[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...]...
samtools的一些问题 samtools在内存与core大量使用时容易出错:如 samtools sort: failed to create temporary file "TCGA-B0-5117-01A-01R-1420-07/hisat2_result/tmp.0000.bam": Cannot send after transport endpoint shutdown 33662 Aborted (core dumped) | samtools sort -@12 - $1/hisat2_result/$1.so...
samtools的一些问题 samtools在内存与core大量使用时容易出错:如 samtools sort: failed to create temporary file "TCGA-B0-5117-01A-01R-1420-07/hisat2_result/tmp.0000.bam": Cannot send after transport endpoint shutdown 33662 Aborted (core dumped) | samtools sort -@12 - $1/hisat2_result/$1.so...
$ samtools sort -@64 -o sort.bam alignments.sam [bam_sort_core] merging from 3392 files and 64 in-memory blocks... [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.1...
Hello, I have been struggling with running samtools because the program can not read the header of my sam file so i get the following error: samtools sort: failed to read header from "20201032.sam" samtools sort: failed to read header fr...
[BioC] Rsamtools: sortBam() and 'samtools sort' does not give the same results 来自 stat.ethz.ch 喜欢 0 阅读量: 19 作者: H Bengtsson 收藏 引用 批量引用 报错 分享 全部来源 求助全文 stat.ethz.ch 相似文献An introduction to Rsamtools The Rsamtools package provides an interface to BAM ...
FAILED. This error must be resolved in order to build HTSlib successfully. 1. 各种方法无法解决后,想到使用conda安装,听说很简单。 2,使用conda安装 conda install samtools 1. 调用samtools,报错 (base) [root@localhost samtools]# samtools samtools: error while loading shared libraries: libcrypto.so.1.0...
samtools index: failed to create index for "Atlas.sort.bam": Numerical result out of range 错误信息表明区域536870922..536871063无法存储在.bai索引中,并建议尝试使用.csi索引。但是 GATK 等一些生信工具不支持 .csi 格式的索引文件。sambamba 能够给最大参考序列长度的 bam 文件构建 bai 索引。
Options: -n sort by read names -r attach RG tag (inferred from file names) -u uncompressed BAM output -f overwrite the output BAM if exist -1 compress level 1 -R STR merge file in the specified region STR [all] -h FILE copy the header in FILE to <out.bam> [in1.bam] ...
samtools index: failed to create indexfor"Atlas.sort.bam": Numerical result out of range 错误信息表明区域536870922..536871063无法存储在.bai索引中,并建议尝试使用.csi索引。但是 GATK 等一些生信工具不支持 .csi 格式的索引文件。sambamba 能够给最大参考序列长度的 bam 文件构建 bai 索引。