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...
In this case samtools view and samtools index failed in open the file "20201032_sorted.sam" , because this file should be the output of samtools sort. Which in turn, cannot can not read the header of the input file "20201032.sam" . The header of the sam file looks as follows: @sqS...
[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....
[M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 67652 sequences (10000283 bp)... [main_samview] fail to read the header from "-". 中划线“-”是前一句命令的,也就是bwa出了错误。 发现错误2 错误2.单独运行bwa程序: /opt/gridview//pbs/dispatcher/mom_priv/jobs/21873...
[main_samview] fail to read the header from "-". 中划线“-”是前一句命令的,也就是bwa出了错误。 发现错误2 错误2.单独运行bwa程序: /opt/gridview//pbs/dispatcher/mom_priv/jobs/21873.node1.SC: line 10: 20117 Bus error (core dumped) ...
[M::process] read 67652 sequences (10000283 bp)... [main_samview] fail to read the header from "-". 中划线“-”是前一句命令的,也就是bwa出了错误。 发现错误2 错误2.单独运行bwa程序: /opt/gridview//pbs/dispatcher/mom_priv/jobs/21873.node1.SC: line 10: 20117 Bus error (core dumped...
fprintf(stderr, "Couldn't read header\n"); goto fail; } sam_hdr_destroy(tmp); } fp = bgzf_fdopen(fd, "w"); if (!fp) { print_error_errno("reheader", "Couldn't open output file"); goto fail; } if (!no_pg && sam_hdr_add_pg(h, "samtools", ...
Sort alignments by leftmost coordinates, or by read name when -n is used. An appropriate @HD-SO sort order header tag will be added or an existing one updated if necessary. The sorted output is written to standard output by default, or to the specified file (out.bam) when -o is used...
Usage:samtools view[options]<in.bam>|<in.sam>[region[...]]默认情况下不加region,则是输出所有的region.Options:-b 默认输出sam格式文件,该参数设置输出bam格式-h 默认输出的sam格式文件不带header,该参数设定输出sam文件时带header信息-H只输出header部分-S默认情况下输入时bam文件,若输入是sam文件,则最好...
header.setSortOrder(htsjdk.samtools.SAMFileHeader.SortOrder.coordinate); header.setSequenceDictionary(dict); return header; } 代码示例来源:origin: broadgsa/gatk-protected protected ReadDestination(final SAMFileHeader header, final String readGroupID) { // prepare the bam header if ( header == null...