[E::hts_idx_check_range] Region 536870752..536870915 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6 [E::sam_index] Read '***' with ref_name='hic_scaffold_1', ref_length=569202264, flags=97, pos=536870753 cannot be indexed samtools ...
[E::hts_idx_check_range] Region 536870922..536871063 cannot be stored in a bai index. Try using a csi index[E::sam_index] Read 'E00548:269:HV7NVCCXY:3:2117:26494:57301' with ref_name='chr1H', ref_length=558535432, flags=81, pos=536870923 cannot be indexed samtools index: failed...
[E::hts_idx_check_range] Region 536870922..536871063 cannot be storedina bai index. Try using a csi index[E::sam_index] Read'E00548:269:HV7NVCCXY:3:2117:26494:57301'with ref_name='chr1H', ref_length=558535432, flags=81, pos=536870923 cannot be indexed samtools index: failed to cr...
I am actually trying to figure out why this bam files can not be read by samtools ( htslib) for ANGSD. We ever indexed the files successfully but no idea why it didn´t work now. Sorry, something went wrong. Copy link Contributor ...
Thesamtools indexcommand can now accept multiple alignment filenames with the new-Moption, and will index each of them separately. (Specifying the output index filename via out.index or the new-ooption is currently only applicable when there is only one alignment file to be indexed.) (PR#...
Usage: samtools [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA index index alignment -- Editing calmd recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header rmdup remove...
thrownewSAMException("BAM cannot be indexed without setting a fileSource for record "+rec); } finalChunknewChunk=((BAMFileSpan)rec.getFileSource().getFilePointer()).getSingleChunk(); finallongstart=newChunk.getChunkStart(); finallongend=newChunk.getChunkEnd(); ...
Linux的管道命令 管道命令(Pipe) 管道命令用"|"来表示,管道命令需要接收前一个命令的输出来进行操作,但...
-f FILE The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razip. [null] -l FILE BED or position list file containing a list of regions or sites where pileup or BCF should be generated [null] -q INT Minimum mapping quality for an alignment ...
-f FILE The faidx-indexed reference fileinthe FASTA format. The file can be optionally compressed by razip. [null] 09 -l FILE BED or position list file containing a list of regions or sites where pileup or BCF should be generated [null] ...