HuTaoJiaZiAckerman
commented
7 months ago Of cause, I have modified according to the issue 11, but I still get these errors.
Closed HuTaoJiaZiAckerman closed 7 months ago
HuTaoJiaZiAckerman
commented
7 months ago Of cause, I have modified according to the issue 11, but I still get these errors.
jkimlab
commented
7 months ago Can you show me your tree file?
On Nov 8, 2023, at 9:53 AM, Ackerman @.***> wrote:
Of cause, I have modified according to the issue 11 https://github.com/jkimlab/DESCHRAMBLER/issues/12, but I still get these errors.
— Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/18#issuecomment-1800818646, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV4XWSTKZ6VOHRY7CCTYDLJXTAVCNFSM6AAAAAA7CBODG6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBQHAYTQNRUGY. You are receiving this because you are subscribed to this thread.
HuTaoJiaZiAckerman
commented
7 months ago Sure!
(Cross:0.00230,NSME:0.00108,(PB:0.00170,(Ossabaw:0.00159,((NingXiang:0.00226,Bama:0.00250)@:0.00015,Meishan:0.00235):0.00145):0.00022):0.00006);Your tree configuration is incorrect.
The ‘@‘ symbol indicates the common ancestor of all ingroup species including the reference. All species outside of ‘@‘ must be outgroup species.
In your tree, the ‘@‘ symbol is placed at the common ancestor of NingXiang and Bama. So one of them must be the reference, and all other species must be outgroup species.
On Nov 8, 2023, at 10:38 AM, Ackerman @.***> wrote:
Sure!
(Cross:0.00230,NSME:0.00108,(PB:0.00170,(Ossabaw:0.00159,((NingXiang:0.00226,Bama:0.00250)@:0.00015,Meishan:0.00235):0.00145):0.00022):0.00006); — Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/18#issuecomment-1800864602, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV76MBPYWFB3ONOHF7LYDLPBXAVCNFSM6AAAAAA7CBODG6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBQHA3DINRQGI. You are receiving this because you commented.
HuTaoJiaZiAckerman
commented
7 months ago Sorry, I can't understand that the symbol @ should put where. Because I adjusted the position of @, but the same error still occurred.
# tree file
(Cross:0.00230,NSME:0.00108,(PB:0.00170,(Ossabaw:0.00159,((NingXiang:0.00226,Bama:0.00250):0.00015,Meishan:0.00235):0.00145):0.00022)@:0.00006);
# error log
Segmentation fault (core dumped)
make: *** [Makefile:33：Orthology.Blocks.pair] 错误 139
readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/estimate_bpdist4.pl line 61.
TREE (Cross:0.00230,NSME:0.00108,(PB:0.00170,(Ossabaw:0.00159,((NingXiang:0.00226,Bama:0.00250,Sscrofall:0.00252):0.00015,Meishan:0.00235):0.00145):0.00022)@:0.00006);
readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 37.
Use of uninitialized value $tmp in scalar chomp at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 39.
Use of uninitialized value $tmp in substr at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 40.
substr outside of string at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 40.
Use of uninitialized value $numblocks in concatenation (.) or string at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 41.
Use of uninitialized value $bdist_f in concatenation (.) or string at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/estparJC.pl line 14.
Sscrofall /home/user/software/68.deschrambler/DESCHRAMBLER6/tree.txt /home/user/software/68.deschrambler/DESCHRAMBLER6/pig_domestic/SFs/bpdist.txt
Use of uninitialized value $bdist_f in string at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/estparJC.pl line 17.
readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/estparJC.pl line 18.
Estimate JC parameter: 0.0001
readLeafGenomes: PB
# no genome for PB
readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/refine_adjprob.pl line 11.
Minimum weight = 0.0001
Conservation score file = /home/user/software/68.deschrambler/DESCHRAMBLER6/pig_domestic/SFs/block_consscores.txt
readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/split_weak_joins.pl line 130.
readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/join_splits.pl line 131.
readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/ext_join_info.pl line 114.
- Totally 0 APCFs
Segmentation fault (core dumped)I guess this problem is reference genome.
I get chain and net file from this tutorial. And I use Sscrofall genome as reference to align other genome, such as Bama, Meishan, NingXiang, and so on. But Sscrofall genome not include in the tree above.
Now, my question is that how to get of chain and net file of spc2 and spc3.
Do you align with spc1 genome using spc2 and spc3?
