broadinstitute/pilon issues and pull requests

#160 - HashMap table size

Issue - State: open - Opened by rivabros2 over 1 year ago

#159 - Java heap space error while running pilon

Issue - State: open - Opened by saras224 over 1 year ago

#158 - Asking for indexed bam file

Issue - State: open - Opened by saras224 over 1 year ago - 1 comment

#157 - pilon error: Exception in thread "main" java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: contig_1

Issue - State: open - Opened by saras224 almost 2 years ago - 1 comment

#156 - Error with very short contig

Issue - State: open - Opened by bartns about 2 years ago

#155 - Segmenting genome for quicker result

Issue - State: open - Opened by tamsinlh over 2 years ago

#154 - How to resume

Issue - State: open - Opened by methylome over 2 years ago

#153 - no bam file

Issue - State: open - Opened by rmormando over 2 years ago - 1 comment

#152 - Question: Are redundant bases inside overlapping ends of paired reads counted once or twice towards consensus?

Issue - State: open - Opened by JohnUrban over 2 years ago

#151 - fasta headers not appended but overwritten

Issue - State: open - Opened by hkaspersen over 2 years ago

#150 - Index -1 out of bounds for length X

Issue - State: open - Opened by anitajnorman over 2 years ago - 1 comment

#149 - Memory usage relation to file size?

Issue - State: open - Opened by snail123815 over 2 years ago - 1 comment

#148 - Make polishing stats machine-readable

Issue - State: open - Opened by kim-fehl over 2 years ago

#147 - --threads argument no longer supported

Issue - State: closed - Opened by cpavloud almost 3 years ago - 1 comment

#146 - Correct spelling mistakes

Pull Request - State: open - Opened by EdwardBetts almost 3 years ago

#145 - VCF format issue

Issue - State: open - Opened by jodyphelan almost 3 years ago

#144 - "main" java.lang.IllegalArgumentException: requirement failed

Issue - State: open - Opened by bioramg almost 3 years ago - 2 comments

#143 - Pilon on haplotype polish: how did pilon deal with haplotype genome assembly?

Issue - State: open - Opened by cjchen5 about 3 years ago

#142 - Fix vcf header def for DP

Pull Request - State: open - Opened by jodyphelan about 3 years ago

#141 - VCF header issue

Issue - State: open - Opened by jodyphelan about 3 years ago

#140 - Problem with executing Pilon

Issue - State: open - Opened by Hai1983 about 3 years ago - 2 comments

#139 - Pilon on transcriptome assembly from tetraploid species

Issue - State: open - Opened by ConcettaDe4 about 3 years ago

#138 - How to run pilon

Issue - State: closed - Opened by leggylas over 3 years ago

#137 - Issues running pilon

Issue - State: open - Opened by myco-bradshaw over 3 years ago

#136 - Discordant Pilon Results for Equivalent Files

Issue - State: open - Opened by cwarden45 over 3 years ago

#135 - Annotate allelic depth?

Issue - State: open - Opened by pgcudahy over 3 years ago - 1 comment

#134 - Ways to speed up pilon

Issue - State: open - Opened by kattweigh over 3 years ago - 1 comment

#133 - trying to polish nanopore with illumina don't understand the error

Issue - State: open - Opened by Ayse1006 almost 4 years ago - 1 comment

#132 - Absurdly long run time and GCLocker

Issue - State: open - Opened by NTNguyen13 almost 4 years ago - 1 comment

#131 - Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: align_filer.bam

Issue - State: open - Opened by zhuanghemu almost 4 years ago - 1 comment

#130 - HI

Issue - State: open - Opened by zhuanghemu almost 4 years ago

#129 - Pilon appearing to make no corrections or confimations of bases

Issue - State: open - Opened by Rob-murphys about 4 years ago - 1 comment

#128 - java.lang.OutOfMemoryError

Issue - State: open - Opened by kjestradag over 4 years ago - 3 comments

#127 - Can you go into more detail about the --threads option? What does "experimental" mean?

Issue - State: open - Opened by lfaller-zymergen over 4 years ago - 2 comments

#126 - Does pilon write to temp files?

