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 from "20201032.sam" samtools sort: failed to read header fr...
[bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "/workspace/home/goat/wangzq/501A.mapped.sorted.bam". 看了一下Facebook上的回答 samtools似乎无法识别自身生成的bam文件,这很奇怪 看看楼下的回答 试着验证 501A.mapped.sorted...
What is the exit code you are getting from that process that has the error fail to read the header from "-". This step is very memory intensive process and I have seen this same error message/empty bam appear if the alignment process has run out of memory. Ensure the global config has...
bam 51977802 + 0 in total (QC-passed reads + QC-failed reads) #总共的reads数 4063860 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 50969572 + 0 mapped (98.06% : N/A) #总体上reads的匹配率 47913942 + 0 paired in sequencing #有多少reads是属于paired reads 23956971 + 0 read1 #...
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。
# 默认下输出的 sam 格式文件不带 header,该参数设定输出sam文件时带 header 信息-HprintSAMheaderonly(no alignments)# 仅仅输出文件的头文件-Sinput isSAM# 默认下输入是BAM文件,若是输入是SAM文件,则最好加该参数,否则有时候会报错。-u uncompressedBAMoutput(force-b)# 该参数的使用需要有-b参数,能节约时间...
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] ...
使用字母r切换显示read name等。 具体的操作说明可以?键查看。 7、flagstat 作用:reads的比对情况统计 Usage: samtools flagstat [--input-fmt-option OPT=VAL] <in.bam> 用法: samtools flagstat test.sort.bam 解释: #总的reads 45456 + 0 in total (QC-passed reads + QC-failed reads) ...
FAILED: 0 WRITTEN: 6352529 格式转换 -- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact...
Usage: samtools sort [option] <in.bam> -o <out.prefix> -n Sort by read name #设定排序方式按short reads的ID排序。默认下是按序列在fasta文件中的顺序(即header)和序列从左往右的位点排序。 -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] # 设置每个线程的最大内存,单位...