naming the S3 bucket and DynamoDB tablename to be used, respectively. The S3 bucket is used to store fileobjects while the DynamoDB table is used to store associationsbetween logically named computations and their concrete output. Notethat S3 bucket names are global, so pick a name that's likely to beunique.
% reflow setup-s3-repository reflow-quickstart-cachereflow: creating s3 bucket reflow-quickstart-cachereflow: created s3 bucket reflow-quickstart-cache% reflow setup-dynamodb-assoc reflow-quickstartreflow: creating DynamoDB table reflow-quickstartreflow: created DynamoDB table reflow-quickstart% reflow configassoc: dynamodb,table=reflow-quickstartrepository: s3,bucket=reflow-quickstart-cache<rest is same as before>The setup commands created the S3 bucket and DynamoDB table asneeded, and modified the configuration accordingly.
Advanced users can also optionallysetup a taskdb.
We're now ready to run our first "hello world" program!
Create a file called "hello.rf" with the following contents:
val Main = exec(image := "ubuntu", mem := GiB) (out file) {"echo hello world >>{{out}}"}and run it:
% reflow run hello.rfreflow: run ID: 6da656d1ec2cluster: 0 instances: (<=$0.0/hr), total{}, waiting{mem:1.0GiB cpu:1 disk:1.0GiBreflow: total n=1 time=0sident n ncache transfer runtime(m) cpu mem(GiB) disk(GiB) tmp(GiB)hello.Main 1 1 0Ba948904fHere, Reflow started a newt2.small instance (Reflow matches the workload withavailable instance types), ranecho hello world inside of an Ubuntu container,placed the output in a file, and returned its SHA256 digest. (Reflow representsfile contents using their SHA256 digest.)
We're now ready to explore Reflow more fully.
Let's explore some of Reflow's features through a simple task:aligning NGS read data from the 1000genomes project. Createa file called "align.rf" with the following. The code is commentedinline for clarity.
// In order to align raw NGS data, we first need to construct an index// against which to perform the alignment. We're going to be using// the BWA aligner, and so we'll need to retrieve a reference sequence// and create an index that's usable from BWA.// g1kv37 is a human reference FASTA sequence. (All// chromosomes.) Reflow has a static type system, but most type// annotations can be omitted: they are inferred by Reflow. In this// case, we're creating a file: a reference to the contents of the// named URL. We're retrieving data from the public 1000genomes S3// bucket.val g1kv37 = file("s3://1000genomes/technical/reference/human_g1k_v37.fasta.gz")// Here we create an indexed version of the g1kv37 reference. It is// created using the "bwa index" command with the raw FASTA data as// input. Here we encounter another way to produce data in reflow:// the exec. An exec runs a (Bash) script inside of a Docker image,// placing the output in files or directories (or both: execs can// return multiple values). In this case, we're returning a// directory since BWA stores multiple index files alongside the raw// reference. We also declare that the image to be used is// "biocontainers/bwa" (the BWA image maintained by the// biocontainers project).//// Inside of an exec template (delimited by {" and "}) we refer to// (interpolate) values in our environment by placing expressions// inside of the {{ and }} delimiters. In this case we're referring// to the file g1kv37 declared above, and our output, named out.//// Many types of expressions can be interpolated inside of an exec,// for example strings, integers, files, and directories. Strings// and integers are rendered using their normal representation,// files and directories are materialized to a local path before// starting execution. Thus, in this case, {{g1kv37}} is replaced at// runtime by a path on disk with a file with the contents of the// file g1kv37 (i.e.,// s3://1000genomes/technical/reference/human_g1k_v37.fasta.gz)val reference = exec(image := "biocontainers/bwa:v0.7.15_cv3", mem := 6*GiB, cpu := 1) (out dir) {"# Ignore failures here. The file from 1000genomes has a trailer# that isn't recognized by gunzip. (This is not recommended practice!)gunzip -c {{g1kv37}} > {{out}}/g1k_v37.fa || truecd {{out}}bwa index -a bwtsw g1k_v37.fa"}// Now that we have defined a reference, we can define a function to// align a pair of reads against the reference, producing an output// SAM-formatted file. Functions compute expressions over a set of// abstract parameters, in this case, a pair of read files. Unlike almost// everywhere else in Reflow, function parameters must be explicitly// typed.