Tabix failed to load the index file

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August undefined, 2024

WebOct 4, 2024 · I get the following error message: $ tabix hg19.15.all.KL.gz chr1:50669400-50669800 [W::hts_idx_load2] The index file is older than the data file: … WebFeb 13, 2016 · tabix chr37.vcf.gz chr37:1-20000 [ti_index_load] wrong magic number [ti_index_load] fail to load the index: chr.37.vcf.gz.tbi [tabix] failed to load the index file I …

How to troubleshoot access to tabix file via http or https?

WebJan 4, 2016 · When I run the load command, it always complaints, ... (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] contig '18' is not defined in the header. (Quick workaround: index the file with tabix.) WebJul 25, 2024 · 1 I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using samtools index, but am running into a couple of errors. I unpacked the original .sra files in the following manner: gwic greyhound racing rules

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WebFeb 2, 2011 · Please help me to fix the three problems followed and give me some tips or directions to merging VCF files. tabix has been in my path. (1). When I want to merge the three example VCF files, I failed. commands: merge-vcf merge-test-a.vcf merge-test-b.vcf merge-test-c.vcf > merg.vcf results: [main] fail to load the index file. The command "tabix ... WebMar 3, 2016 · You ll have to run the prerequisites of tabix (bgzip, index) before the query actually.They are not included in the tb.query. if your file is already zipped ,you should … WebJun 27, 2024 · Hello, I'm trying to use tabix on a bed file and it seems that tabix is unable to parse my file. Here is my file : Code: chr7 1000 5000 name1 1 + chr7 15000 25000 name3 4 + chr7 35000 75000 name4 8 + chr7 57373 987412 name5 16 -. my commands are : $ bgzip example_sort.bed. $ tabix -p bed example_sort.bed.gz. and the outputs are : boys and girls club st augustine fl

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[Vcftools-help] [tabix] failed to load the index file. vcftools

WebVCF data files must be indexed for viewing in IGV, either by using igvtools or by using Tabix. igvtools can be run from the command line or IGV itself (Tools>Run igvtools...) After launching, choose the Index command and browse to your .vcf file. The index file (.idx) will be created in the same directory as the .vcf file. WebIf the file is gzipped (ends with .vcf.gz), it must have an accompanying Tabix index (see below). VCF Requirements. IGV supports VCF Version 4. VCF data files must be indexed … gwich gls white 1000 hiline base white cabWebJan 16, 2011 · FASTA indexing allows even very large FASTA files to be downloaded into JBrowse "on demand" e.g. only downloading the sequence required for a certain view. The FASTA index will be a file called volvox.fa.fai. Then we'll move these files into a "data directory" that JBrowse can use. Then create the file data/tracks.conf with this file content. boys and girls club staunton va

"WebJan 13, 2024 · This index acts lke a table of contents, helping tabix jump around the .gz file quickly. The index file is called .tbi and will be put adjacent to your .gz file. Now you can check for the existence of a variant like so. Its important to remember, while you’re doing this, that a polymorphism being in the VCF file is not synonymous with being ... " - Tabix failed to load the index file

Tabix failed to load the index file

python - tabix.TabixError: query failed - Stack Overflow

WebJun 16, 2024 · This is intentional — hts_open() was originally for opening SAM/BAM/CRAM/VCF/BCF files, and having it fail to open index files improves the error … WebDec 9, 2012 · The files you attached are not valid VCF files. I am surprised VCFtools would work at all, as they contain no header information and do not conform with the VCF specification. ... [tabix] failed to load the index > file" ) > > I would be very thankful if you could tell me what I am doing wrong. An > alternative option to convert my .vcf files ...

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Web错误原因:我新建了一个folder,然后在下面新建一个file ,两者name一样,但是我应该是没有修改某些配置,只能识别index.js. 修改方法:给新建的file rename 成index.js..... (不要喷我,真的是新手,本职工作水平都不怎么厉害,又在学习新的... 有好的教程或教学视频的,请推荐我,谢谢) WebTabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file ( in.tab.bgz.tbi or in.tab.bgz.csi ) when region is absent from the command-line. The input …

WebThe data is block-gzipped to allow indexing and to save disk space. The fragments.tsv.gz.tbi file is a tabix index of the fragment intervals facilitating random access to records from an arbitrary genomic interval. The tabix index is created with --preset=bed . Positions in the fragments.tsv.gz file, as in a BED file, are 0-based. WebFeb 26, 2024 · tabix 0.2.6-2. links: PTS, VCS area: main; in suites: jessie, jessie-kfreebsd; size: 384 kB; ctags: 521; sloc: ansic: 3,759; java: 309; python: 126; perl: 91 ...

WebSep 4, 2024 · I believe the `.idx` index is for uncompressed VCF s. The `.tbi` tabix index is for block-compressed `.gz` VCF s. Be sure you are tabix indexing a block-compressed vcf. To upload here, just change the `.vcf` extension (of the uncompressed file) to `.txt`. You can do this on a Mac by right-clicking on a file, then selecting Get Info. WebOct 4, 2024 · In response to Jonathan Moore's comment, I wget the bgzip-ed gz archive and its associated tbi index, and then try to query the file locally (not via http, but directly via the filesystem). $ tabix hg19.15.all.KL.gz chr1:50669400-50669800 [W::hts_idx_load2] The index file is older than the data file: hg19.15.all.KL.gz.tbi.

WebJan 10, 2013 · [Vcftools-help] VCFTools or Tabix problem - [tabix] the index file either does not exist or is older than the vcf file. Please reindex

WebJan 9, 2024 · How to index a VCF file with tabix? If you get the above error messages, you have to first sort your VCF file, and you can do it in several ways using the sort command and compressing it using bgzip and finally applying bcftools index or … boys and girls club spruce st lawrence njWebSep 29, 2011 · Hi Hasani, it looks as if you were at the same time trying to index (-f) and to query the VCF. Please try first to index and then to run your query, in two separate commands. boys and girls club stamfordWebDec 11, 2013 · Hi, I followed the vcftools instructions and compressed and indexed the vcf as follows. bgzip my_file.vcf tabix -p vcf my_file.vcf.gz After using these commands a … boys and girls club statisticsWebJun 7, 2024 · As written in the documentation of the function CreateChromatinAssay, the fragments = file should be a tabix file (ending in .tbi) containing the index with fragments of your data, or a Fragments object in R. Apparently, first you will need to create the Fragments object in R from your tsv data, using the function CreateFragmentObject (). boys and girls club spruce st ewing njWebFeb 25, 2024 · Below are the outputs. It didn't show which version of libcurl I was using. By the way, it is really slow for me to download the index file from ftp.ncbi.nih.gov. I'm not … boys and girls clubs scotlandWebsamtools index output.sorted.bam Step 5: Removing duplicates java -jar picard.jar MarkDuplicates I=output.sorted.bam O=output.sorted.dedup.bam METRICS_FILE=metrics.txt VALIDATION_STRINGENCY=LENIENT boys and girls club st albansWebcreate tabix index for the vcf file created in step 1 tabix -p vcf chr1.vcf The next step is executed in R vcffile = open(VcfFile(file = "chr1.vcf", index = "chr1.vcf.bgz.tbi", yieldSize = … boys and girls club steinhatchee