Javan Okendo

Yes I work on HPC environment. On Sat, 27 Aug 2022, 16:55 Fernando Puente-Sánchez, < ***@***.***> wrote: > No, it should be faster. Are you writing the databases into a...

What could be causing the following error: ``` [0 seconds]: STEP17 -> CHECKING BINS: 17.checkM_batch.pl Evaluating bins with CheckM (Parks et al 2015, Genome Res 25, 1043-55) Reading /users/javanokendo/.conda/envs/SqueezeMeta/SqueezeMeta/data/alltaxlist.txt Looking...

How to I restart it at step 19? Because if I use restart script it fails....could you provide the command to start at a specific step? On Sun, 4 Sept...

I also have 160GB data and I have 232GB RAM but it is still failing. Is there a trick around the solve this problem?

`head mc.vcf` shows the following: ``` ##fileformat=VCFv4.2 ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ```

@pontushojer Thanks for getting back to me. I tried this and it did not work. I am sending my `sorted bam and vcf` for you to have a look and...

Do you think if I run the standard GATK on the sorted BAM file I will be able to get the SV information. Or which tool do you suggest I...

@pontushojer thanks for the pointers. I was able to use `manta` and got the right vcf file.

Could you provide a small "wiki" on how to run this program?

I have the illumina fastq files for the F0. I can use that to do variant calling. How is it possible to use this variant files to do a simultaneous...