aquaskyline/SOAPdenovo2 issues and pull requests

#97 - compilation is not working

Issue - State: open - Opened by CodeBlack589 2 months ago

#96 - compilation is not working on EL/rocky 9

Issue - State: open - Opened by eylenth 5 months ago

#95 - get_scafSeq_to_fasta.pl script

Issue - State: open - Opened by Wyclif3 6 months ago - 1 comment

#93 - cannot open *.kmerFreq file after pregraph, then exit

Issue - State: open - Opened by cqh1 about 1 year ago

#92 - Challenges with Scaffold Statistics in SOAPdenovo2 Assembly: Number_of_contigs_in_scaffolds

Issue - State: open - Opened by Simon602 about 1 year ago

#91 - Using a compressed file during the "pregraph" process may lead to program exit

Issue - State: open - Opened by shiinachaos about 1 year ago

#90 - cgroup out-of-memory handler

Issue - State: open - Opened by cnxiaobo94 over 1 year ago

#89 - SOAPdenovo parameter -K

Issue - State: open - Opened by 17863952296 over 1 year ago

#88 - SOAPdenovo2 installation error

Issue - State: open - Opened by AbRawoof over 1 year ago - 3 comments

#87 - Negative number of edges in pregraph

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

#86 - compilation from source failed on debian11, gcc11.2 - patch added

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

#85 - Ran out of memory while applying -64982367872bytes

Issue - State: open - Opened by WJT0925 about 2 years ago

#84 - soap didn't read fastq files in Pregraph and Contig

Issue - State: closed - Opened by sqwwww over 2 years ago - 2 comments

#83 - Getting the following Error during SOAPdenovo installation

Issue - State: closed - Opened by bandana98 over 2 years ago

#82 - question about the output file .scafSeq file when using SOAPdenovo2

Issue - State: closed - Opened by wangc1106 over 2 years ago

#81 - Are the new releases really new releases?

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

#80 - not resolved gaps of 1 nucleotide

Issue - State: closed - Opened by glopatriello about 3 years ago - 1 comment

#79 - soapaligner is not working

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

#78 - final link failed: Nonrepresentable section on output

Issue - State: closed - Opened by iquasere over 3 years ago - 1 comment

#77 - GapCloser: Segmentation fault (core dumped)

Issue - State: closed - Opened by iquasere over 3 years ago - 1 comment

#76 - operation

Issue - State: closed - Opened by BAOjinbo over 3 years ago - 6 comments

#75 - Empty fastq input results in infinite "air_return error" loop

Issue - State: closed - Opened by magcurly over 3 years ago - 1 comment

#74 - Dealing graph with too many edges

Issue - State: closed - Opened by dfguan almost 4 years ago - 1 comment
Labels: enhancement

#73 - About the err.txt

Issue - State: closed - Opened by Otis-chan almost 4 years ago - 2 comments

#72 - Tag r242

Issue - State: closed - Opened by njbooher about 4 years ago - 2 comments

#71 - Soap denovo with multiple libraries

Issue - State: closed - Opened by jvkheni about 4 years ago

#70 - Small N50 due to read length cutoff

Issue - State: closed - Opened by shanewidanagama over 4 years ago - 2 comments

#69 - Compilation error

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

#68 - High gap percentage in scaffold assembly

Issue - State: closed - Opened by shanewidanagama over 4 years ago

#67 - segmentation fault (core dumped)

Issue - State: closed - Opened by bioramg over 4 years ago - 2 comments

#66 - No arcs being generated, resulting in zero scaffolds

Issue - State: closed - Opened by mchaney1 over 4 years ago - 3 comments

#65 - Cannot find SOAPdenovo2/SOAPdenovo2/GapCloser

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

#64 - In Makefile compilation do not considere CFLAGS arguments

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

#63 - reading too few reads? Not supporting gz format?!

Issue - State: closed - Opened by bitcometz over 5 years ago - 3 comments

#62 - standardPregraph/hashFunction.c

Pull Request - State: closed - Opened by xusailor over 5 years ago

#61 - incompatible libbam.a

Issue - State: closed - Opened by xqhuang1018 over 5 years ago - 1 comment

#60 - Error while Installation $make

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

#59 - Config file

Issue - State: closed - Opened by SIlviaHinojosa over 5 years ago - 3 comments

#58 - Make error with Ubuntu 18.04 LTS

Issue - State: closed - Opened by elvenwhite over 5 years ago - 2 comments

#57 - Scaff step crashes because of long gzip command

Issue - State: closed - Opened by sturgman over 5 years ago

#56 - SOAPdenovo-fusion

Issue - State: closed - Opened by garfring over 5 years ago

#55 - much larger genome size

Issue - State: closed - Opened by zdz1989 over 5 years ago

#54 - 16435 Segmentation fault during pregraph step

Issue - State: closed - Opened by AllisonStander almost 6 years ago

#53 - Segmentation fault during contig step

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

#52 - make err

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

#51 - Segmentation fault while reading fastq files

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

#50 - Crashed building contigs

Issue - State: closed - Opened by shanesturrock about 6 years ago - 10 comments

#49 - SOAPdenovo-fusion (command not found...)

Issue - State: closed - Opened by ptsij over 6 years ago - 4 comments

#48 - About the setting of parameters

Issue - State: closed - Opened by Xuelei-Dai over 6 years ago

#47 - Makefile:65: recipe for target 'SOAPdenovo-63mer' failed

Issue - State: closed - Opened by BenjaminGuinet over 6 years ago

#46 - set proper input

Issue - State: closed - Opened by mossishahi over 6 years ago - 1 comment

#45 - "make install" is not available anymore

Issue - State: closed - Opened by hlfernandez over 6 years ago - 2 comments

#44 - Respect CC/CXX/CFLAGS/CXXFLAGS variables. Respect site-wide samtools.