It is important that for select reference and outgroup genome. Could you tell me that
As example, spc1 is reference genome, which not have chain and net file. Should I prepare file with following structure, and then reconstructed tree file by mashtree.
examples/
└── chainNet
└── Sscrofall
├── Bama
│ ├── chain
│ │ ├── chr10.chain
│ │ ├── chr11.chain
│ │ ├── chr12.chain
│ │ ├── chr13.chain
│ │ ├── chr14.chain
│ │ ├── chr15.chain
│ │ ├── chr16.chain
│ │ ├── chr17.chain
│ │ ├── chr18.chain
│ │ ├── chr1.chain
│ │ ├── chr2.chain
│ │ ├── chr3.chain
│ │ ├── chr4.chain
│ │ ├── chr5.chain
│ │ ├── chr6.chain
│ │ ├── chr7.chain
│ │ ├── chr8.chain
│ │ └── chr9.chain
│ └── net
│ ├── chr10.net
│ ├── chr11.net
│ ├── chr12.net
│ ├── chr13.net
│ ├── chr14.net
│ ├── chr15.net
│ ├── chr16.net
│ ├── chr17.net
│ ├── chr18.net
│ ├── chr1.net
│ ├── chr2.net
│ ├── chr3.net
│ ├── chr4.net
│ ├── chr5.net
│ ├── chr6.net
│ ├── chr7.net
│ ├── chr8.net
│ └── chr9.net
├── Cross
│ ├── chain
│ │ ├── chr10.chain
│ │ ├── chr11.chain
│ │ ├── chr12.chain
│ │ ├── chr13.chain
│ │ ├── chr14.chain
│ │ ├── chr15.chain
│ │ ├── chr16.chain
│ │ ├── chr17.chain
│ │ ├── chr18.chain
│ │ ├── chr1.chain
│ │ ├── chr2.chain
│ │ ├── chr3.chain
│ │ ├── chr4.chain
│ │ ├── chr5.chain
│ │ ├── chr6.chain
│ │ ├── chr7.chain
│ │ ├── chr8.chain
│ │ └── chr9.chain
│ └── net
│ ├── chr10.net
│ ├── chr11.net
│ ├── chr12.net
│ ├── chr13.net
│ ├── chr14.net
│ ├── chr15.net
│ ├── chr16.net
│ ├── chr17.net
│ ├── chr18.net
│ ├── chr1.net
│ ├── chr2.net
│ ├── chr3.net
│ ├── chr4.net
│ ├── chr5.net
│ ├── chr6.net
│ ├── chr7.net
│ ├── chr8.net
│ └── chr9.net
├── Meishan
│ ├── chain
│ │ ├── chr10.chain
│ │ ├── chr11.chain
│ │ ├── chr12.chain
│ │ ├── chr13.chain
│ │ ├── chr14.chain
│ │ ├── chr15.chain
│ │ ├── chr16.chain
│ │ ├── chr17.chain
│ │ ├── chr18.chain
│ │ ├── chr1.chain
│ │ ├── chr2.chain
│ │ ├── chr3.chain
│ │ ├── chr4.chain
│ │ ├── chr5.chain
│ │ ├── chr6.chain
│ │ ├── chr7.chain
│ │ ├── chr8.chain
│ │ └── chr9.chain
│ └── net
│ ├── chr10.net
│ ├── chr11.net
│ ├── chr12.net
│ ├── chr13.net
│ ├── chr14.net
│ ├── chr15.net
│ ├── chr16.net
│ ├── chr17.net
│ ├── chr18.net
│ ├── chr1.net
│ ├── chr2.net
│ ├── chr3.net
│ ├── chr4.net
│ ├── chr5.net
│ ├── chr6.net
│ ├── chr7.net
│ ├── chr8.net
│ └── chr9.net
├── NingXiang
│ ├── chain
│ │ ├── chr10.chain
│ │ ├── chr11.chain
│ │ ├── chr12.chain
│ │ ├── chr13.chain
│ │ ├── chr14.chain
│ │ ├── chr15.chain
│ │ ├── chr16.chain
│ │ ├── chr17.chain
│ │ ├── chr18.chain
│ │ ├── chr1.chain
│ │ ├── chr2.chain
│ │ ├── chr3.chain
│ │ ├── chr4.chain
│ │ ├── chr5.chain
│ │ ├── chr6.chain
│ │ ├── chr7.chain
│ │ ├── chr8.chain
│ │ └── chr9.chain
│ └── net
│ ├── chr10.net
