Ecosyste.ms: Issues

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GitHub / Nextomics/NextDenovo issues and pull requests

#100 - compare v2.4 with v2.2-beta.0

Issue - State: open - Opened by HanKMU over 3 years ago - 6 comments

#99 - How can I get more information of the random assembly nd.asm.p.fasta ?

Issue - State: closed - Opened by tinyfallen over 3 years ago - 2 comments

#98 - Segmentation fault

Issue - State: closed - Opened by Johnsonzcode almost 4 years ago - 15 comments

#97 - ARM support

Issue - State: closed - Opened by starskyzheng almost 4 years ago - 1 comment

#96 - the question about nd.asm.p.fasta

Issue - State: closed - Opened by WenhaoLiu0218 almost 4 years ago - 5 comments

#95 - minmap align is too slow！！

Issue - State: closed - Opened by yangzhou0916 almost 4 years ago

#94 - Low BUSCO completeness value

Issue - State: open - Opened by fengyuanli304 almost 4 years ago - 2 comments

#93 - assembly graph

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

#92 - an unknown error

Issue - State: open - Opened by yangzhuang0916 almost 4 years ago - 1 comment

#91 - seed_cns failed

Issue - State: closed - Opened by linshengnan2020 almost 4 years ago - 11 comments

#90 - ctg_align aborting

Issue - State: closed - Opened by fengyuanli304 almost 4 years ago - 2 comments

#89 - Asking for parameters suggestion for NextDenovo using

Issue - State: open - Opened by LeoCao-X almost 4 years ago - 4 comments

#88 - How to check random_round results in Nextdenovo v2.3.1

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

#87 - “stop” at the cns_align step

Issue - State: closed - Opened by WenhaoLiu0218 about 4 years ago - 4 comments

#86 - Segmentation fault (core dumped)

Issue - State: open - Opened by Morriyaty about 4 years ago - 6 comments

#84 - too many step to run

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

#83 - the disk consuming for raw reads correction

Issue - State: open - Opened by longzhangnation about 4 years ago - 3 comments

#82 - Pulling corrected long reads with v2.3.0

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

#81 - version `GLIBC_2.14' not found

Issue - State: closed - Opened by unique379 about 4 years ago - 5 comments

#80 - What do contig types 'junction' and 'breakpoint' mean?

Issue - State: closed - Opened by zhangrengang about 4 years ago - 1 comment

#78 - NextDenovo stops running but doesn't exit when a sub-job fails.

Issue - State: closed - Opened by TypicalSEE about 4 years ago - 4 comments
Labels: bug

#77 - How to run nextdenovo on a set of cloud service with SGE?

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

#76 - The assembled genome is much smaller than predicted, pacbio reads

Issue - State: closed - Opened by Jin-Sun-OUC about 4 years ago - 2 comments

#75 - nextdenovo correct pacbio subreads

Issue - State: closed - Opened by licheng0921 about 4 years ago - 5 comments

#74 - How to get genome assembly larger than 3.5G?

Issue - State: closed - Opened by pengbo233 about 4 years ago - 1 comment

#73 - Unexplained status when I run

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

#72 - assembly big genome

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

#71 - Suggested length cutoff: 0 bp

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

#69 - OverflowError: cannot serialize a string larger than 2 GiB

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

#68 - nextdenovo+wtdbg2

Issue - State: closed - Opened by fengyuanli304 over 4 years ago - 24 comments

#67 - Failed in regional assembly by NextDenovo.

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

#66 - Does NextDenovo apply to diploid genome assembly?

Issue - State: closed - Opened by huangyixian123 over 4 years ago - 3 comments

#65 - too slow in minimap2-nd step

Issue - State: closed - Opened by ucassee over 4 years ago - 12 comments

#64 - sort_align failed

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

#63 - LSF memory request reports a bug and the fixing func

Issue - State: closed - Opened by haoliu1213 over 4 years ago - 9 comments

#62 - GLIBC2.14 not found

Issue - State: closed - Opened by Lyang556 over 4 years ago - 19 comments

#61 - Reducing RAM usage on a desktop

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

#60 - more raw data used to assembly

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

#59 - Can NextDenovo be used for metagenomic samples? (Nanopore data)

Issue - State: closed - Opened by jinhao94 over 4 years ago - 2 comments

#58 - NextDenovo on SLURM

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

#57 - time not found

Issue - State: closed - Opened by 000generic over 4 years ago - 3 comments

#56 - Resume the job when terminated unexpectedly

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

#55 - the problem of software running in v2.2-beta.0 version

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

#54 - Can not get_cns

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

#53 - Question about -b, --blacklist

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

#52 - nextgraph, could it run with multi thread?

Issue - State: closed - Opened by fangdm over 4 years ago - 8 comments

#51 - Raw align failed

Issue - State: closed - Opened by kinglyyang over 4 years ago - 10 comments

#49 - Questions about "seed_cutoff" option

Issue - State: open - Opened by TypicalSEE over 4 years ago - 10 comments

#48 - processes have been killed by the cgroup out-of-memory handler.

Issue - State: closed - Opened by biowackysci over 4 years ago - 10 comments

#47 - nextgraph: asg.c:1270: update_graph: Assertion `mode == 10' failed.

Issue - State: closed - Opened by huangyixian123 over 4 years ago - 3 comments

#46 - how to select a prefect results

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

#45 - main: Assertion `opts.max_mem > 100000000' failed

Issue - State: closed - Opened by shehongbing almost 5 years ago - 2 comments

#44 - assemble result

Issue - State: closed - Opened by shehongbing almost 5 years ago - 9 comments

#43 - how to run on LSF system?