//// (Note that we're using a syntactic short-hand here: parameter lists can // be abbreviated. "r1, r2 file" is equivalent to "r1 file, r2 file".)//// The implementation of align is a straightforward invocation of "bwa mem".// Note that "r1" and "r2" inside of the exec refer to the function arguments,// thus align can be invoked for any set of r1, r2.func align(r1, r2 file) = exec(image := "biocontainers/bwa:v0.7.15_cv3", mem := 20*GiB, cpu := 16) (out file) {"bwa mem -M -t 16 {{reference}}/g1k_v37.fa {{r1}} {{r2}} > {{out}}"}// We're ready to test our workflow now. We pick an arbitrary read// pair from the 1000genomes data set, and invoke align. There are a// few things of note here. First is the identifier "Main". This// names the expression that's evaluated by `reflow run` -- the// entry point of the computation. Second, we've defined Main to be// a block. A block is an expression that contains one or more// definitions followed by an expression. The value of a block is the// final expression. Finally, Main contains a @requires annotation.// This instructs Reflow how many resources to reserve for the work// being done. Note that, because Reflow is able to distribute work,// if a single instance is too small to execute fully in parallel,// Reflow will provision additional compute instances to help along.// @requires thus denotes the smallest possible instance// configuration that's required for the program.@requires(cpu := 16, mem := 24*GiB, disk := 50*GiB)val Main = {r1 := file("s3://1000genomes/phase3/data/HG00103/sequence_read/SRR062640_1.filt.fastq.gz")r2 := file("s3://1000genomes/phase3/data/HG00103/sequence_read/SRR062640_2.filt.fastq.gz")align(r1, r2)}Now we're ready to run our module. First, let's runreflow doc.This does two things. First, it typechecks the module (and anydependent modules), and second, it prints documentation for thepublic declarations in the module. Identifiers that begin with anuppercase letter are public (and may be used from other modules);others are not.
% reflow doc align.rfDeclarationsval Main (out file) We're ready to test our workflow now. We pick an arbitrary read pair from the 1000genomes data set, and invoke align. There are a few things of note here. First is the identifier "Main". This names the expression that's evaluated by `reflow run` -- the entry point of the computation. Second, we've defined Main to be a block. A block is an expression that contains one or more definitions followed by an expression. The value of a block is the final expression. Finally, Main contains a @requires annotation. This instructs Reflow how many resources to reserve for the work being done. Note that, because Reflow is able to distribute work, if a single instance is too small to execute fully in parallel, Reflow will provision additional compute instances to help along. @requires thus denotes the smallest possible instance configuration that's required for the program.Then let's run it:
% reflow run align.rfreflow: run ID: 82e63a7aec2cluster: 1 instances: c5.4xlarge:1 (<=$0.7/hr), total{mem:29.8GiB cpu:16 disk:250.0GiB intel_avx512:16}, waiting{}, pending{}82e63a7a: elapsed: 2m30s, executing:1, completed: 3/5 align.reference: exec ..101f9a082e1679c16d23787c532a0107537c9c # Ignore failures here. The f..bwa index -a bwtsw g1k_v37.fa 2m4sReflow launched a new instance: the previously launched instance (at2.small) was not big enough to fit the requirements of align.rf.Note also that Reflow assigns a run name for eachreflow runinvocation. This can be used to look up run details with thereflow info command. In this case:
% reflow info 82e63a7a82e63a7aee201d137f8ade3d584c234b856dc6bdeba00d5d6efc9627bd988a68 (run) time: Wed Dec 12 10:45:04 2018 program: /Users/you/align.rf phase: Eval alloc: ec2-34-213-42-76.us-west-2.compute.amazonaws.com:9000/5a0adaf6c879efb1 resources: {mem:28.9GiB cpu:16 disk:245.1GiB intel_avx:16 intel_avx2:16 intel_avx512:16} log: /Users/you/.reflow/runs/82e63a7aee201d137f8ade3d584c234b856dc6bdeba00d5d6efc9627bd988a68.execlogHere we see that the run is currently being performed on the alloc namedec2-34-213-42-76.us-west-2.compute.amazonaws.com:9000/5a0adaf6c879efb1.An alloc is a resource reservation on a single machine. A run canmake use of multiple allocs to distribute work across multiplemachines. The alloc is a URI, and the first component is the realhostname. You can ssh into the host in order to inspect what's going on.Reflow launched the instance with your public SSH key (as long as it wasset up byreflow setup-ec2, and$HOME/.ssh/id_rsa.pub existed at that time).
