seryrzu / centroflye Goto Github PK

Dear author, I recently tried to go through the process in the way of your article, but I had a problem in the first step, my code is:
bash /home/Mpzhang/HpDu/centroFlye-master/scripts/read_recruitment/run_read_recruitment.sh rel2.fastq.gz results_cenX/centromeric_reads 50 11100000
,but reported the wrong, I looked carefully, do not understand where their mistakes, can give me advice on how to correct

Fallow your code ,I had a problem identifying the rare kmer

I downloaded the link you provided "https://s3.amazonaws.com/nanopore-human-wgs/chm13/nanopore/rel2/rel2_to_GRCh38.cram
But the last error reported at runtime,Couldn't find the reason for this cram?

But my script is running out, and I want to know where I can generated this step. Can you provide a code link for this step? I didn't see it in the scripts

Hello,

I am trying to construct the human ChrX centromere as demonstrated in your paper, except with reads from our own sample: 87X of regular Pacbio Sequel II CLR reads (N50=28.3k, 10X of >50k reads). May I ask what are the parameters that I should adjust besides the ones below?

error-mode=pacbio
min-coverage=2
coverage=3

Thanks for creating such a valuable tool,
Tim

Hi seryrzu:
Thanks for the great job of T2T assembling. I have question about the centroFlye using in other species, such as bovine. We do not know the HOR unit and monomor in chromosomeX, but easier to get prexfix reads and suffix reads. How could we assembly this centromere, Will the centroFlye mono mode could help to assemble the genome? Thanks a lot if you could reply.
Best
Huanfa

Hi @seryrzu ,
thank you for your great work.
When I do the read_recruitment part, I got this error:

xargs -I '{}' -P 150 /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/9.gap/completeness/centroFlye/scripts/read_recruitment/rr /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/9.gap/completeness/centroFlye/data/GgDNA_chr1_cen1_repeat_sequence.fasta '{}' '../split_rr/{}_cen.fasta' 350
rr: rr.cpp:24: char complement(char): Assertion `false' failed.
rr: rr.cpp:24: char complement(char): Assertion `false' failed.
rr: rr.cpp:24: char complement(char): Assertion `false' failed.
rr: rr.cpp:24: char complement(char): Assertion `false' failed.
rr: rr.cpp:24: char complement(char): Assertion `false' failed.
rr: rr.cpp:24: char complement(char): Assertion `false' failed.
xargs: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/9.gap/completeness/centroFlye/scripts/read_recruitment/rr: terminated by signal 6
xargs: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/9.gap/completeness/centroFlye/scripts/read_recruitment/rr: terminated by signal 6
rr: rr.cpp:24: char complement(char): Assertion `false' failed.
rr: rr.cpp:24: char complement(char): Assertion `false' failed.

and my code is :

bash scripts/read_recruitment/run_read_recruitment.sh data/Chicken_ONT_93X.fa results_cen1/centromeric_reads 150 7700000 data/GgDNA_chr1_cen1_repeat_sequence.fasta 350

then I check the rr.cpp

#include <cassert>
#include <algorithm>
#include <cstdio>
#include <cstdlib>
#include <zlib.h>
#include "edlib.h"
#include "kseq/kseq.h"
KSEQ_INIT(gzFile, gzread)


char complement(char n)
{
    switch(n)
    {
    case 'A':
        return 'T';
    case 'T':
        return 'A';
    case 'G':
        return 'C';
    case 'C':
        return 'G';
    }
    assert(false);
    return ' ';
}

It seems something went wrong, so the code arrived at assert(), but I don't know why, looking forward to your answer.

Thank you sincerely
Johnson

Hello,
I'd like to try to run cen6 pipeline but it doesn't work because scripts/ext/stringdecomposer/longreads_decomposer.py is not included in ext folder in the current master HEAD(a1a314d). How should I handle this?
Thanks in advance.

Dear author
Using the data you provided, your software ran through the assembly of centromeres in the article,But I'm also trying to use manual assembly of centromeres,Want to Verify each other,Would you please provide a ID of these reads across centromeres,Since I used the reads ID provided in T2T article to find that it was not found in your centromere.fasta reads, only 1 out of 10 reads can be found, I guess it might be data is different version .
I saw that T2T used 12 reads to assemble the centromere,And so I'd like to ask if you can provide reads ID, across centromeres(assembly),I want to use a manual method to verify

Hello!