Issue - State: open - Opened by lfaller-zymergen over 4 years ago - 1 comment

#125 - Expected memory usage

Issue - State: closed - Opened by nhartwic over 4 years ago - 4 comments

#124 - Exception in thread "main" java.nio.BufferUnderflowException

Issue - State: open - Opened by francescodc87 over 4 years ago - 2 comments

#123 - Pilon on Nanopore assembly of tetraploid organism

Issue - State: closed - Opened by ms-gx over 4 years ago - 1 comment

#122 - Out of memory?

Issue - State: open - Opened by stanislasmorand almost 5 years ago - 7 comments

#121 - Asymmetric mapping in two repeat areas

Issue - State: open - Opened by YiweiZhu almost 5 years ago - 5 comments

#120 - java.lang.ArrayIndexOutOfBoundsException: -5 ERROR

Issue - State: open - Opened by francicco almost 5 years ago - 1 comment

#119 - No output file or directory

Issue - State: open - Opened by cmaggior almost 5 years ago - 3 comments

#118 - pilon

Issue - State: closed - Opened by marjorie2205 almost 5 years ago

#117 - New htsjdk and options *-list

Pull Request - State: open - Opened by SergejN almost 5 years ago - 2 comments

#116 - Alternate genotype with no alternate allele in VCF output

Issue - State: open - Opened by tatumdmortimer about 5 years ago - 1 comment

#115 - Pilon with 10x bam ( longranger )

Issue - State: open - Opened by ViriatoII about 5 years ago

#114 - long runtime

Issue - State: closed - Opened by dcopetti about 5 years ago - 3 comments

#113 - a bam file contains single-end and paired-end reads

Issue - State: open - Opened by lancer-lu about 5 years ago - 1 comment

#112 - Is it OK to run Pilon multiple times by adding shortreads?

Issue - State: closed - Opened by chelidphile about 5 years ago

#111 - bam doesn't have sequence

Issue - State: open - Opened by emmannaemeka about 5 years ago - 2 comments

#110 - Exception in thread "main"

Issue - State: closed - Opened by Tdanis about 5 years ago - 2 comments

#109 - Not detecting 100bp insertion

Issue - State: open - Opened by ybendana over 5 years ago

#108 - Runtime estimates

Issue - State: open - Opened by henkela over 5 years ago

#107 - About the "diploid" option

Issue - State: open - Opened by hungweichen0327 over 5 years ago

#106 - Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException:

Issue - State: open - Opened by jhcaddisfly over 5 years ago - 3 comments

#105 - Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException

Issue - State: open - Opened by SvitlanaLukicheva over 5 years ago - 1 comment

#104 - Strand bias report

Issue - State: open - Opened by carlosmag over 5 years ago

#103 - Disable CCxGG motif skipping for bacteria / PCR amplified DNA ?

Issue - State: open - Opened by tseemann over 5 years ago

#102 - Exception in thread "main" java.lang.reflect.InvocationTargetException

Issue - State: open - Opened by nsgarcia27 over 5 years ago - 1 comment

#101 - How to get polished reads after Pilon has run?

Issue - State: open - Opened by tayabsoomro over 5 years ago - 2 comments

#100 - Install/command not found?

Issue - State: closed - Opened by Firedrops over 5 years ago - 1 comment

#99 - use --targets but return complete input assembly (including non-polished regoins)

Issue - State: open - Opened by dwinter over 5 years ago

#98 - No output after scanning BAMs

Issue - State: open - Opened by nicolasalexandre21 over 5 years ago - 2 comments

#97 - Pilon spiking and using multiple cores on cluster

Issue - State: open - Opened by swlong over 5 years ago - 3 comments

#96 - Support for CSI indices

Issue - State: open - Opened by SergejN over 5 years ago - 1 comment

#95 - Error Exception in thread "main" java.lang.IllegalStateException: Inappropriate call if not paired read

Issue - State: open - Opened by drs357 over 5 years ago - 1 comment

#94 - marking reads duplication before pilon running

Issue - State: open - Opened by baoxingsong over 5 years ago - 1 comment

#93 - pilon fails on Falcon unzip assemblies

Issue - State: open - Opened by dgordon562 almost 6 years ago

#92 - Hard-coded memory

Issue - State: open - Opened by CristianRiccio almost 6 years ago - 1 comment

#91 - pilon running error

Issue - State: open - Opened by emmannaemeka almost 6 years ago - 1 comment

#90 - obtain gfa after polishing

Issue - State: open - Opened by MChiaraC almost 6 years ago

#89 - Error Pilon - Array

Issue - State: open - Opened by KristinaGagalova almost 6 years ago - 1 comment

#88 - --targets list reading error

Issue - State: open - Opened by KristinaGagalova almost 6 years ago - 2 comments

#87 - Multimapped read behaviour

Issue - State: open - Opened by francicco almost 6 years ago

#86 - Best practices - Is it necessary to use trimmed illumina reads as input for polishing?

