Samtools index is corrupted or unsorted
WebI converted the sam output to sorted bam with this command: samtools view -bh@ 15 in.sam samtools sort -T tmp -@ 15 -o out.sorted.bam - When I try to index the sorted … WebSamtools is a set of utilities that manipulate alignments in the SAM (Sequence Alignment/Map), BAM, and CRAM formats. It converts between the formats, does sorting, merging and indexing, and can retrieve reads in any regions swiftly. Samtools is designed to work on a stream.
Samtools index is corrupted or unsorted
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Websamtools index: "SORT.0.bam" is corrupted or unsorted when I check the last lines of the file, it effectively has mapped reads at the end, instead of the unmapped reads. The last 194 … Websamtools index: "SORT.0.bam" is corrupted or unsorted (I assume SORT.0.bam is the same file as out.sorted.bam?) “16” refers to 6B_concat, probably the last record that you saw …
WebNov 20, 2013 · samtools “index” Indexing a genome sorted BAM file allows one to quickly extract alignments overlapping particular genomic regions. Moreover, indexing is required by genome viewers such as IGV so that the viewers can quickly display alignments in each genomic region to which you navigate. samtools index sample.sorted.bam WebSamtools can only create coordinate-sorted BAM indexes in Galaxy. Picard has a queryname sort function and that always outputs a SAM file (even when BAM is input). The Samtools Sort tool will be modified soon. The queryname sort/BAM output should be a failed result and could be considered a bug.
http://quinlanlab.org/tutorials/samtools/samtools.html WebThe exit code >> does not indicate a failure > > The lack of error reporting here is something that has been improved since 1.2. Samtools built from the current develop branch reports …
WebThe BAM formatis a compressed version of the SAM format(which is a plain text) and cannot thus being seen as a text. To explore the BAM file, we have to convert it to the SAM format by using samtools. Note that we use the parameter -hto show also the header that is hidden by default.
WebThe problem is that when I write: samtools view myfile.bam 1 (for example, to just view the data for chromosome 1) I get the following error message: [bam_index_load] fail to load … front of mind campaignWebSamtools built from the current develop branch reports for this file: > > [bam_index] corrupted or unsorted input file > > and exits with failure. ... This can't be indexed with samtools index, and I'll change the message for this case to make it easier to diagnose. (A bgzipped SAM file could be indexed with tabix, but unfortunately such an ... front of mind definitionWebMar 28, 2012 · If you had let samtools view convert the .bam to .sam for a little while, you could have looked at that .sam, and just confirmed that yes, the file is not corrupted, yes, most of the reads really did align, yes, the chromosome names in the .sam match the chromosome names of my reference file, and yes, there are supposed to be reads visible … front of lower legWebpython-pysam: FTBFS: samtools index: "ex2_truncated.bam" is corrupted or unsorted Package: src:python-pysam ; Maintainer for src:python-pysam is Debian Med Packaging … ghost recon white razor mission successWebThis is because samtools sort -n has been used to sort the reads by name instead. Remove -n to sort by position, which is what is needed to prepare a BAM file for indexing with … ghost recon what is hdgWebI have a bam file which appears to be corrupted but I can't understand where and why. ... JdkDeflater WARNING 2014-08-20 10:45:08 SinglePassSamProgram File reports sort order 'unsorted', assuming it's coordinate sorted anyway. ... It seems samtools-1.0 idxstats index incorrectly reports the number of unmapped reads as reported in this thread ... front of mind in a sentenceWebNov 1, 2024 · Looked in some of the bam logs and found the following error: samtools sort: couldn't allocate memory for bam_mem On both occasions where dDocent invokes samtools sort, I added the flag -m 100M... ghost recon wiki breakpoint