% ssh core@ec2-34-213-42-76.us-west-2.compute.amazonaws.com...As the run progresses, Reflow prints execution status of each task on theconsole.
...align.Main.r2: intern s3://1000genomes/phase3/data/HG00103/sequence_read/SRR062640_2.filt.fastq.gz 23salign.Main.r1: intern done 1.8GiB 23salign.g1kv37: intern done 851.0MiB 23salign.reference: exec ..101f9a082e1679c16d23787c532a0107537c9c # Ignore failures here. The f..bwa index -a bwtsw g1k_v37.fa 6sHere, Reflow started downloading r1 and r2 in parallel with creating the reference.Creating the reference is an expensive operation. We can examine it while it's runningwithreflow ps:
% reflow ps 3674721e align.reference 10:46AM 0:00 running 4.4GiB 1.0 6.5GiB bwaThis tells us that the only task that's currently running is bwa to compute the reference.It's currently using 4.4GiB of memory, 1 cores, and 6.5GiB GiB of disk space. By passing the -loption, reflow ps also prints the task's exec URI.
% reflow ps -l3674721e align.reference 10:46AM 0:00 running 4.4GiB 1.0 6.5GiB bwa ec2-34-213-42-76.us-west-2.compute.amazonaws.com:9000/5a0adaf6c879efb1/3674721e2d9e80b325934b08973fb3b1d3028b2df34514c9238be466112eb86eAn exec URI is a handle to the actual task being executed. Itglobally identifies all tasks, and can be examined withreflow info:
% reflow info ec2-34-213-42-76.us-west-2.compute.amazonaws.com:9000/5a0adaf6c879efb1/3674721e2d9e80b325934b08973fb3b1d3028b2df34514c9238be466112eb86eec2-34-213-42-76.us-west-2.compute.amazonaws.com:9000/5a0adaf6c879efb1/3674721e2d9e80b325934b08973fb3b1d3028b2df34514c9238be466112eb86e (exec) state: running type: exec ident: align.reference image: index.docker.io/biocontainers/bwa@sha256:0529e39005e35618c4e52f8f56101f9a082e1679c16d23787c532a0107537c9c cmd: "\n\t# Ignore failures here. The file from 1000genomes has a trailer\n\t# that isn't recognized by gunzip. (This is not recommended practice!)\n\tgunzip -c {{arg[0]}} > {{arg[1]}}/g1k_v37.fa || true\n\tcd {{arg[2]}}\n\tbwa index -a bwtsw g1k_v37.fa\n" arg[0]: .: sha256:8b6c538abf0dd92d3f3020f36cc1dd67ce004ffa421c2781205f1eb690bdb442 (851.0MiB) arg[1]: output 0 arg[2]: output 0 top: bwa index -a bwtsw g1k_v37.faHere, Reflow tells us that the currently running process is "bwaindex...", its template command, and the SHA256 digest of its inputs.Programs often print helpful output to standard error while working;this output can be examined withreflow logs:
% reflow logs ec2-34-221-0-157.us-west-2.compute.amazonaws.com:9000/0061a20f88f57386/3674721e2d9e80b325934b08973fb3b1d3028b2df34514c9238be466112eb86egzip: /arg/0/0: decompression OK, trailing garbage ignored[bwa_index] Pack FASTA... 18.87 sec[bwa_index] Construct BWT for the packed sequence...[BWTIncCreate] textLength=6203609478, availableWord=448508744[BWTIncConstructFromPacked] 10 iterations done. 99999990 characters processed.[BWTIncConstructFromPacked] 20 iterations done. 199999990 characters processed.[BWTIncConstructFromPacked] 30 iterations done. 299999990 characters processed.[BWTIncConstructFromPacked] 40 iterations done. 399999990 characters processed.[BWTIncConstructFromPacked] 50 iterations done. 499999990 characters processed.[BWTIncConstructFromPacked] 60 iterations done. 599999990 characters processed.[BWTIncConstructFromPacked] 70 iterations done. 699999990 characters processed.[BWTIncConstructFromPacked] 80 iterations done. 799999990 characters processed.[BWTIncConstructFromPacked] 90 iterations done. 899999990 characters processed.[BWTIncConstructFromPacked] 100 iterations done. 999999990 characters processed.[BWTIncConstructFromPacked] 110 iterations done. 1099999990 characters processed.