Totally 0 APCFs

[aaannaw]

Hello, Professor Recently I used DESCHRAMBLER to reconstruct the ancestral chromosome fragments for two species （Ma and Mp) from the same genus with the outgroup of a species of related genus (Efon). Taking Maas reference, we built the pair alignmentbetween Ma and Mp, Efon using lastz and lastal pipeline respectively. When I ran DESCHRAMBLER taking the chain andnet files from lastal pipeline, I got the error:

0 Ma /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/tree.txt /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/SFs/bpdist.txt Illegal division by zero at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/estparJC.pl line 41, line 1. Estimate JC parameter: inferAdjProb - inferring the posterior probability of block adjacency usage: inferAdjProb refspc parameter-alpha tree-file genome-file readline() on closed filehandle F at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/SFs/block_consscores.txt Totally 0 APCFs sh: line 1: 3279879 Segmentation fault (core dumped) /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../code/makeBlocks/createCarFile /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/SFs/config.file /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/Ancestor.APCF /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/SFs/Conserved.Segments > /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/APCFs

Then I input the chain and net files from lastz pipeline to run DESCHRAMBLER, I got too much blocks as follows:
Moreover, professor Marco Corbo suggested a more recent version allowed for the the use of multiple reference genomes to strengthen the analysis. Could you give me any suggestions. Looking forward with your reply. Best wishes! Na wan

[jkimlab]

Hi Na wan,

I am not sure but the synteny blocks were not constructed correctly. Can you share the SFs.log file in the output directory and the parameter file?

On Dec 5, 2023, at 9:10 PM, aaannaw @.***> wrote:

Hello, Professor Recently I used DESCHRAMBLER to reconstruct the ancestral chromosome fragments for two species （Ma and Mp) from the same genus with the outgroup of a species of related genus (Efon). Taking Ma as reference, we built the pair alignment between Ma and Mp, Efon using lastz and lastal pipeline respectively. When I ran DESCHRAMBLER taking the chain and net files from lastal pipeline, I got the error:

0 Ma /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/tree.txt /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/SFs/bpdist.txt Illegal division by zero at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/estparJC.pl line 41, line 1. Estimate JC parameter: inferAdjProb - inferring the posterior probability of block adjacency usage: inferAdjProb refspc parameter-alpha tree-file genome-file readline() on closed filehandle F at /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/SFs/block_consscores.txt Totally 0 APCFs sh: line 1: 3279879 Segmentation fault (core dumped) /data/01/user158/kuangzhuoran/software/DESCHRAMBLER/script/../code/makeBlocks/createCarFile /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/SFs/config.file /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/Ancestor.APCF /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/SFs/Conserved.Segments > /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/result/APCFs

Then I input the chain and net files from lastz pipeline to run DESCHRAMBLER, I got too much blocks as follows: image.png (view on web) https://github.com/jkimlab/DESCHRAMBLER/assets/109299053/2a624fae-063c-4074-9c12-aef73f8c3654 Moreover, professor Marco Corbo suggested a more recent version allowed for the the use of multiple reference genomes to strengthen the analysis. Could you give me any suggestions. Looking forward with your reply. Best wishes! Na wan

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[aaannaw]

Hello, professor I am sorry for late response. I will show you these files based on the nets and chains from lastz and lastal respectively: files from analysis based on lastz :

params.txt:
# Reference species
REFSPC=Ma

# Output directory
OUTPUTDIR=APCFs.300K
#OUTPUTDIR=Out_RACA.anctest

# Block resolution (bp)
RESOLUTION=300000

# Newick tree file
# Refer to the sample file 'tree.txt'.

TREEFILE=tree.txt

# Minimum adjacency scores
MINADJSCR=0.0001

# Config and make files for syntenic fragment construction
# Refer to the sample files 'config.SFs' and 'Makefile.SFs'.
# You need to change settings in the sample configuration file (config.SFs) according to your data
# You don't need to change anything in the Makefile.SFs.
CONFIGSFSFILE=config.SFs
MAKESFSFILE=Makefile.SFs

config.SFs
# path of a net files 
>netdir
/data/01/user158/kuangzhuoran/wanna/Last2AncKary/chainNet

# path of a chain files 
>chaindir
/data/01/user158/kuangzhuoran/wanna/Last2AncKary/chainNet

# species-name tag1 tag2
# tag1 (0: ref-species, 1: descendents, 2: outgroup)
# tag2 (1: chromosome assembly, 0: others)
# Warning for tag2: Use the value 1 only when a chromosome name starts with "chr". 
>species
Ma 0 0
Mp 1 0
Efon 2 0 

# block resolution (bp): DO NOT CHANGE
>resolution
<resolutionwillbechanged>

Tree.txt：
 (Efon:0.01009,(Mp:0.00552,Ma:0.00585)@:0.00647);

Files from analysis based on lastal:

config.SFs
# path of a net files 
>netdir
/data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/chainNet

# path of a chain files 
>chaindir
/data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/chainNet

# species-name tag1 tag2
# tag1 (0: ref-species, 1: descendents, 2: outgroup)
# tag2 (1: chromosome assembly, 0: others)
# Warning for tag2: Use the value 1 only when a chromosome name starts with "chr". 
>species
Ma 0 0
Mp 1 0 
Efon 2 0 

# block resolution (bp): DO NOT CHANGE
>resolution
<resolutionwillbechanged>

params.txt
# Reference species
REFSPC=Ma

# Output directory
OUTPUTDIR=result
#OUTPUTDIR=Out_RACA.anctest

# Block resolution (bp)
RESOLUTION=300000

# Newick tree file
# Refer to the sample file 'tree.txt'.
TREEFILE=tree.txt

# Minimum adjacency scores
MINADJSCR=0.0001

# Config and make files for syntenic fragment construction
# Refer to the sample files 'config.SFs' and 'Makefile.SFs'.
# You need to change settings in the sample configuration file (config.SFs) according to your data
# You don't need to change anything in the Makefile.SFs.
CONFIGSFSFILE=config.SFs
MAKESFSFILE=Makefile.SFs

tree.txt:
(Efon:0.01009,(Mp:0.00552,Ma:0.00585)@:0.00647);

The log files will be added with upload files. lastal.run.log lastz.run.log

[jkimlab]

I also need the SFs.log file in the output directory.

