broadinstitute pilon issues

broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool

GNU General Public License v2.0

342 stars 60 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

OutOfMemoryError: Java heap space

#174 Ppatel09-wq opened 2 months ago
0
BUG pilon renames headers in fasta, adds "|pilon"

#173 Luky1228 closed 4 months ago
1
What does "Large collapsed region" mean in standard output?

#172 ryanskiba opened 4 months ago
0
Pilon died mid-run

#171 drdna opened 5 months ago
0
Polish a large genome with Pilon

#170 enriquepola1996 opened 6 months ago
2
Pilon Killed with no other error message

#169 dorie8 opened 7 months ago
1
Java out of memory

#168 JWang52md opened 8 months ago
0
Memory problem

#167 Wanjie-Feng opened 10 months ago
0
Pilon is running but no .changes file in output

#166 NicMAlexandre closed 5 months ago
0
pilon freezes and doesnt respond

#165 Vasudha-pai opened 1 year 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 1 year ago
0
pilon error:Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded

#163 smoothyly opened 1 year ago
0
Exception in thread "main" java.lang.NoSuchMethodError: java.nio.ByteBuffer.position(I)Ljava/nio/ByteBuffer;

#162 karthickbrlab closed 1 year ago
0
unable to access jarfile pilon-1.24.jar

#161 tbazilegith opened 1 year ago
2
HashMap table size

#160 rivabros2 opened 1 year 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 2 years ago
0
How to resume

#154 methylome opened 2 years ago
0
no bam file

#153 rmormando opened 2 years ago
1
Question: Are redundant bases inside overlapping ends of paired reads counted once or twice towards consensus?

#152 JohnUrban opened 2 years ago
0
fasta headers not appended but overwritten

#151 hkaspersen opened 2 years 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 3 years ago
2
Pilon on transcriptome assembly from tetraploid species

#139 ConcettaDe4 opened 3 years ago
0
How to run pilon

#138 leggylas closed 3 years ago
2
Issues running pilon

#137 myco-bradshaw opened 3 years ago
0
Discordant Pilon Results for Equivalent Files

#136 cwarden45 opened 3 years ago
0
Annotate allelic depth?

#135 pgcudahy opened 3 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 4 years ago
1
java.lang.OutOfMemoryError

#128 kjestradag opened 4 years ago
3
Can you go into more detail about the --threads option? What does "experimental" mean?

#127 lfaller-zymergen opened 4 years ago
2
Does pilon write to temp files?

#126 lfaller-zymergen opened 4 years ago
1
Expected memory usage

#125 nhartwic closed 3 years ago
4