[BWTIncConstructFromPacked] 120 iterations done. 1199999990 characters processed.[BWTIncConstructFromPacked] 130 iterations done. 1299999990 characters processed.[BWTIncConstructFromPacked] 140 iterations done. 1399999990 characters processed.[BWTIncConstructFromPacked] 150 iterations done. 1499999990 characters processed.[BWTIncConstructFromPacked] 160 iterations done. 1599999990 characters processed.[BWTIncConstructFromPacked] 170 iterations done. 1699999990 characters processed.[BWTIncConstructFromPacked] 180 iterations done. 1799999990 characters processed.[BWTIncConstructFromPacked] 190 iterations done. 1899999990 characters processed.[BWTIncConstructFromPacked] 200 iterations done. 1999999990 characters processed.[BWTIncConstructFromPacked] 210 iterations done. 2099999990 characters processed.[BWTIncConstructFromPacked] 220 iterations done. 2199999990 characters processed.[BWTIncConstructFromPacked] 230 iterations done. 2299999990 characters processed.[BWTIncConstructFromPacked] 240 iterations done. 2399999990 characters processed.[BWTIncConstructFromPacked] 250 iterations done. 2499999990 characters processed.[BWTIncConstructFromPacked] 260 iterations done. 2599999990 characters processed.[BWTIncConstructFromPacked] 270 iterations done. 2699999990 characters processed.[BWTIncConstructFromPacked] 280 iterations done. 2799999990 characters processed.[BWTIncConstructFromPacked] 290 iterations done. 2899999990 characters processed.[BWTIncConstructFromPacked] 300 iterations done. 2999999990 characters processed.[BWTIncConstructFromPacked] 310 iterations done. 3099999990 characters processed.[BWTIncConstructFromPacked] 320 iterations done. 3199999990 characters processed.[BWTIncConstructFromPacked] 330 iterations done. 3299999990 characters processed.[BWTIncConstructFromPacked] 340 iterations done. 3399999990 characters processed.[BWTIncConstructFromPacked] 350 iterations done. 3499999990 characters processed.[BWTIncConstructFromPacked] 360 iterations done. 3599999990 characters processed.[BWTIncConstructFromPacked] 370 iterations done. 3699999990 characters processed.[BWTIncConstructFromPacked] 380 iterations done. 3799999990 characters processed.[BWTIncConstructFromPacked] 390 iterations done. 3899999990 characters processed.[BWTIncConstructFromPacked] 400 iterations done. 3999999990 characters processed.[BWTIncConstructFromPacked] 410 iterations done. 4099999990 characters processed.[BWTIncConstructFromPacked] 420 iterations done. 4199999990 characters processed.[BWTIncConstructFromPacked] 430 iterations done. 4299999990 characters processed.[BWTIncConstructFromPacked] 440 iterations done. 4399999990 characters processed.[BWTIncConstructFromPacked] 450 iterations done. 4499999990 characters processed.At this point, it looks like everything is running as expected.There's not much more to do than wait. Note that, while creating anindex takes a long time, Reflow only has to compute it once. Whenit's done, Reflow memoizes the result, uploading the resulting datadirectly to the configured S3 cache bucket. The next time thereference expression is encountered, Reflow will use the previouslycomputed result. If the input file changes (e.g., we decide to useanother reference sequence), Reflow will recompute the index again.The same will happen if the command (or Docker image) that's used tocompute the index changes. Reflow keeps track of all the dependenciesfor a particular sub computation, and recomputes them only whendependencies have changed. This way, we always know what is beingcomputed is correct (the result is the same as if we had computed theresult from scratch), but avoid paying the cost of redundantcomputation.