Could you please help me install centroFlye?

1. I'm trying to clong the centroFlye into CentOS 7.0 server with the following command but it failed

command1

git clone --verbose --progress --recurse-submodules --single-branch --branch cF_NatBiotech_paper_Xv0.8.3-6v0.1.3 [email protected]:seryrzu/centroFlye.git

error1

Cloning into 'centroFlye'...
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

.

2. I tried the master branch and I got the following error

command2

git clone --verbose --progress --recurse-submodules --single-branch  https://github.com/seryrzu/centroFlye.git

error2

Cloning into 'centroFlye'...
POST git-upload-pack (204 bytes)
remote: Enumerating objects: 685, done.
remote: Total 685 (delta 0), reused 0 (delta 0), pack-reused 685
Receiving objects: 100% (685/685), 2.45 MiB | 1.45 MiB/s, done.
Resolving deltas: 100% (432/432), done.
Submodule 'scripts/ext/stringdecomposer' ([email protected]:ablab/stringdecomposer.git) registered for path 'scripts/ext/stringdecomposer'
Submodule 'scripts/ext/tandemQUAST' ([email protected]:ablab/tandemQUAST.git) registered for path 'scripts/ext/tandemQUAST'
Cloning into 'scripts/ext/stringdecomposer'...
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Clone of '[email protected]:ablab/stringdecomposer.git' into submodule path 'scripts/ext/stringdecomposer' failed

3. I can clone the centroFlye when I remove --recurse-submodules option

4. I am unable to clone the the connected submodules that can be accessed through here

5. Could you please help me install the centroFlye on my server?

With regards,
Jin-Young

Dear author, I recently tried to go through the process in the way of your article, but I had a problem in the first step, my code is:
bash /home/Mpzhang/HpDu/centroFlye-master/scripts/read_recruitment/run_read_recruitment.sh rel2.fastq.gz results_cenX/centromeric_reads 50 11100000
,but reported the wrong, I looked carefully, do not understand where their mistakes, can give me advice on how to correct

I tried cenX assembly on my sample but getting error messages on the final tandemquast step.

It seems to be due to the same reads are recruited twice.

In my sample, 4 reads were reported to be duplicated.

Is it okay if I manually remove this duplicate or does this mean something is wrong?

command1

grep "^>" centromeric_reads.fasta | sort | uniq -c | awk '$1>1'

stdout1

      2 >322f6dbf-c5bf-4486-8e2c-e764ea4947bf
      2 >507fbfdd-3676-4c83-bfc2-2cf2073ea27a
      2 >56d4b6ec-9491-4c3c-8d74-d727a6bb3a4c
      2 >5e4107b0-c80b-48d4-bbad-fceb11f48b3b

command2

head -n 10000 split_fasta_0.fasta | grep -n 322f6dbf-c5bf-4486-8e2c-e764ea4947bf

stdout2

2065:>322f6dbf-c5bf-4486-8e2c-e764ea4947bf runid=869182ee9e718c030eb89012b70e7246ee05373c read=38 ch=2666 start_time=2020-08-11T09:13:23Z flow_cell_id=PAF10281 protocol_group_id=20200811 sample_id=test
9088:>322f6dbf-c5bf-4486-8e2c-e764ea4947bf runid=869182ee9e718c030eb89012b70e7246ee05373c read=38 ch=2666 start_time=2020-08-11T09:13:23Z flow_cell_id=PAF10281 protocol_group_id=20200811 sample_id=test

Hi,
In our project we are currently having issues with the asssembly of long repetitive regions of the genome and we would like to know if your approach (centroflye) would work on repetitive regions others then centromers.
If this is the case I would appreciate if you could explain to me how to make the reference file necessary for running centrofly.
We have long (Nanopore) reads.

Thanks,
j.

Dear author
When I run to this step, there is an error, the error is the above picture, what is the reason, how should I do
Looking forward to your reply

Dear author, when I run this line of code,

This error occurred in the run, This file was not found


I did not generate this file.But I followed this centroFlye.py script, why did it happen,Looking forward to your reply

Can you tag a release? That'll make it easier to put this in bioconda.