Failed to find fasta index file

Author: uugh

August undefined, 2024

WebOct 15, 2024 · ERROR: Unable to open index file: ucsc.hg19.fa, yet it's in the current directory. #107. Open jamesdalg opened this issue Oct 15, 2024 · 2 comments ... You have to have the genome fasta indexed with both bwa and samtools faidx. I’d run or rerun those on the genomes and try again. ... WebAug 9, 2024 · CreateSequenceDictionary (Picard) Follow. Creates a sequence dictionary for a reference sequence. This tool creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, …

Remove from Multi-FASTA by Sequence ID - Bioinformatics Stack Exchange

WebAn fai index file is a text file consisting of lines each with five TAB-delimited columns for a FASTA file and six for FASTQ: NAME. Name of this reference sequence. LENGTH. … WebPairwise sequence alignment methods such as BLAST and FASTA use position-independent subsitution score matrices such as BLOSUM and PAM, but the desirability of position-speciﬁc models was recog-nized even before BLAST and FASTA were written.3 Several groups 3 R. F. Doolittle. Similar amino acid se-quences: Chance or common … matthew simonet runde

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WebWe can see 5 new files, all having the same basename as the original reference sequence file. These are the index files required by BWA. Note: If the reference is greater than 2GB, you need to specify a different algorithm when building the BWA index, as follows: bwa index -a bwtsw WebJun 19, 2024 · We use the faidx command in samtools to prepare the fasta index file. This file describes byte offsets in the fasta file for each contig, allowing us to compute exactly … herend 2 rabbits

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[ERROR] The FastA is not index - please index file first and run …

WebMay 29, 2024 · colsen commented on May 29, 2024. Confirm that docker see this file: Run a similar command: Run another program to make sure the the fasta file is well-formed. to join this conversation on GitHub . Already have an account? WebJan 2, 2024 · First, start by removing the transcriptome data folder, rm -rf transcriptome_data. Then: bowtie2-build Tcas.fa Tcas. # this will create Tcas*bt2 in the current directory. # now create the ... matthew simonds pa attorneyWebDriver reports warning: Contigs in the vcf file XXX do not match any contigs in the reference¶ The root cause for this warning is that the input VCF file is incompatible with … heren crossbody tas leer

"WebApr 19, 2015 · ../scripts/Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 2 If you would like to refer to this comment somewhere else in this project, copy and paste the following link: " - Failed to find fasta index file

Failed to find fasta index file

[Samtools-help] faidx error_could not build fai index

http://www.htslib.org/doc/samtools-faidx.html WebFeb 25, 2024 · Paul Henry Asks: Unable to see Samba shares in Windows 10 I have a NAS server running Ubuntu server 14.04.5 (Trusty Tahr) and Samba 4.3.11. To be honest I don't know all the complexities of Samba, and I set the NAS up by watching a …

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WebApr 14, 2024 · Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... WebSep 5, 2024 · I am facing this issue while running genotyphi. File path is correct and it is a fasta file [fai_build] fail to open the FASTA file temp_reference.fasta Could not build fai index temp_reference.fasta.fai Traceback (most recent call last)...

WebMay 21, 2015 · Biopython is just perfect for these kinds of tasks. The Seq-Object stores a sequence and info about it.Reading the fasta file format is straight forward. You can access the sequence like a simple list and, hence, access certain positions straight forward as well: WebJun 10, 2014 · Hi, You can run searches with bowtie2 v2.2.3. However it is not yet compatible with tophat. Tophat developers are working to address this issue.

http://eddylab.org/software/hmmer/Userguide.pdf WebIndex reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, faidx will index the file and create .fai on the disk. If regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format. The input file can be compressed in the BGZF …

WebFeb 28, 2024 · The -o option is to set an output file, and you seem to be trying to overwrite an existing fasta index (.fai) file. Did you mean to use -f to give the genome (which would be resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta and not resources-broad-hg38-v0-Homo_sapiens_assembly38.fasta.fai)? $\endgroup$ –

WebFeb 28, 2024 · The -o option is to set an output file, and you seem to be trying to overwrite an existing fasta index (.fai) file. Did you mean to use -f to give the genome (which … herend anchorWebStep 2: Manually check contig_list.txt and custom_genome.fa using your preferred method (e.g. less, nano, vi, or cat are all good command-line options) to confirm if both the contig entry name and sequence are duplicated or if just the contig entry name is duplicated. Step 3: Once the FASTA file is corrected remake the reference library using ... herend asian gardenWebDear Sir/Madam, I met a problem while running samtools faidx command. It shows like: $ cd /biotool/samtools-1.3.1 $ ./samtools faidx /data/hg19.fasta [fai_build] fail to open the FASTA file /data/hg19.fasta Could not build fai index /data/hg19.fasta.fai I tried 3 reference genomes respectively: hg19.fasta, ucsc.hg19.fasta and hg19.fa. matthew simonsen dollar general