After a little while, the reference will have finished generating,and Reflow begins alignment. Here, Reflow reports that the referencetook 52 minutes to compute, and produced 8 GiB of output.
align.reference: exec done 8.0GiB 52m37s align.align: exec ..101f9a082e1679c16d23787c532a0107537c9c bwa mem -M -t 16 {{reference}..37.fa {{r1}} {{r2}} > {{out}} 4sIf we query ("info") the reference exec again, Reflow reports precisely whatwas produced:
% reflow info ec2-34-221-0-157.us-west-2.compute.amazonaws.com:9000/0061a20f88f57386/3674721e2d9e80b325934b08973fb3b1d3028b2df34514c9238be466112eb86eec2-34-221-0-157.us-west-2.compute.amazonaws.com:9000/0061a20f88f57386/3674721e2d9e80b325934b08973fb3b1d3028b2df34514c9238be466112eb86e (exec) state: complete type: exec ident: align.reference image: index.docker.io/biocontainers/bwa@sha256:0529e39005e35618c4e52f8f56101f9a082e1679c16d23787c532a0107537c9c cmd: "\n\t# Ignore failures here. The file from 1000genomes has a trailer\n\t# that isn't recognized by gunzip. (This is not recommended practice!)\n\tgunzip -c {{arg[0]}} > {{arg[1]}}/g1k_v37.fa || true\n\tcd {{arg[2]}}\n\tbwa index -a bwtsw g1k_v37.fa\n" arg[0]: .: sha256:8b6c538abf0dd92d3f3020f36cc1dd67ce004ffa421c2781205f1eb690bdb442 (851.0MiB) arg[1]: output 0 arg[2]: output 0 result: list[0]: g1k_v37.fa: sha256:2f9cd9e853a9284c53884e6a551b1c7284795dd053f255d630aeeb114d1fa81f (2.9GiB) g1k_v37.fa.amb: sha256:dd51a07041a470925c1ebba45c2f534af91d829f104ade8fc321095f65e7e206 (6.4KiB) g1k_v37.fa.ann: sha256:68928e712ef48af64c5b6a443f2d2b8517e392ae58b6a4ab7191ef7da3f7930e (6.7KiB) g1k_v37.fa.bwt: sha256:2aec938930b8a2681eb0dfbe4f865360b98b2b6212c1fb9f7991bc74f72d79d8 (2.9GiB) g1k_v37.fa.pac: sha256:d62039666da85d859a29ea24af55b3c8ffc61ddf02287af4d51b0647f863b94c (739.5MiB) g1k_v37.fa.sa: sha256:99eb6ff6b54fba663c25e2642bb2a6c82921c931338a7144327c1e3ee99a4447 (1.4GiB)In this case, "bwa index" produced a number of auxiliary indexfiles. These are the contents of the "reference" directory.
We can again query Reflow for running execs, and examine thealignment. We see now that the reference is passed in (argument 0),along side the read pairs (arguments 1 and 2).
