[E::idx_find_and_load] Could not retrieve index file for '/home/ali/Dokumente/RPractise/Run_alle_features/Velocity/PythonCodes/B2_HET/possorted_genome_bam.bam' So you need index your bam file to get possorted_genome_bam.bam.bai first. ...
MalformedFile ( "Could not read sequence dictionary from given fasta stream " + fastaDictionaryStream ); } return header.getSequenceDictionary(); } Example #13Source File: VariantWalkerSpark.java From gatk with BSD 3-Clause "New" or "Revised" License 6 votes @Override public SAMSequence...
Samtools is also able to open a BAM (not SAM) file on a remote FTP or HTTP server if the BAM file name starts with `ftp://' or `http://'. Samtools checks the current working directory for the index file and will download the index upon absence. Samtools does not retrieve the entir...
i+1 : i-1; if ( out[j].comparator!=filters_cmp_id ) error("Error: could not parse the expression. Note that the \"@file_name\" syntax can be currently used with ID column only.\n"); } if ( out[i].tok_type==TOK_OR || out[i].tok_type==TOK_OR_VEC ) out[i].func =...
private void loadFASTAIndex() { try { this.fasta = new IndexedFastaSequenceFile(new File(options.getPathReferenceFASTA())); } catch (FileNotFoundException e) { throw new UncheckedJannovarException("Could not load FASTA index", e); } if (this.fasta.getSequenceDictionary() == null) { throw...
[%s:%d %s] Could not parse the expression: %s\n", __FILE__,__LINE__,__FUNCTION__, filter->str); if ( !out[ival].key ) error("Comparison between samples is not supported, sorry!\n"); // assign correct setters and unify expressions, eg ar->ra, HOM->hom, etc if ( !