│ ├── chr11.net
│ ├── chr12.net
│ ├── chr13.net
│ ├── chr14.net
│ ├── chr15.net
│ ├── chr16.net
│ ├── chr17.net
│ ├── chr18.net
│ ├── chr1.net
│ ├── chr2.net
│ ├── chr3.net
│ ├── chr4.net
│ ├── chr5.net
│ ├── chr6.net
│ ├── chr7.net
│ ├── chr8.net
│ └── chr9.net
├── NSME
│ ├── chain
│ │ ├── chr10.chain
│ │ ├── chr11.chain
│ │ ├── chr12.chain
│ │ ├── chr13.chain
│ │ ├── chr14.chain
│ │ ├── chr15.chain
│ │ ├── chr16.chain
│ │ ├── chr17.chain
│ │ ├── chr18.chain
│ │ ├── chr1.chain
│ │ ├── chr2.chain
│ │ ├── chr3.chain
│ │ ├── chr4.chain
│ │ ├── chr5.chain
│ │ ├── chr6.chain
│ │ ├── chr7.chain
│ │ ├── chr8.chain
│ │ └── chr9.chain
│ └── net
│ ├── chr10.net
│ ├── chr11.net
│ ├── chr12.net
│ ├── chr13.net
│ ├── chr14.net
│ ├── chr15.net
│ ├── chr16.net
│ ├── chr17.net
│ ├── chr18.net
│ ├── chr1.net
│ ├── chr2.net
│ ├── chr3.net
│ ├── chr4.net
│ ├── chr5.net
│ ├── chr6.net
│ ├── chr7.net
│ ├── chr8.net
│ └── chr9.net
├── Ossabaw
│ ├── chain
│ │ ├── chr10.chain
│ │ ├── chr11.chain
│ │ ├── chr12.chain
│ │ ├── chr13.chain
│ │ ├── chr14.chain
│ │ ├── chr15.chain
│ │ ├── chr16.chain
│ │ ├── chr17.chain
│ │ ├── chr18.chain
│ │ ├── chr1.chain
│ │ ├── chr2.chain
│ │ ├── chr3.chain
│ │ ├── chr4.chain
│ │ ├── chr5.chain
│ │ ├── chr6.chain
│ │ ├── chr7.chain
│ │ ├── chr8.chain
│ │ └── chr9.chain
│ └── net
│ ├── chr10.net
│ ├── chr11.net
│ ├── chr12.net
│ ├── chr13.net
│ ├── chr14.net
│ ├── chr15.net
│ ├── chr16.net
│ ├── chr17.net
│ ├── chr18.net
│ ├── chr1.net
│ ├── chr2.net
│ ├── chr3.net
│ ├── chr4.net
│ ├── chr5.net
│ ├── chr6.net
│ ├── chr7.net
│ ├── chr8.net
│ └── chr9.net
└── PB
├── chain
│ ├── chr10.chain
│ ├── chr11.chain
│ ├── chr12.chain
│ ├── chr13.chain
│ ├── chr14.chain
│ ├── chr15.chain
│ ├── chr16.chain
│ ├── chr17.chain
│ ├── chr18.chain
│ ├── chr1.chain
│ ├── chr2.chain
│ ├── chr3.chain
│ ├── chr4.chain
│ ├── chr5.chain
│ ├── chr6.chain
│ ├── chr7.chain
│ ├── chr8.chain
│ └── chr9.chain
└── net
├── chr10.net
├── chr11.net
├── chr12.net
├── chr13.net
├── chr14.net
├── chr15.net
├── chr16.net
├── chr17.net
├── chr18.net
├── chr1.net
├── chr2.net
├── chr3.net
├── chr4.net
├── chr5.net
├── chr6.net
├── chr7.net
├── chr8.net
└── chr9.netYour configuration is still incorrect.
The reference must be one of the species under ‘@‘ in your tree file. You want to use Sscrofall as the reference, but it is not in your tree.
For chain/net files, if your reference is Sscrofall, you have to make chain/net files using Sscrofall against each of the other species. For example, Sscrofall vs. Cross, Sscrofall, vs. NSME, Sscrofall vs. PB, and so on.
The chain/net directory structure must be as follows.
Sscrofall Cross chain net NSME chain net PB chain net ...
