broadinstitute pilon issues

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool

GNU General Public License v2.0

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Pilon died mid-run

#171 drdna opened 2 weeks ago
0
Polish a large genome with Pilon

#170 enriquepola1996 opened 1 month ago
2
Pilon Killed with no other error message

#169 dorie8 opened 2 months ago
1
Java out of memory

#168 JWang52md opened 4 months ago
0
Memory problem

#167 Wanjie-Feng opened 5 months ago
0
Pilon is running but no .changes file in output

#166 NicMAlexandre closed 3 weeks ago
0
pilon freezes and doesnt respond

#165 Vasudha-pai opened 7 months ago
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 sugarsaman opened 8 months ago
0
pilon error:Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded

#163 smoothyly opened 8 months ago
0
Exception in thread "main" java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer;

#162 karthickbrlab closed 10 months ago
0
unable to access jarfile pilon-1.24.jar

#161 tbazilegith opened 10 months ago
2
HashMap table size

#160 rivabros2 opened 11 months ago
0
Java heap space error while running pilon

#159 saras224 opened 1 year ago
0
Asking for indexed bam file

#158 saras224 opened 1 year ago
1
pilon error: Exception in thread "main" java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequenceDictionary: contig_1

#157 saras224 opened 1 year ago
1
Error with very short contig

#156 bartns opened 1 year ago
0
Segmenting genome for quicker result

#155 tamsinlh opened 1 year ago
0
How to resume

#154 methylome opened 1 year ago
0
no bam file

#153 rmormando opened 1 year ago
1
Question: Are redundant bases inside overlapping ends of paired reads counted once or twice towards consensus?

#152 JohnUrban opened 1 year ago
0
fasta headers not appended but overwritten

#151 hkaspersen opened 1 year ago
0
Index -1 out of bounds for length X

#150 anitajnorman opened 2 years ago
1
Memory usage relation to file size?

#149 snail123815 opened 2 years ago
1
Make polishing stats machine-readable

#148 kim-fehl opened 2 years ago
0
--threads argument no longer supported

#147 cpavloud closed 1 year ago
1
Correct spelling mistakes

#146 EdwardBetts opened 2 years ago
0
VCF format issue

#145 jodyphelan opened 2 years ago
0
"main" java.lang.IllegalArgumentException: requirement failed

#144 bioramg opened 2 years ago
2
Pilon on haplotype polish: how did pilon deal with haplotype genome assembly?

#143 cjchen5 opened 2 years ago
0
Fix vcf header def for DP

#142 jodyphelan opened 2 years ago
0
VCF header issue

#141 jodyphelan opened 2 years ago
0
Problem with executing Pilon

#140 Hai1983 opened 2 years ago
2
Pilon on transcriptome assembly from tetraploid species

#139 ConcettaDe4 opened 2 years ago
0
How to run pilon

#138 leggylas closed 2 years ago
2
Issues running pilon

#137 myco-bradshaw opened 2 years ago
0
Discordant Pilon Results for Equivalent Files

#136 cwarden45 opened 2 years ago
0
Annotate allelic depth?

#135 pgcudahy opened 2 years ago
1
Ways to speed up pilon

#134 kattweigh opened 3 years ago
1
trying to polish nanopore with illumina don't understand the error

#133 Ayse1006 opened 3 years ago
2
Absurdly long run time and GCLocker

#132 NTNguyen13 opened 3 years ago
1
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.FileNotFoundException: align_filer.bam

#131 zhuanghemu opened 3 years ago
1
HI

#130 zhuanghemu opened 3 years ago
0
Pilon appearing to make no corrections or confimations of bases

#129 Rob-murphys opened 3 years ago
1
java.lang.OutOfMemoryError

#128 kjestradag opened 3 years ago
3
Can you go into more detail about the --threads option? What does "experimental" mean?

#127 lfaller-zymergen opened 3 years ago
2
Does pilon write to temp files?

#126 lfaller-zymergen opened 3 years ago
1
Expected memory usage

#125 nhartwic closed 3 years ago
4
Exception in thread "main" java.nio.BufferUnderflowException

#124 francescodc87 opened 4 years ago
2
Pilon on Nanopore assembly of tetraploid organism

#123 ms-gx closed 3 years ago
1
Out of memory?

#122 stanislasmorand opened 4 years ago
7