% reflow ps -l6a6c36f5 align.align 5:12PM 0:00 running 5.9GiB 12.3 0B bwa ec2-34-221-0-157.us-west-2.compute.amazonaws.com:9000/0061a20f88f57386/6a6c36f5da6ee387510b0b61d788d7e4c94244d61e6bc621b43f59a73443a755% reflow info ec2-34-221-0-157.us-west-2.compute.amazonaws.com:9000/0061a20f88f57386/6a6c36f5da6ee387510b0b61d788d7e4c94244d61e6bc621b43f59a73443a755ec2-34-221-0-157.us-west-2.compute.amazonaws.com:9000/0061a20f88f57386/6a6c36f5da6ee387510b0b61d788d7e4c94244d61e6bc621b43f59a73443a755 (exec) state: running type: exec ident: align.align image: index.docker.io/biocontainers/bwa@sha256:0529e39005e35618c4e52f8f56101f9a082e1679c16d23787c532a0107537c9c cmd: "\n\t\tbwa mem -M -t 16 {{arg[0]}}/g1k_v37.fa {{arg[1]}} {{arg[2]}} > {{arg[3]}}\n\t" arg[0]: g1k_v37.fa: sha256:2f9cd9e853a9284c53884e6a551b1c7284795dd053f255d630aeeb114d1fa81f (2.9GiB) g1k_v37.fa.amb: sha256:dd51a07041a470925c1ebba45c2f534af91d829f104ade8fc321095f65e7e206 (6.4KiB) g1k_v37.fa.ann: sha256:68928e712ef48af64c5b6a443f2d2b8517e392ae58b6a4ab7191ef7da3f7930e (6.7KiB) g1k_v37.fa.bwt: sha256:2aec938930b8a2681eb0dfbe4f865360b98b2b6212c1fb9f7991bc74f72d79d8 (2.9GiB) g1k_v37.fa.pac: sha256:d62039666da85d859a29ea24af55b3c8ffc61ddf02287af4d51b0647f863b94c (739.5MiB) g1k_v37.fa.sa: sha256:99eb6ff6b54fba663c25e2642bb2a6c82921c931338a7144327c1e3ee99a4447 (1.4GiB) arg[1]: .: sha256:0c1f85aa9470b24d46d9fc67ba074ca9695d53a0dee580ec8de8ed46ef347a85 (1.8GiB) arg[2]: .: sha256:47f5e749123d8dda92b82d5df8e32de85273989516f8e575d9838adca271f630 (1.7GiB) arg[3]: output 0 top: /bin/bash -e -l -o pipefail -c ..bwa mem -M -t 16 /arg/0/0/g1k_v37.fa /arg/1/0 /arg/2/0 > /return/0 . bwa mem -M -t 16 /arg/0/0/g1k_v37.fa /arg/1/0 /arg/2/0Note that the read pairs are files. Files in Reflow do not havenames; they are just blobs of data. When Reflow runs a process thatrequires input files, those anonymous files are materialized on disk,but the filenames are not meaningful. In this case, we can see fromthe "top" output (these are the actual running processes, as reportedby the OS), that the r1 ended up being called "/arg/1/0" and r2"/arg/2/0". The output is a file named "/return/0".
Finally, alignment is complete. Aligning a single read pair tookaround 19m, and produced 13.2 GiB of output. Upon completion, Reflowprints runtime statistics and the result.
reflow: total n=5 time=1h9m57s ident n ncache transfer runtime(m) cpu mem(GiB) disk(GiB) tmp(GiB) align.align 1 0 0B 17/17/17 15.6/15.6/15.6 7.8/7.8/7.8 12.9/12.9/12.9 0.0/0.0/0.0 align.Main.r2 1 0 0B align.Main.r1 1 0 0B align.reference 1 0 0B 51/51/51 1.0/1.0/1.0 4.4/4.4/4.4 6.5/6.5/6.5 0.0/0.0/0.0 align.g1kv37 1 0 0Bbecb0485Reflow represents file values by the SHA256 digest of the file'scontent. In this case, that's not very useful: you want the file,not its digest. Reflow provides mechanisms to export data. In thiscase let's copy the resulting file to an S3 bucket.
