[E::hts_open_format] Failed to open file "2_5_merged.sort.bam.tmp.1020.bam" : Too many open files 原脚本 samtools sort -o w.sort.bam w.merged.bam 排查原因:临时文件生成太多导致,改善方法就是增大临时文件可写入的大小来减少文件个数 $ samtools sort Usage: samtools sort [options...]...
Caused by: java.io.FileNotFoundException: /tmp/anjie/CSPI.tmp5012020104068677848/3581.tmp (Too many open files) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298) at java.base/java.io.FileOutputStream.<init>(File...
--overflow-list-size=OVERFLOW_LIST_SIZE:增加大小会减少创建的临时文件的数量。 如果出现 Too many open files 报错,需要通过使用ulimit -n 8000或添加--overflow-list-size=600000来解决 扫码关注微信公众号【生信F3】获取文章完整内容,分享生物信息学最新知识。 本文由mdnice多平台发布...
如果出现 Too many open files 报错,需要通过使用ulimit -n 8000或添加--overflow-list-size=600000来解决 扫码关注微信公众号【生信F3】获取文章完整内容,分享生物信息学最新知识。
[E::hts_open_format] Failed to open file /tmp/sort.bam.RX8hvv.1020.bam samtools sort: fail to open "/projects/btl_scratch/sjackman/redcedar/tmp/sort.bam.RX8hvv.1020.bam": Too many open files $ ulimit -n 1024 I'll try increasing -m from the default value of 768 MB to 16 ...
1M is aminimumvalue for when users try to drive the memory limit too low. It is most definitely not the default nor recommended. As for a maximum number of files, this may work, but I'm wary of something low as many file systems are quite capable of dealing with 100k files, just not...
2313 'select()' returned 1:many mapping between keys and columns 2314 Filtering counts using DRIMSeq. 2315 Error in dmDSdata(counts = counts, samples = coldata) : 2316 mode(counts) %in% "numeric" is not TRUE 2317 Calls: dmDSdata -> stopifnot 2318 Execution halted 2319 2320 Work dir: ...
Fix a bug wich caused incorrect FORMAT/BCSQ formatting at sites with too many per-sample consequences Fix a bug which incorrectly handled the --ncsq parameter and could clash with reserved BCF values, consequently producing truncated or even incorrect output of the %TBCSQ formatting expression in...
open("tmp.Chr09_18095464_18242300.q13Q10.vcf.gz.tbi", O_RDONLY) = -1 EMFILE (Too many open files) open("tmp.Chr09_18095464_18242300.q13Q10.vcf.tbi", O_RDONLY) = -1 EMFILE (Too many open files) write(2, "Failed to open tmp.NC_024339.1_R"..., 91Failed to open tmp.Chr09_18...
if (num_columns > sizeof(scanf_components)) { fprintf(stderr, "[amplicon] error: too many columns in line %d of %s.\n" "Found %d columns, but only up to %zu are expected.\n", line_count, infile, num_columns, sizeof(scanf_components) / sizeof(scanf_components[0])); ...