On Nov 8, 2023, at 12:56 PM, Ackerman @.***> wrote:
Sorry, I can't understand that the symbol @ should put where. Because I adjusted the position of @, but the same error still occurred.
tree file
(Cross:0.00230,NSME:0.00108,(PB:0.00170,(Ossabaw:0.00159,((NingXiang:0.00226,Bama:0.00250):0.00015,Meishan:0.00235):0.00145):0.00022)@:0.00006);
error log
Segmentation fault (core dumped) make: *** [Makefile:33：Orthology.Blocks.pair] 错误 139 readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/estimate_bpdist4.pl line 61. TREE (Cross:0.00230,NSME:0.00108,(PB:0.00170,(Ossabaw:0.00159,((NingXiang:0.00226,Bama:0.00250,Sscrofall:0.00252):0.00015,Meishan:0.00235):0.00145):0.00022)@:0.00006);
readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 37. Use of uninitialized value $tmp in scalar chomp at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 39. Use of uninitialized value $tmp in substr at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 40. substr outside of string at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 40. Use of uninitialized value $numblocks in concatenation (.) or string at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/wrap_recon_apcf.pl line 41. Use of uninitialized value $bdist_f in concatenation (.) or string at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/estparJC.pl line 14. Sscrofall /home/user/software/68.deschrambler/DESCHRAMBLER6/tree.txt /home/user/software/68.deschrambler/DESCHRAMBLER6/pig_domestic/SFs/bpdist.txt Use of uninitialized value $bdist_f in string at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/estparJC.pl line 17. readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/estparJC.pl line 18. Estimate JC parameter: 0.0001 readLeafGenomes: PB
no genome for PB
readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/refine_adjprob.pl line 11. Minimum weight = 0.0001 Conservation score file = /home/user/software/68.deschrambler/DESCHRAMBLER6/pig_domestic/SFs/block_consscores.txt readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/split_weak_joins.pl line 130. readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/join_splits.pl line 131. readline() on closed filehandle F at /home/user/software/68.deschrambler/DESCHRAMBLER6/script/ext_join_info.pl line 114.
- Totally 0 APCFs Segmentation fault (core dumped) I guess this problem is reference genome. I get chain and net file from this tutorial https://biochen.org/cn/blog/2021/%E4%B8%A4%E5%9F%BA%E5%9B%A0%E7%BB%84%E6%AF%94%E5%AF%B9/. And I use Sscrofall genome as reference to align other genome, such as Bama, Meishan, NingXiang, and so on. But Sscrofall genome not include in the tree above.
Now, my question is that how to get of chain and net file of spc2 and spc3. Do you align with spc1 genome using spc2 and spc3? It is important that for select reference and outgroup genome. Could you tell me that
As example, spc1 is reference genome, which not have chain and net file. Should I prepare file with following structure, and then reconstructed tree file by mashtree.
