masurca 3.4.1 33.54% Success

Executables

add_pb_seq Failed add_missing_mates Failed break_contigs Failed create_merged_mega_reads Failed create_merged_sequences Failed create_end_pairs Failed create_end_pairs Failed create_sr_frg Failed evaluate_splits Failed extractJoinableAndNextPassReadsFromJoinKUnitigs Failed extract_merges Failed extract_merges_mega_reads Failed extract_single_best_match_coords_file Failed extract_unique_mega_reads Failed extract_unjoined_pairs Failed extractreads Failed extractreads_not Failed fastqToFasta Failed fill_unaligned_gaps Failed filter_delta_file_for_qrys Failed filter_redundancy Failed find_contained_reads Failed fix_consensus_from_vcf Failed getEndSequencesOfContigs Failed getLengthStatisticsForKUnitigsFile Failed getMeanAndStdevByGCCount Failed get_super_read_sizes Failed homo_trim Failed introduce_errors_fasta_file Failed join_mega_reads_trim Failed join_mega_reads_trim Failed join_mega_reads_trim Failed killBadKUnitigs Failed makeAdjustmentFactorsForNumReadsForAStatBasedOnGC Failed makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2 Failed mergeSuperReadsUniquely Failed merge_contigs Failed merge_mega_reads Failed merge_matches_and_tile_coords_file Failed merge_sequences_simple Failed outputJoinedPairs Failed process_scaffold_gaps Failed reconcile_consensus Failed recover_scaffolds Failed resolve_trio Failed restore_ns Failed reverse_complement Failed splitFileAtNs Failed splitLongKUnitigs Failed splitFileByPrefix Failed splitScaffoldsAtNs Failed split_reads_to_join Failed split_matches_file Failed translateReduceFile Failed translate_reduced_reads Failed trim_by_kunitigs Failed trim_mega_reads Failed ufasta Succeeded MasurcaCelera Failed MasurcaCommon Failed MasurcaConf Failed MasurcaPaths Failed MasurcaSoap Failed MasurcaSuperReads Failed addSurrogatesToFrgCtgFile Failed addSurrogatesToFrgctg Succeeded blast_self_alignment_filter Failed bloom_query Succeeded chromosome_scaffolder Succeeded classify_reads Failed closeGaps Failed closeGaps Failed closeGapsInScaffFastaFile Succeeded closeGapsLocally Succeeded closeGaps Succeeded close_gaps Failed close_scaffold_gaps Succeeded collectReadSequencesForLocalGapClosing Succeeded compute_sr_cov Failed compute_sr_cov Failed createFastaSuperReadSequences Failed createKUnitigMaxOverlaps Succeeded createSuperReadSequenceAndPlacementFileFromCombined Succeeded createSuperReadsForDirectory Succeeded create_k_unitigs_large_k Succeeded create_k_unitigs_large_k2 Succeeded create_mega_reads Succeeded create_sr_frg Failed deduplicate_contigs Succeeded deduplicate_unitigs Failed determineUnjoinablePacbioSubmegas Succeeded eliminateBadSuperReadsUsingList Failed error_corrected2frg Succeeded expand_fastq Succeeded extendSuperReadsBasedOnUniqueExtensions Succeeded extendSuperReadsForUniqueKmerNeighbors Succeeded fasta2frg Failed fasta2frg_m Failed fasta_make_Nbase_bed Failed filter_alt Failed filter_library Failed filter_overlap_file Succeeded findGapsInCoverageOfPacbios Succeeded findMatchesBetweenKUnitigsAndReads Succeeded fix_unitigs Failed fragScaff Failed fragScaff Succeeded getATBiasInCoverageForIllumina_v2 Failed getGCBiasStatistics Failed getMeanAndStdevForGapsByGapNumUsingCeleraAsmFile Succeeded getMeanAndStdevForGapsByGapNumUsingCeleraTerminatorDirectory Succeeded getNumBasesPerReadInFastaFile Succeeded getSequenceForClosedGaps Failed getSequenceForLocallyClosedGaps Failed getSuperReadInsertCountsFromReadPlacementFile Succeeded getSuperReadInsertCountsFromReadPlacementFileTwoPasses Succeeded getSuperReadPlacements Failed getUnitigTypeFromAsmFile Succeeded get_super_read_sizes Succeeded jf_aligner Succeeded joinKUnitigs_v3 Succeeded longest_path Succeeded make_mate_frg Failed make_mr_frg Failed masurca Succeeded masurca_superreads Succeeded mega_reads_assemble_cluster Succeeded mega_reads_assemble_nomatch Succeeded mega_reads_assemble_ref Succeeded merge_contigs Succeeded merge_coords Succeeded outputAlekseysJellyfishReductionFile Failed outputRecordsNotOnList Failed output_reconciled_scaffolds Failed parallel_delta_filter Succeeded polca Succeeded polish_with_illumina_assembly Succeeded recompute_astat_superreads Failed recompute_astat_superreads_CA8 Failed reconcile_alignments Failed reconcile_matches Failed reconciliate_mega_reads Failed reduce_sr Succeeded refine Failed refine_alignments Failed rename_filter_fastq Succeeded rename_filter_fastq Failed runByDirectory Succeeded runSRCA Succeeded run_ECR Failed samToDelta Failed sample_mate_pairs Failed sorted_merge Succeeded split_long_unitigs Failed ufasta_arg Succeeded ufasta_cmd Succeeded compute_coverage Failed freebayes Succeeded