broadinstitute/pilon

Issues

• OutOfMemoryError: Java heap space

  #174 opened 3 months ago by Ppatel09-wq
  0

• BUG pilon renames headers in fasta, adds "|pilon"

  #173 opened 4 months ago by Luky1228
  1

• What does "Large collapsed region" mean in standard output?

  #172 opened 4 months ago by ryanskiba
  0

• Polish a large genome with Pilon

  #170 opened 6 months ago by enriquepola1996
  2

• Pilon died mid-run

  #171 opened 5 months ago by drdna
  0

• Pilon is running but no .changes file in output

  #166 opened 5 months ago by NicMAlexandre
  0

• How to run pilon

  #138 opened 3 years ago by leggylas
  2

• Pilon Killed with no other error message

  #169 opened 7 months ago by dorie8
  1

• Java out of memory

  #168 opened 9 months ago by JWang52md
  0

• trying to polish nanopore with illumina don't understand the error

  #133 opened 4 years ago by Ayse1006
  2

• Memory problem

  #167 opened 10 months ago by Wanjie-Feng
  0

• pilon freezes and doesnt respond

  #165 opened a year ago by Vasudha-pai
  0

• an error?I use pilon to polish my ONT—data assembly genome. Then I got the line: Exception in thread "main" java.lang.IllegalStateException: Inappropriate call if not paired read.so what can I do next.my bam file has some error?

  #164 opened a year ago by sugarsaman
  0

• pilon error:Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded

  #163 opened a year ago by smoothyly
  0

• Exception in thread "main" java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer;

  #162 opened a year ago by karthickbrlab
  0

• unable to access jarfile pilon-1.24.jar

  #161 opened a year ago by tbazilegith
  2

• Memory usage relation to file size?

  #149 opened 2 years ago by snail123815
  1

• HashMap table size

  #160 opened a year ago by rivabros2
  0

• Java heap space error while running pilon

  #159 opened a year ago by saras224
  0

• Asking for indexed bam file

  #158 opened 2 years ago by saras224
  1

• "main" java.lang.IllegalArgumentException: requirement failed

  #144 opened 3 years ago by bioramg
  2

• no bam file

  #153 opened 2 years ago by rmormando
  1

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

  #157 opened 2 years ago by saras224
  1

• Index -1 out of bounds for length X

  #150 opened 2 years ago by anitajnorman
  1

• --threads argument no longer supported

  #147 opened 2 years ago by cpavloud
  1

• Error with very short contig

  #156 opened 2 years ago by bartns
  0

• Absurdly long run time and GCLocker

  #132 opened 4 years ago by NTNguyen13
  1

• Segmenting genome for quicker result

  #155 opened 2 years ago by tamsinlh
  0

• How to resume

  #154 opened 2 years ago by methylome
  0

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

  #152 opened 2 years ago by JohnUrban
  0

• fasta headers not appended but overwritten

  #151 opened 2 years ago by hkaspersen
  0

• Make polishing stats machine-readable

  #148 opened 3 years ago by kim-fehl
  0

• VCF format issue

  #145 opened 3 years ago by jodyphelan
  0

• Pilon on haplotype polish: how did pilon deal with haplotype genome assembly?

  #143 opened 3 years ago by cjchen5
  0

• VCF header issue

  #141 opened 3 years ago by jodyphelan
  0

• java.lang.OutOfMemoryError

  #128 opened 4 years ago by kjestradag
  3

• Problem with executing Pilon

  #140 opened 3 years ago by Hai1983
  2

• Pilon on transcriptome assembly from tetraploid species

  #139 opened 3 years ago by ConcettaDe4
  0

• Issues running pilon

  #137 opened 3 years ago by myco-bradshaw
  0

• Discordant Pilon Results for Equivalent Files

  #136 opened 3 years ago by cwarden45
  0

• Ways to speed up pilon

  #134 opened 3 years ago by kattweigh
  1

• Annotate allelic depth?

  #135 opened 3 years ago by pgcudahy
  1

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

  #131 opened 4 years ago by zhuanghemu
  1

• HI

  #130 opened 4 years ago by zhuanghemu
  0

• Expected memory usage

  #125 opened 4 years ago by nhartwic
  4

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

  #127 opened 4 years ago by lfaller-zymergen
  2

• Pilon on Nanopore assembly of tetraploid organism

  #123 opened 4 years ago by ms-gx
  1

• Does pilon write to temp files?

  #126 opened 4 years ago by lfaller-zymergen
  1

• Pilon appearing to make no corrections or confimations of bases

  #129 opened 4 years ago by Rob-murphys
  1

• Exception in thread "main" java.nio.BufferUnderflowException

  #124 opened 4 years ago by francescodc87
  2