2024 Fail to open index file for merged.bcf

Fail to open index file for merged.bcf

Author: gjbh

August undefined, 2024

WebJul 21, 2024 · That shows the CRAM file being opened, returning file descriptor 3 (it'd be -1 if it errored). You could also try using egrep ENOENT instead. You'll likely see lots of harmless things while the program and libraries speculatively look for things, but in there somewhere should be the smoking gun. WebAbout BCFtools. BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. In order to avoid tedious repetion, throughout this document we will use "VCF" and "BCF" interchangeably ...

bcftools call -c : unknown file type #1129 - GitHub

Webbcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf bcftools annotate [OPTIONS]FILE This command allows to add or remove annotations. -a, --annotationsfile Bgzip-compressed and tabix-indexed file with annotations. can be VCF, BED, or a tab-delimited file with mandatory columns CHROM, POS http://samtools.github.io/bcftools/howtos/index.html red nose pitbull breed

bcftools mpileup "Failed to open the file" questions

WebMay 29, 2024 · Failed to open a_certain_variant_file.vcf.gz: could not load index I believe the problem is that too many files are opened. For each vcf also the index (.tbi) file is … WebJun 24, 2024 · Too many open files in merge simply means we need to do sub-merges and save to temporary files to avoid running out of file descriptors. This is what the proposed … rich bedding homasassa bbb

bcftools concat: Failed to open variants.vcf.gz: could not load …

Failed to read index file - how to solve related issues - Opster

WebWhen this option is in use, the input file may not be sorted. -T, --targets FILE Similar to -R but the entire input will be read sequentially and regions not listed in FILE will be skipped. -D Do not download the index file before opening it. Valid for remote files only. --cache INT Set the BGZF block cache size to INT megabytes. [10] WebMerge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file. For example, when merging file A.vcf.gz containing samples S1 , S2 and S3 and … red nose pit bullsWebDec 5, 2024 · VCF or BCF input files (File format is determined by file extension), or a file having a '.list' suffix containing the path to the files, one per line.--OUTPUT -O: null: The merged VCF or BCF file. File format is determined by file extension. Optional Tool Arguments--arguments_file [] read one or more arguments files and add them to the … rich bedding nightfall

"WebDec 27, 2024 · 首先因为我的vcf并不是标准的vcf，我用的这些vcf是通过python拼凑了几个call snp软件的结果，所以遇到了各种问题，开帖记录一下。要对多个vcf文件进行合并， … " - Fail to open index file for merged.bcf

Fail to open index file for merged.bcf

bcftools concat could not load index! #1045 - Github

WebDec 27, 2024 · 1 2 这下压缩时就没有报错了，接下来进行index bcftools index sample.vcf.gz [E::hts_idx_push] Unsorted positions on sequence #1: 59033730 followed by 2730114 index: failed to create index for "ERR3378452.vcf.gz" 1 2 3 4 然后说我的位置信息没排过序，于是再加上位置的排序： WebDec 6, 2024 · I also had problems when merging thousands of vcf files with bcftools. In my case, the problem was the number of open files. You may need to increase the open file limit. Try these commands: # check soft limit ulimit -Sn #check hard limit ulimit -Hn #set soft limit ulimit -Sn Share Improve this answer Follow

Did you know?

WebI am having an issue when trying to perform bcftools merge. I get these errors with the first file in the list, [E::hts_hopen] Failed to open file filename1.bcf.csi [E::hts_open_format] Failed to open file filename1.bcf.csi Failed to open filename1.bcf.csi Exec format error WebThis may occur if the file is corrupted or if the storage device hosting the file is damaged. To resolve this error, you can try the following steps: (1) Check the storage device hosting …

WebDec 14, 2024 · I first compress my VCF files in bgzip format with bgzip -ci infileA.vcf > outfileA.vcf.gz. I next attempt to merge the files with bcftools merge outfileA.vcf.gz outfileB.vcf.gz outfileC.vcf.gz. But I get an error … WebJan 16, 2024 · "Failed to open ." You probably mistyped a filename, included a file extension when you shouldn't have (e.g. --bfile ), or failed to include a file extension when you should have (e.g. --vcf ). "Line <1-based …

WebDec 5, 2024 · The vcf files has been generated using GATK and converted to bcf and indexed by bcftools. The bcftools proceeds to analyze 20% of the data but it keeps … WebNov 8, 2024 · A character(1) file path for the header information to be used in the merged BAM file. addRG: A logical(1) indicating whether the file name should be used as RG (read group) tag in the merged BAM file. compressLevel1: A logical(1) indicating whether the merged BAM file should be compressed to zip level 1. maxMemory

WebThe VCF IDs are matched between tumor and control. Thus, you can merge both files using bcftools. bcftools merge -m id -O b -o tumor_control.bcf tumor.bcf control.bcf. Somatic filtering requires a tab-delimited sample description file where the first column is the sample id (as in the VCF/BCF file) and the second column is either tumor or control.

WebJul 8, 2024 · The latter is quite easy: run gdb --args bcftools mpileup -f ref_genbank/ref_genbank.fasta -o /dev/null ref494_aligned.sorted.bam, then type run … red nose pitbull puppies for adoptionWebWrite merged output to FILE , specifying the filename via an option rather than as the first filename argument. When -o is used, all non-option filename arguments specify input files to be merged. -t TAG. The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given). -R STR. rich bedding furniture outlethttp://www.htslib.org/doc/1.1/bcftools.html red nose pitbull whiteWebDec 23, 2024 · Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files Failed to read from standard input: unknown file type I used to run this command before, maybe there's an issue with the versions? rich beddingWebMay 29, 2024 · Failed to open a_certain_variant_file.vcf.gz: could not load index. I believe the problem is that too many files are opened. For each vcf also the index (.tbi) file is opened, which turns out to be more than the number of files your operating system allows you to open. You can check that using ulimit -u, which in my case is 1024. rich bedding homosassaWebI can't merge my BCF files together using bcftools. Below are the details of my pipeline. After running the pipeline, I created a subdirectory that has 2 *.bcf files to try and merge … red nose pit mixed with labhttp://www.htslib.org/doc/samtools-merge.html rich become richer