We'll make use of the "files" system module to copy the aligned fileto an external S3 bucket. Modify align.rf'sMain to the following(but pick an S3 bucket you own), and then run it again. Commentary isinline for clarity.
@requires(cpu := 16, mem := 24*GiB, disk := 50*GiB)val Main = {r1 := file("s3://1000genomes/phase3/data/HG00103/sequence_read/SRR062640_1.filt.fastq.gz")r2 := file("s3://1000genomes/phase3/data/HG00103/sequence_read/SRR062640_2.filt.fastq.gz")// Instantiate the system modules "files" (system modules begin// with $), assigning its instance to the "files" identifier. To// view the documentation for this module, run `reflow doc// $/files`.files := make("$/files")// As before.aligned := align(r1, r2)// Use the files module's Copy function to copy the aligned file to// the provided destination.files.Copy(aligned, "s3://marius-test-bucket/aligned.sam")}And run it again:
% reflow run align.rfreflow: run ID: 9f0f3596reflow: total n=2 time=1m9s ident n ncache transfer runtime(m) cpu mem(GiB) disk(GiB) tmp(GiB) align_2.align 1 1 0B align_2.Main 1 0 13.2GiBval<.=becb0485 13.2GiB>Here we see that Reflow did not need to recompute the aligned file;it is instead retrieved from cache. The reference index generation isskipped altogether. Status lines that indicate "xfer" (instead of"run") means that Reflow is performing a cache transfer in place ofrunning the computation. Reflow claims to have transferred a 13.2 GiBfile tos3://marius-test-bucket/aligned.sam. Indeed it did:
% aws s3 ls s3://marius-test-bucket/aligned.sam2018-12-13 16:29:49 14196491221 aligned.sam.This code was modularized and generalized in1000align. Here,fastq, bam, and alignment utilities are split into their ownparameterized modules. The toplevel module, 1000align, isinstantiated from the command line. Command line invocations (reflow run) can pass module parameters through flags (strings, booleans,and integers):
% reflow run 1000align.rf -helpusage of 1000align.rf: -out string out is the target of the output merged BAM file (required) -sample string sample is the name of the 1000genomes phase 3 sample (required)For example, to align the full sample from above, we can invoke1000align.rf with the following arguments:
% reflow run 1000align.rf -sample HG00103 -out s3://marius-test-bucket/HG00103.bamIn this case, if your account limits allow it, Reflow will launchadditional EC2 instances in order to further parallelize the work tobe done. (Since we're aligning multiple pairs of FASTQ files).In this run, we can see that Reflow is aligning 5 pairs in parallelacross 2 instances (four can fit on the initial m4.16xlarge instance).
% reflow ps -le74d4311 align.align.sam 11:45AM 0:00 running 10.9GiB 31.8 6.9GiB bwa ec2-34-210-201-193.us-west-2.compute.amazonaws.com:9000/6a7ffa00d6b0d9e1/e74d4311708f1c9c8d3894a06b59029219e8a545c69aa79c3ecfedc1eeb898f659c561be align.align.sam 11:45AM 0:00 running 10.9GiB 32.7 6.4GiB bwa ec2-34-210-201-193.us-west-2.compute.amazonaws.com:9000/6a7ffa00d6b0d9e1/59c561be5f627143108ce592d640126b88c23ba3d00974ad0a3c801a32b50fbeba688daf align.align.sam 11:47AM 0:00 running 8.7GiB 22.6 2.9GiB bwa ec2-18-236-233-4.us-west-2.compute.amazonaws.com:9000/ae348d6c8a33f1c9/ba688daf5d50db514ee67972ec5f0a684f8a76faedeb9a25ce3d412e3c94c75c0caece7f align.align.sam 11:47AM 0:00 running 8.7GiB 25.9 3.4GiB bwa ec2-18-236-233-4.us-west-2.compute.amazonaws.com:9000/ae348d6c8a33f1c9/0caece7f38dc3d451d2a7411b1fcb375afa6c86a7b0b27ba7dd1f9d43d94f2f90b59e00c align.align.sam 11:47AM 0:00 running 10.4GiB 22.9 926.6MiB bwa ec2-18-236-233-4.us-west-2.compute.amazonaws.com:9000/ae348d6c8a33f1c9/0b59e00c848fa91e3b0871c30da3ed7e70fbc363bdc48fb09c3dfd61684c5fd9When it completes, an approximately 17GiB BAM file is deposited to s3:
% aws s3 ls s3://marius-test-bucket/HG00103.bam2018-12-14 15:27:33 18761607096 HG00103.bam.Reflow comes with a built-in cluster manager, which is responsiblefor elastically increasing or decreasing required compute resources.The AWS EC2 cluster manager keeps track of instance type availabilityand account limits, and uses these to launch the most appropriate setof instances for a given job. When instances become idle, they willterminate themselves if they are idle for more than 10 minutes; idleinstances are reused when possible.
