The single command mode

[wushyer]

Hi could I ask when the single command mode be used?
I tried the single command mode but failed as some bugs in the main script.

Best,

[mawad89]

Hi, thanks for report this. We did a lot of modification on our scripts. So, could you share the reported bugs with us to solve the problem

[wushyer]

Hi, thanks for the quick reply.

1. The first problem I found with the main script is the variable definition. The main script can not run the below draft_comp.sh as the variable does not add in this script. This could be easily fixed by adding the absolute path in the sh files.

ie
mkdir -p preliminary_comparison
cd preliminary_comparison
minimap2 -x asm5 $draft01 $draft02 > draft01vsdraft02.paf
minimap2 -x asm5 $draft01 $draft03 > draft01vsdraft03.paf
minimap2 -x asm5 $draft01 $ref > draft01vsref.paf
minimap2 -x asm5 $draft02 $draft01 > draft02vsdraft01.paf
minimap2 -x asm5 $draft02 $draft03 > draft02vsdraft03.paf
minimap2 -x asm5 $draft02 $ref > draft02vsref.paf
minimap2 -x asm5 $draft03 $draft01 > draft03vsdraft01.paf
minimap2 -x asm5 $draft03 $draft02 > draft03vsdraft02.paf
minimap2 -x asm5 $draft03 $ref > draft03vsref.paf
minimap2 -x asm5 $ref $draft01 > refvsdraft01.paf
minimap2 -x asm5 $ref $draft02 > refvsdraft02.paf
minimap2 -x asm5 $ref $draft03 > refvsdraft03.paf

2. when I use the Step-by-Step Mode, I test 4 assemblies from different assemblers (Centromere arabidopsis paper data, Hicanu/wtdbg2/flye/hifiasm). I also add the TAIR10 reference in the draft.txt as the manual set in the human pipeline. I found quite strange reads arrangement produced by ccm.

cat scaffolds_new_ref.scaff
Scaffolds List:

scaff_1 5_2_awad 5_1_awad 3_2_awad 3_4_awad 3_6_awad5_3_awad 3_11_awad 3_8_awad 3_5_awad 3_1_awad 3_7_awad5_5_awad 3_3_awad 5_4_awad 3_9_awad 50403612
scaff_2 1_1_awad 1_10_awad 1_3_awad 1_8_awad 1_5_awad1_9_awad 1_6_awad 1_7_awad 1_4_awad 1_2_awad 30427671
scaff_3 2_1_awad 4_1_awad Mt_awad 2_4_awad 2_3_awad 2_2_awad 2_6_awad 3_10_awad 23148673
scaff_4 4_5_awad 4_3_awad 4_2_awad 4_4_awad 15531776

Single Contigs:

2_5_awad 1540
Pt_awad 154478

The HIFI data accession is ERR6210723, if you have time to check I could send you the 4 draft assemblies.

Best,
Shuangyang

[mawad89]

Hi Shuangyang;

I can see where the problem is. I think you use different accessions, so the MDM module reports some false misassemblies. But this is not the problem because CCM merges them again -which is one of CCM's advantages - to correct the errors of MDM.

The problem is I see a merging of Chr 5 and 3 in Scaff_1 and a wrong merge for the short arm of chromosome 4 and mitochondrial genome to chr2 scaff_3.

The problems of scaff_3 are understandable, and I think the problem may be in the parameters of CCM. But for Scaff_1, I think something is going wrong in the MDM module with one of the preliminary assemblies.
Could you please send me the set of original preliminary assemblies and the comparison folder?

You can upload it here or send it to my mail.
awad@mpipz.mpg.de

Best
Mohamed