Open bostanict opened 7 years ago
if you are sure the results from the earlier step is done, you can just comment out the command and re-run the script. get_read_ctg_map
generates 2-asm-falcon/read_maps/pread_ids
, raw_read_ids
, read_to_contig_map
. rr_ctg_track
generates 2-asm-falcon/read_maps/rawread_to_contigs
and pr_ctg_track
generates 2-asm-falcon/read_maps/pr_ctg_track
. The fetch_reads
generates all files inside 3-unzip/reads/
.
You can delete the files and regenerate them.
Moreover, is there any folder we might need to remove after each re-run? like falcon that we needed to remove mywatcher?
Yes, for now you also need to remove mypwatcher/
.
ok. I got a little bit confused.
if you are sure the results from the earlier step is done, you can just comment out the command and re-run the script.
which earlier commands you mean? Falcon assembly? or there are other commands before these for the unzip.
so to be clear. I did the falcon assembly and I have the whole folder. I want now to run unzip to separate the haplotypes. before I ram only:
python -m falcon_kit.mains.get_read_ctg_map
python -m falcon_kit.mains.rr_ctg_track
python -m falcon_kit.mains.pr_ctg_track
mkdir -p 3-unzip/reads/
python -m falcon_kit.mains.fetch_reads
nothing more, nothing less and I have the result. So if I want to have the haploypes from the unzip, should I run the falcon_unzip or there is any way to use the results from these few lines mentioned.
you can just comment out the command and re-run the script.
where? in falcon unzip code? or there is any sh file for that so I comment out. Just to say, I am using slurm as the job scheduler.
You can delete the files and regenerate them.
the files you mentioned here right?
sorry if the questions are confusing. First time using unzip :)
Thanks alot~
nothing more, nothing less and I have the result. So if I want to have the haploypes from the unzip, should I run the falcon_unzip or there is any way to use the results from these few lines mentioned.
yes
where? in falcon unzip code? or there is any sh file for that so I comment out. Just to say, I am using slurm as the job scheduler.
No , I meant something like:
#python -m falcon_kit.mains.get_read_ctg_map
#python -m falcon_kit.mains.rr_ctg_track
python -m falcon_kit.mains.pr_ctg_track
mkdir -p 3-unzip/reads/
python -m falcon_kit.mains.fetch_reads
if you already get pread_ids
, raw_read_ids
, read_to_contig_map
, rr_ctg_track
.
the files you mentioned here right?
yes
ok.
I ran fc_unzip.py fc_unzip.cfg
before and it created the file track_reads.sh
SO if I got it right, I will comment the commands:
#python -m falcon_kit.mains.get_read_ctg_map
#python -m falcon_kit.mains.rr_ctg_track
#python -m falcon_kit.mains.pr_ctg_track
#mkdir -p 3-unzip/reads/
#python -m falcon_kit.mains.fetch_reads
in the track_reads.sh file since I already have them run before. Then I run only:
fc_quiver.py fc_unzip.cfg
to get the results.
right? thanks
in another topic in falcon ( https://github.com/PacificBiosciences/FALCON/issues/472 ) I asked the way I can get the unassembled reads from falcon. As sugested I ran:
now that I am trying to run falcon_unzip,
I see that the first step is this tracker. Since I have already this files and did it before, is there anyway I can continue from this point and avoid reduing them?
Moreover, is there any folder we might need to remove after each re-run? like falcon that we needed to remove mywatcher..
Thanks