Francesco Cicconardi

Hi, This is the new log. ESC[0;35m###### Wed Apr 22 05:43:48 BST 2020: Running layoutESC[0m INPUT reads lis mates PLACEMENT CONFLICT ASSEMBLY OUTPUT ESC[0;35m###### Sun Apr 26 17:18:38 BST 2020: Running consensusESC[0m Entering 'Amos_supercontigs.bnk' Found CTG bank unlocking 'r 432968 tk19812' Found FRG bank Found LAY bank Found LIB bank Found RED bank Found SCF bank Found UNV bank IFOs found: 7 File locks: 0 Bank locks: 1 Starting on Sun Apr 26 17:18:38 2020 Read bank is Amos_supercontigs.bnk Alignment...

I'm suspecting it's a memory issue. Is there any chance I can split the delta file to run part of that and reconnect them after? Cheers F

Now I don't have it anymore, but the log file was just listing the different stages of the job like: INPUT reads lis ... till the end without returning any expicit error. F

Hi, I think consensus fails because layout didn't generate the file. layout also finishes without error messages Thanks a lot F

casm-layout ERROR

Hi Pasi, Thanks for your help. Apparently the small change in the assembly generated a mis-joining in the LM. I'm sure probably to a repeat region in those flanking areas. One scaffolder was able to solve it the other not. I also used the good LM to break down scaffolds, re-scaffold and gap filling them, re compute che LM and use it fo a final scaffolding. Now it looks really good. A final gap filling closed most of the LM gaps. Now I should be quite happy with it. As I'm not familiar with the sensitivity...

Hi Pasi, I'm having a problem with the linkadge map. The fist run produced a satisfied result, but, for reason that I'm not explaining here I went back to my assembly and I build a different version of the draft using a different software to perform the scaffolding. I then generated the LM for the new assembly version and the draft before the scaffolding. Comparing the 3 LMs it seems like the draft and the second scaffolding procedure produced comparable results which prodced worst results than the...

Ok, will do it. Is it in LMPlot section of your wiki? Something to mention is that AllMaps found this ambiguities: 11:26:59 [__init__] CACHEDIR=/home/fc464/.cache/matplotlib 11:26:59 [font_manager] Using fontManager instance from /home/fc464/.cache/matplotlib/fontList.json 11:26:59 [__init__] backend agg version v2.2 11:26:59 [base] Load file `../EisaPacBio.LMmale.bed` 11:27:02 [allmaps] Map contains 184033 markers in 31 linkage groups. 11:27:03 [allmaps] Retained 162,372 of 184,033 (88.2%) clean...