On Dec 11, 2023, at 11:57 AM, aaannaw @.***> wrote:

Hello, professor I am sorry for late response. I will show you these files based on the nets and chains from lastz and lastal respectively: files from analysis based on lastz :

params.txt:

Reference species

REFSPC=Ma

Output directory

OUTPUTDIR=APCFs.300K

OUTPUTDIR=Out_RACA.anctest

Block resolution (bp)

RESOLUTION=300000

Newick tree file

Refer to the sample file 'tree.txt'.

TREEFILE=tree.txt

Minimum adjacency scores

MINADJSCR=0.0001

Config and make files for syntenic fragment construction

Refer to the sample files 'config.SFs' and 'Makefile.SFs'.

You need to change settings in the sample configuration file (config.SFs) according to your data

You don't need to change anything in the Makefile.SFs.

CONFIGSFSFILE=config.SFs MAKESFSFILE=Makefile.SFs config.SFs

path of a net files

netdir /data/01/user158/kuangzhuoran/wanna/Last2AncKary/chainNet

path of a chain files

chaindir /data/01/user158/kuangzhuoran/wanna/Last2AncKary/chainNet

species-name tag1 tag2

tag1 (0: ref-species, 1: descendents, 2: outgroup)

tag2 (1: chromosome assembly, 0: others)

Warning for tag2: Use the value 1 only when a chromosome name starts with "chr".

species Ma 0 0 Mp 1 0 Efon 2 0

block resolution (bp): DO NOT CHANGE

resolution

Tree.txt： (Efon:0.01009,(Mp:0.00552,Ma:0.00585)@:0.00647); Files from analysis based on lastal:

config.SFs

path of a net files

netdir /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/chainNet

path of a chain files

chaindir /data/01/user158/kuangzhuoran/wanna/Last2AncKary/2023.12/10.DESCHRAMBLER/chainNet

species-name tag1 tag2

tag1 (0: ref-species, 1: descendents, 2: outgroup)

tag2 (1: chromosome assembly, 0: others)

Warning for tag2: Use the value 1 only when a chromosome name starts with "chr".

species Ma 0 0 Mp 1 0 Efon 2 0

block resolution (bp): DO NOT CHANGE

resolution

params.txt # Reference species REFSPC=Ma

Output directory

OUTPUTDIR=result

OUTPUTDIR=Out_RACA.anctest

Block resolution (bp)

RESOLUTION=300000

Newick tree file

Refer to the sample file 'tree.txt'.

TREEFILE=tree.txt

Minimum adjacency scores

MINADJSCR=0.0001

Config and make files for syntenic fragment construction

Refer to the sample files 'config.SFs' and 'Makefile.SFs'.

You need to change settings in the sample configuration file (config.SFs) according to your data

You don't need to change anything in the Makefile.SFs.

CONFIGSFSFILE=config.SFs MAKESFSFILE=Makefile.SFs tree.txt: (Efon:0.01009,(Mp:0.00552,Ma:0.00585)@:0.00647); The log files will be added with upload files. lastal.run.log https://github.com/jkimlab/DESCHRAMBLER/files/13630512/lastal.run.log lastz.run.log https://github.com/jkimlab/DESCHRAMBLER/files/13630513/lastz.run.log — Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/21#issuecomment-1849246956, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PVYMCGGFR4ADEGLCXW3YIZZCZAVCNFSM6AAAAABAHSNBFOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBZGI2DMOJVGY. You are receiving this because you commented.

[aaannaw]

Sorry， Professor, I can not find the SFs.log fille in the output directory. I also run the example file provided and I can likely not find SFs.log file. Maybe it has other naming?

[jkimlab]

OK. Did you see any error messages when you ran the example data? If not, it may be caused by an incorrect value of the resolution parameter.

Your assemblies are scaffolds, not chromosome-level sequences. In that case, the default 300Kbp resolution may be too large especially if your assemblies are highly fragmented.

Decrease the resolution, say 50Kbp or smaller, and try again.

On Dec 11, 2023, at 4:14 PM, aaannaw @.***> wrote:

Sorry， Professor, I can not find the SFs.log fille in the output directory. I also run the example file provided and I can likely not find SFs.log file. Maybe it has other naming? image.png (view on web) https://github.com/jkimlab/DESCHRAMBLER/assets/109299053/1ef80a91-c0af-4914-9f80-5bb40a480d0f image.png (view on web) https://github.com/jkimlab/DESCHRAMBLER/assets/109299053/1a966ec2-80f5-448c-9964-6307a3e6de49 image.png (view on web) https://github.com/jkimlab/DESCHRAMBLER/assets/109299053/e8fb57c6-0e43-44da-a0ef-9596a8df84a7 — Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/21#issuecomment-1849450578, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV5PWUGJLY3EYXSV443YI2XFTAVCNFSM6AAAAABAHSNBFOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBZGQ2TANJXHA. You are receiving this because you commented.