Issue - State: open - Opened by elor77 almost 6 years ago

#85 - pilon for rna-seq

Issue - State: closed - Opened by manuelsmendoza almost 6 years ago - 2 comments

#84 - java.lang.ArithmeticException: / by zero

Issue - State: closed - Opened by MichelMoser about 6 years ago - 1 comment

#83 - unknown option --nanopore

Issue - State: open - Opened by MichelMoser about 6 years ago

#82 - The error caused by the Xxm**G setting problem, the existence of two types of errors

Issue - State: open - Opened by Hongchang-Gu about 6 years ago - 2 comments

#78 - Possible to set minimum indel length for correction?

Issue - State: open - Opened by rorycraig337 over 6 years ago - 1 comment
Labels: enhancement

#76 - Handling of single "N" characters in reference genome

Issue - State: open - Opened by ewilbanks over 6 years ago - 1 comment
Labels: enhancement

#69 - Fix Ambiguous Bases - finding, possibly fixing, but not writing changes

Issue - State: closed - Opened by Roli-Wilhelm about 7 years ago - 4 comments

#67 - advice for finishing a pacbio sequel yeast genome asm

Issue - State: closed - Opened by splaisan about 7 years ago

#66 - pilon will call snpindel in repeat region of ref sequence ？

Issue - State: closed - Opened by orangeSi about 7 years ago

#65 - Exception in thread "main" java.lang.reflect.InvocationTargetException

Issue - State: closed - Opened by wenjiexiaomeng about 7 years ago - 1 comment

#64 - Multiple rounds of polishing using pilon

Issue - State: closed - Opened by efratca about 7 years ago - 1 comment

#63 - Coverage is always 0

Issue - State: closed - Opened by CVan19 about 7 years ago - 3 comments

#62 - GATK Indel Realigner

Issue - State: closed - Opened by ArashBayat about 7 years ago - 1 comment

#61 - Caused by: java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary:

Issue - State: closed - Opened by tiramisutes over 7 years ago - 1 comment

#60 - using 250bp paired reads in pilon (which the reads of a pair may overlap each other)

Issue - State: closed - Opened by dgordon562 over 7 years ago - 1 comment

#59 - [Question] Impact of kmer size (--K) in correction

Issue - State: closed - Opened by ghost over 7 years ago - 1 comment

#58 - Pilon with MP + PE cuses too many cpus and memory

Issue - State: closed - Opened by jaworskicoline over 7 years ago - 1 comment

#57 - use pilon to polish cause error

Issue - State: closed - Opened by lijingjing1 over 7 years ago - 1 comment

#56 - Dovetail data for Pilon

Issue - State: closed - Opened by dcopetti over 7 years ago - 1 comment

#55 - pilon on sge cluster

Issue - State: closed - Opened by dcopetti over 7 years ago - 1 comment

#54 - Crash correcting single contig

Issue - State: closed - Opened by TomHarrop over 7 years ago - 2 comments
Labels: bug

#48 - VCF output exception "Can't fetch base outside region"

Issue - State: closed - Opened by pd3 over 7 years ago - 3 comments
Labels: bug

#46 - dies with Invalid reference index -1

Issue - State: closed - Opened by dcopetti over 7 years ago - 3 comments
Labels: bug

#44 - Issue running pilon : java.lang.OutOfMemoryError: Java heap space

Issue - State: closed - Opened by RxLoutre over 7 years ago - 10 comments

#31 - Clean metagenomics contigs

Issue - State: closed - Opened by davidvilanova about 8 years ago - 2 comments

GitHub / broadinstitute/pilon issues and pull requests