Pull Request - State: closed - Opened by mmokrejs over 6 years ago

#43 - Update Makefile

Pull Request - State: closed - Opened by aquaskyline over 6 years ago

#42 - Update Makefile

Pull Request - State: closed - Opened by aquaskyline over 6 years ago

#41 - Update Makefile

Pull Request - State: closed - Opened by aquaskyline over 6 years ago

#40 - Spkieliu

Pull Request - State: closed - Opened by aquaskyline over 6 years ago

#39 - Error during compilation

Issue - State: closed - Opened by michaelgruenstaeudl over 6 years ago - 6 comments

#38 - When reading in ".links" file, the first line with real data will be ignored.

Issue - State: closed - Opened by spikeliu over 6 years ago - 3 comments

#37 - clarify if megahit is usable for mammalian de novo assembly

Issue - State: closed - Opened by antonkulaga almost 7 years ago - 3 comments

#36 - should have a real config.example

Issue - State: closed - Opened by spikeliu almost 7 years ago - 1 comment

#35 - It seems that with very low numbers of edges, insufficient memory is …

Pull Request - State: closed - Opened by twmccart almost 7 years ago

#34 - GapCloser max read size?

Issue - State: closed - Opened by r1corre almost 7 years ago - 1 comment

#33 - how to choose the kmer number for the genome assembly.

Issue - State: closed - Opened by fhu2008-tio almost 7 years ago - 1 comment

#32 - Error reading FASTA files

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

#31 - fixed issue #15. infinate loop if input file is not correct fastq format

Pull Request - State: closed - Opened by cchd0001 about 7 years ago - 1 comment

#30 - bug report

Pull Request - State: closed - Opened by cchd0001 about 7 years ago

#29 - fixed small bugs in sparse module.

Pull Request - State: closed - Opened by cchd0001 about 7 years ago - 1 comment

#28 - SOAPdenovo-127mer going only to kmer of 63

Issue - State: closed - Opened by opatty over 7 years ago - 4 comments

#27 - Segmentation fault with scaff step when use different MEGAHIT's output

Issue - State: closed - Opened by YiweiNiu over 7 years ago - 5 comments

#26 - How to use SOAPdenovo-fusion scaffold the output of MEGAHIT?

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

#25 - for SOAPdenovo-fusion

Issue - State: closed - Opened by SiyuanZhangB over 7 years ago - 2 comments

#24 - When I used fusion module no Arc file is created

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

#23 - finalFusion: not enough memory error (but enough is available)

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

#22 - version `GLIBCXX_3.4.20' not found

Issue - State: closed - Opened by aersoares81 over 7 years ago - 1 comment

#21 - Sequence orientation of the output?

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

#20 - Need assistance

Issue - State: closed - Opened by sagnikbanerjee15 over 7 years ago - 1 comment

#19 - Updated top level Makefile for appropriate making of -127mer binary.

Pull Request - State: closed - Opened by ibio-project over 7 years ago - 2 comments

#18 - binaries of newer versions

Issue - State: closed - Opened by KamilSJaron almost 8 years ago - 8 comments

#17 - Segmentation faul with scaff step after fusion and map

Issue - State: closed - Opened by astridboehne almost 8 years ago - 14 comments

#16 - Please add release tags

Issue - State: closed - Opened by tillea almost 8 years ago - 2 comments

#15 - aio_return error

Issue - State: closed - Opened by dcopetti about 8 years ago - 11 comments

#14 - glibc detected error on cluster

Issue - State: closed - Opened by andreyurch about 8 years ago - 1 comment

#13 - The header in SOAPdenovo output ?

Issue - State: closed - Opened by ptranvan over 8 years ago - 3 comments

#12 - GapCloser development

Issue - State: closed - Opened by sklages over 8 years ago - 1 comment

#11 - segment fault when use staff -F option

Issue - State: closed - Opened by starnight0 almost 9 years ago - 1 comment

#10 - segmentation fault when running SOAPdenovo2 with low k-mer size and sparse pregraph

Issue - State: closed - Opened by jvollme almost 9 years ago - 1 comment

#9 - how to use multi-kmer option: setting kmer step size and minimum k-mer size

Issue - State: closed - Opened by jvollme almost 9 years ago - 1 comment

#8 - example config file missing ?

Issue - State: closed - Opened by blaiseli about 9 years ago - 1 comment

#7 - contig failing on bubble pinching

Issue - State: closed - Opened by travc about 9 years ago - 2 comments

#6 - standard pregraph bug when using large number of threads

Issue - State: closed - Opened by travc about 9 years ago - 2 comments

#4 - Added missing "#include <unistd.h>" in several souces

Pull Request - State: closed - Opened by chenghlee over 9 years ago

#3 - make error

Issue - State: closed - Opened by macmanes over 9 years ago - 3 comments

#2 - Fix undefined reference to `call_pregraph_sparse'

Pull Request - State: closed - Opened by bmpvieira about 10 years ago

#1 - Does not build on Mac OS: error: 'spinLock.h' file not found

Issue - State: closed - Opened by sjackman almost 11 years ago - 15 comments

GitHub / aquaskyline/SOAPdenovo2 issues and pull requests