ALLHiC

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第7步Optimize步骤中sample.clean.bam文件打不开

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您好，我目前正在用此软件组装三倍体同源基因组，前面的每一步骤都有做，在进行第7步优化时，程序报错。 运行命令如下： /share/appspace_data/shared_groups/01.Softwares/03.Soft_ALL/ALLHiC-221024/bin/allhic extract /share/home/07.ALLHic/04.optimize/sample.clean.bam /share/home/07.ALLHic/04.optimize/sample.contigs.fasta --RE GATC 报错信息如下： extractContigLinks | ERROR Cannot open bamfile `/share/home/07.ALLHic/04.optimize/sample.clean.bam` (sam: reference already used) 我查阅了您网页下的所有问题，暂时没有此类问题的相关解决办法，所以才冒昧打扰您，希望您在百忙之中能够解答一下该问题。 注：在这步之前的Rescue步骤，也用到了sample.clean.bam该文件，在Rescue步骤中此文件是能够正常读取的，运行过程中没有报错，所以我觉得应该不是bam文件有误，fa文件的索引文件也都在同一目录下。

zhangm1212

ALLHiC_plot: error

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[14:52:18] Step1: Get chromosome length [14:52:18] Step2: Get signal matrix [15:57:46] Step3: Draw heatmap [15:57:46] Drawing with bin size 500k Traceback (most recent call last): File "/home/xb/ALLHiC/ALLHiC/bin/ALLHiC_plot", line 250, in...

MonsterLaplace

Thank you for developing ALLHIC. I did an HiC mount for the autotetraploid assembly I assembled according to the wiki, and there was no error, but when the result was...

xujialupaoli

Group1 optimization step has been running for 43 days for a genome assembly. I previously used AllHIC for another assembly, and the optimization step took about 2 days. Is there...

hans-vg

有个真菌杂合二倍体，现在用hifiasm 组装获得了两个单倍型contig级别基因组，现在把hap1和hap2合并，跑all-hic 挂载，想看下hifiasm有没有分错，是跑简单二倍体流程吗，目前该真菌还没有染色体级别可供参考的基因组。

Hanjiangna

Hi there, I am looking forward to seeing the results from this tool, however I am having some troubles running it. Is the partition stage meant to produce two files...

Rhia15

Hi, I am really keen to use this tool, however I am struggling with understanding and making the allele table. Please could I see what the gff3 format and .bed...

Rhia15

Hi, I want to ask how to set group counts in male? 23, 24(X and Y) or 25(X, Y and mitochondria)? Best wishes.

DayTimeMouse

Hi, thanks for develop this tool to improve the assembly for polyploid plant genome. This is really helpful, just a bit confusing about the draft genome. Normally we use hifiasm...

ifoo1213

When I run the script PreprocessSAMs.pl unique.bam asm.fa MBOI, I get an error. The following error message is displayed, what is the problem with me? 

tky199996