The cluster manager may be configured under the "ec2cluster" key inReflow's configuration. Its parameters are documented bygodoc.(Formal documentation is forthcoming.)
Setting up a TaskDB is entirely optional. The TaskDB is used to store a record of reflow runs,their sub-tasks (mainlyexecs), the EC2 instances that were instantiated, etc.It provides the following benefits:
Tools such as
reflow infowill work better, especially in a multi-user environment.That is, if you have a single AWS account and share it with other users to run
reflow, thena TaskDB allows you to monitor and query info about all runs within the account (usingreflow ps,reflow info, etc)Determine cost of a particular run (included in the output of
reflow info)Determine cost of the cluster (
reflow ps -p- see documentation usingreflow ps --help)
The following command can be used to setup a TaskDB (refer documentation:
% reflow setup-taskdb -helpNote that the same dynamodb table and S3 bucket which were used to setup the cache (see above),could optionally be used here. But note that this (TaskDB) feature comes with a cost (DynamoDB),and by keeping them separate, the costs can be managed independently.
Example:
% reflow setup-taskdb <table_name> <s3_bucket_name>reflow: attempting to create DynamoDB table ...reflow: created DynamoDB table ...reflow: waiting for table to become active; current status: CREATINGreflow: created secondary index Date-Keepalive-indexreflow: waiting for table to become active; current status: UPDATINGreflow: waiting for index Date-Keepalive-index to become active; current status: CREATING...reflow: created secondary index RunID-indexreflow: waiting for table to become active; current status: UPDATINGreflow: waiting for index RunID-index to become active; current status: CREATING...Reflow is implemented in Go, and its packages are go-gettable.Reflow is also aGo moduleand uses modules to fix its dependency graph.
After checking out the repository,the usualgo commands should work, e.g.:
% go test ./...The packagegithub.com/grailbio/reflow/cmd/reflow(or subdirectorycmd/reflow in the repository)defines the main command for Reflow.Because Reflow relies on being able todistribute its current build,the binary must be built using thebuildreflow toolinstead of the ordinary Go tooling.Commandbuildreflow acts likego build,but also cross compiles the binaryfor the remote target (Linux/amd64 currently supported),and embeds the cross-compiled binary.
% cd $CHECKOUT/cmd/reflow% go install github.com/grailbio/reflow/cmd/buildreflow% buildreflowThe$HOME/.reflow/runs directory contains logs, traces and otherinformation for each Reflow run. If the run you're looking for isno longer there, theinfo andcat tools can be used if you havethe run ID:
% reflow info 2fd5a9b6runid user start end RunLog EvalGraph Trace2fd5a9b6 username 4:41PM 4:41PM 29a4b506 90f40bfc 4ec75aac% reflow cat 29a4b506 > /tmp/29a4b506.runlog# fetch the evalgraph data, pass to the dot tool to generate an svg image (viewable in your browser)% reflow cat 90f40bfc | dot -Tsvg > /tmp/90f40bfc.svgFor more information about tracing, see:doc/tracing.md.
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A language and runtime for distributed, incremental data processing in the cloud