3

我正在尝试随机采样一个大型 FASTQ 文件并将其写入标准输出。我不断收到“超出 GC 开销限制”错误，我不确定自己做错了什么。我试过在 leiningen 增加 Xmx 但这没有帮助。这是我的代码：

(ns fastq-sample.core
  (:gen-class)
  (:use clojure.java.io))

(def n-read-pair-lines 8)

(defn sample? [sample-rate]
  (> sample-rate (rand)))

;
; Agent for writing the reads asynchronously
;

(def wtr (agent (writer *out*)))

(defn write-out [r]
  (letfn [(write [out msg] (.write out msg) out)]
    (send wtr write r)))

(defn write-close []
  (send wtr #(.close %))
  (await wtr))

;
; Main
;

(defn reads [file]
  (->>
    (input-stream file)
    (java.util.zip.GZIPInputStream.)
    (reader)
    (line-seq)))

(defn -main [fastq-file sample-rate-str]
  (let [sample-rate (Float. sample-rate-str)
        in-reads    (partition n-read-pair-lines (reads fastq-file))]
    (doseq [x (filter (fn [_] (sample? sample-rate)) in-reads)]
      (write-out (clojure.string/join "\n" x)))
    (write-close)
    (shutdown-agents)))
4

1 回答 1

1

当我尝试将无限序列合并到一个简单的数据结构（如地图或向量）中时，我经常会遇到这种症状。这通常意味着内存紧张，垃圾收集器无法满足对新对象的需求。wtr 代理很可能对于内存来说太大了。也许您可能不想通过更改将打印结果存储在原子中

(write [out msg] (.write out msg) out)

至

(write [out msg] (.write out msg))
于 2013-10-01T17:04:16.353 回答