Issue - State: closed - Opened by huangyixian123 almost 5 years ago - 1 comment

#42 - analysis tasks done but the following pipeline died (KeyError: '009')

Issue - State: closed - Opened by DengHAU almost 5 years ago - 5 comments

#41 - how to restart the whole pipeline when some tasks is failed?

Issue - State: closed - Opened by ryys1122 almost 5 years ago - 1 comment

#40 - Add GFA in output

Issue - State: closed - Opened by xuzhougeng almost 5 years ago - 2 comments

#39 - how can I reduce the number of process and storage at raw align step？

Issue - State: closed - Opened by zhenzhenS almost 5 years ago - 1 comment

#38 - ovl_sort.c:688: main: Assertion `opts.max_mem > 100000000' failed

Issue - State: closed - Opened by wook2014 almost 5 years ago - 1 comment

#37 - there is not enough disk space

Issue - State: closed - Opened by shehongbing almost 5 years ago - 6 comments

#36 - self.drmaa.exit() stuck

Issue - State: closed - Opened by lskfs almost 5 years ago - 3 comments

#35 - Assemble the genome with corrected fasta using NextDenovo2.1

Issue - State: closed - Opened by jiahaow123456 almost 5 years ago - 2 comments

#34 - What is the memory requirement for nodes when run a huge input fastq?

Issue - State: closed - Opened by zengpeng2012 almost 5 years ago - 5 comments

#33 - Raw data or corrected data ??

Issue - State: closed - Opened by shehongbing almost 5 years ago - 1 comment

#32 - Cann't get the cns.fasta

Issue - State: closed - Opened by shehongbing almost 5 years ago - 6 comments

#31 - How to get genome assembly larger than 3.5G?

Issue - State: closed - Opened by zijiangyang almost 5 years ago - 1 comment

#30 - The question of error cerrection

Issue - State: closed - Opened by mida5730 almost 5 years ago - 1 comment

#29 - NextDenovo/bin/seq_dump: cannot execute binary file

Issue - State: closed - Opened by YongZhou2019 almost 5 years ago - 2 comments

#28 - Running error assembling Pacbio data

Issue - State: closed - Opened by Dichromatism almost 5 years ago - 1 comment

#27 - task assemble error

Issue - State: closed - Opened by BoWangXJTU almost 5 years ago - 4 comments

#26 - NextDenovo assemble has no result file

Issue - State: closed - Opened by ruanyingfei almost 5 years ago - 5 comments

#25 - task = ？

Issue - State: closed - Opened by BoWangXJTU almost 5 years ago - 4 comments

#24 - The error of the seed_cutoff

Issue - State: closed - Opened by shehongbing almost 5 years ago - 2 comments

#23 - jobs in step 02.cns_align/02.cns_align.sh.work runs extremely slow

Issue - State: closed - Opened by zijiangyang almost 5 years ago - 1 comment

#22 - Ask help for software usage

Issue - State: closed - Opened by panbei123 almost 5 years ago - 2 comments

#21 - about the bug in nextdenovo2.0

Issue - State: closed - Opened by wangzhongkai1 almost 5 years ago - 9 comments
Labels: bug

#20 - How to run nextdenovo on lsf system

Issue - State: closed - Opened by zzlzef almost 5 years ago - 1 comment

#19 - A problem I met when running NextDenovo

Issue - State: closed - Opened by zjwang0831 almost 5 years ago - 7 comments

#18 - Segmentation fault

Issue - State: closed - Opened by SC-Duan almost 5 years ago - 6 comments
Labels: question

#17 - Parallel job parameter of NextDenovo when run in local mode

Issue - State: closed - Opened by xuzhougeng almost 5 years ago - 1 comment

#16 - How do I run NextDenovo on my SLURM / SGE / PBS / LSF / Torque system?

Issue - State: closed - Opened by Rachel-pku almost 5 years ago - 23 comments

#15 - test run is finished, but assembly file is none

Issue - State: closed - Opened by bioone almost 5 years ago - 1 comment

#14 - Assembly size is smaller than estimated genome size

Issue - State: closed - Opened by yilunhuangyue almost 5 years ago - 3 comments

#13 - minimap2 option "-I"

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

#12 - Problem: ValueError: zero length field name in format

Issue - State: closed - Opened by li081766 about 5 years ago - 4 comments

#11 - some questions of output files

Issue - State: closed - Opened by Axolotl233 about 5 years ago - 1 comment

#10 - read_cuoff = 1k 应为 read_cutoff = 1k 问一下现在的参数设置

Issue - State: closed - Opened by hyliu87 about 5 years ago - 1 comment
Labels: enhancement

#9 - python3 ?

Issue - State: closed - Opened by colindaven about 5 years ago - 4 comments

#8 - only few reads were left

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

#7 - get_cns error

Issue - State: closed - Opened by JHAO12321 about 5 years ago - 16 comments

#6 - About data size after processing nextdenovo

Issue - State: closed - Opened by HeymaxHY about 5 years ago - 4 comments
Labels: question

#5 - sort_overlap error

Issue - State: closed - Opened by northbio about 5 years ago - 6 comments
Labels: question

#4 - NextDenovo is unfinished

Issue - State: closed - Opened by SC-Duan over 5 years ago - 6 comments
Labels: bug

#3 - multithreading in local

Issue - State: closed - Opened by SC-Duan over 5 years ago - 1 comment
Labels: question

#2 - Problem with NextDenovo

Issue - State: closed - Opened by WeipengMO over 5 years ago - 3 comments
Labels: question

#1 - The SGE Option

Issue - State: closed - Opened by chenshixuan over 5 years ago - 2 comments
Labels: enhancement