when I use the command 'samtools view -bS GSM653001_BMM_KO_aligned.SAM > GSM653001_BMM_KO_aligned.bam' I got an error as follows: [E::sam_parse1] missing SAM header [W::sam_read1] Parse error at line 3 [main_samview] truncated file. the ...
With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header by default). You may specify one or more space-separated region specifications after the input filename to restrict...
samtools sort: failed to read header from "20201032.sam" srun: error: node2-069: tasks 0-3: Exited with exit code 1 [E::hts_open_format] Failed to open file "20201032_sorted.sam" : No such file or directory samtools view: failed to open "20201032_sorted.sam" for reading: No such...
@SQ SN:chr3 LN:198022430 M5:fdfd811849cc2fadebc929bb925902e5 UR:file:///data/ck/samtool/fasta/hg19.fa AS:/data/ck/samtool/fasta/hg19.dict @SQ SN:chr4 LN:191154276 M5:23dccd106897542ad87d2765d28a19a1 UR:file:///data/ck/samtool/fasta/hg19.fa AS:/data/ck/samtool/fasta/hg19....
head test.sam The first 10 lines on your terminal after typing "head test.sam", should be lines starting with an "@" sign, which is an indicator for a header line. If you don't see lines starting with the "@" sign, the header information is most likely missing. ...
修业/Bioinformatics/Algorithm/Mapping/Software/samtools/使用`samtools view`命令将SAM转换为BAM文件时遇到“no SQ lines present in the header”报错.md · BioX-Lab/BIClass.biox - Gitee.com #samtools #SA…
This command will exit with a non-zero exit code if any input files don't have a valid header or are missing an EOF block. Otherwise it will exit successfully (with a zero exit code). Options: -v Verbose output: will additionally print the names of all input files that don't pass ...
本文整理了Java中htsjdk.samtools.SAMFileHeader.setTextHeader()方法的一些代码示例,展示了SAMFileHeader.setTextHeader()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台,是从一些精选项目中提取出来的代码,具有较强的参考意义,能在一定程度帮忙到你。SAMFileHeader.setTextHeader()方法的具体详情如下...
2_fixup_orphan.sam /usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected /usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected.err /usr/share/samtools/test/addrprg/3_fixup.sam.expected /usr/share/samtools/test/addrprg/3_fixup.sam.expected.err /usr/share/samtools/test/...
* Sam-Spec under the SA tag. No protection against missing values (for cigar, and NM tag). * (Might make sense to move this to htsJDK.) * * @param rec SAMRecord whose alignment information will be encoded * @return String encoding rec's alignment information according to SA tag in th...