examples/ └── chainNet └── Sscrofall ├── Bama │ ├── chain │ │ ├── chr10.chain │ │ ├── chr11.chain │ │ ├── chr12.chain │ │ ├── chr13.chain │ │ ├── chr14.chain │ │ ├── chr15.chain │ │ ├── chr16.chain │ │ ├── chr17.chain │ │ ├── chr18.chain │ │ ├── chr1.chain │ │ ├── chr2.chain │ │ ├── chr3.chain │ │ ├── chr4.chain │ │ ├── chr5.chain │ │ ├── chr6.chain │ │ ├── chr7.chain │ │ ├── chr8.chain │ │ └── chr9.chain │ └── net │ ├── chr10.net │ ├── chr11.net │ ├── chr12.net │ ├── chr13.net │ ├── chr14.net │ ├── chr15.net │ ├── chr16.net │ ├── chr17.net │ ├── chr18.net │ ├── chr1.net │ ├── chr2.net │ ├── chr3.net │ ├── chr4.net │ ├── chr5.net │ ├── chr6.net │ ├── chr7.net │ ├── chr8.net │ └── chr9.net ├── Cross │ ├── chain │ │ ├── chr10.chain │ │ ├── chr11.chain │ │ ├── chr12.chain │ │ ├── chr13.chain │ │ ├── chr14.chain │ │ ├── chr15.chain │ │ ├── chr16.chain │ │ ├── chr17.chain │ │ ├── chr18.chain │ │ ├── chr1.chain │ │ ├── chr2.chain │ │ ├── chr3.chain │ │ ├── chr4.chain │ │ ├── chr5.chain │ │ ├── chr6.chain │ │ ├── chr7.chain │ │ ├── chr8.chain │ │ └── chr9.chain │ └── net │ ├── chr10.net │ ├── chr11.net │ ├── chr12.net │ ├── chr13.net │ ├── chr14.net │ ├── chr15.net │ ├── chr16.net │ ├── chr17.net │ ├── chr18.net │ ├── chr1.net │ ├── chr2.net │ ├── chr3.net │ ├── chr4.net │ ├── chr5.net │ ├── chr6.net │ ├── chr7.net │ ├── chr8.net │ └── chr9.net ├── Meishan │ ├── chain │ │ ├── chr10.chain │ │ ├── chr11.chain │ │ ├── chr12.chain │ │ ├── chr13.chain │ │ ├── chr14.chain │ │ ├── chr15.chain │ │ ├── chr16.chain │ │ ├── chr17.chain │ │ ├── chr18.chain │ │ ├── chr1.chain │ │ ├── chr2.chain │ │ ├── chr3.chain │ │ ├── chr4.chain │ │ ├── chr5.chain │ │ ├── chr6.chain │ │ ├── chr7.chain │ │ ├── chr8.chain │ │ └── chr9.chain │ └── net │ ├── chr10.net │ ├── chr11.net │ ├── chr12.net │ ├── chr13.net │ ├── chr14.net │ ├── chr15.net │ ├── chr16.net │ ├── chr17.net │ ├── chr18.net │ ├── chr1.net │ ├── chr2.net │ ├── chr3.net │ ├── chr4.net │ ├── chr5.net │ ├── chr6.net │ ├── chr7.net │ ├── chr8.net │ └── chr9.net ├── NingXiang │ ├── chain │ │ ├── chr10.chain │ │ ├── chr11.chain │ │ ├── chr12.chain │ │ ├── chr13.chain │ │ ├── chr14.chain │ │ ├── chr15.chain │ │ ├── chr16.chain │ │ ├── chr17.chain │ │ ├── chr18.chain │ │ ├── chr1.chain │ │ ├── chr2.chain │ │ ├── chr3.chain │ │ ├── chr4.chain │ │ ├── chr5.chain │ │ ├── chr6.chain │ │ ├── chr7.chain │ │ ├── chr8.chain │ │ └── chr9.chain │ └── net │ ├── chr10.net │ ├── chr11.net │ ├── chr12.net │ ├── chr13.net │ ├── chr14.net │ ├── chr15.net │ ├── chr16.net │ ├── chr17.net │ ├── chr18.net │ ├── chr1.net │ ├── chr2.net │ ├── chr3.net │ ├── chr4.net │ ├── chr5.net │ ├── chr6.net │ ├── chr7.net │ ├── chr8.net │ └── chr9.net ├── NSME │ ├── chain │ │ ├── chr10.chain │ │ ├── chr11.chain │ │ ├── chr12.chain │ │ ├── chr13.chain │ │ ├── chr14.chain │ │ ├── chr15.chain │ │ ├── chr16.chain │ │ ├── chr17.chain │ │ ├── chr18.chain │ │ ├── chr1.chain │ │ ├── chr2.chain │ │ ├── chr3.chain │ │ ├── chr4.chain │ │ ├── chr5.chain │ │ ├── chr6.chain │ │ ├── chr7.chain │ │ ├── chr8.chain │ │ └── chr9.chain │ └── net │ ├── chr10.net │ ├── chr11.net │ ├── chr12.net │ ├── chr13.net │ ├── chr14.net │ ├── chr15.net │ ├── chr16.net │ ├── chr17.net │ ├── chr18.net │ ├── chr1.net │ ├── chr2.net │ ├── chr3.net │ ├── chr4.net │ ├── chr5.net │ ├── chr6.net │ ├── chr7.net │ ├── chr8.net │ └── chr9.net ├── Ossabaw │ ├── chain │ │ ├── chr10.chain │ │ ├── chr11.chain │ │ ├── chr12.chain │ │ ├── chr13.chain │ │ ├── chr14.chain │ │ ├── chr15.chain │ │ ├── chr16.chain │ │ ├── chr17.chain │ │ ├── chr18.chain │ │ ├── chr1.chain │ │ ├── chr2.chain │ │ ├── chr3.chain │ │ ├── chr4.chain │ │ ├── chr5.chain │ │ ├── chr6.chain │ │ ├── chr7.chain │ │ ├── chr8.chain │ │ └── chr9.chain │ └── net │ ├── chr10.net │ ├── chr11.net │ ├── chr12.net │ ├── chr13.net │ ├── chr14.net │ ├── chr15.net │ ├── chr16.net │ ├── chr17.net │ ├── chr18.net │ ├── chr1.net │ ├── chr2.net │ ├── chr3.net │ ├── chr4.net │ ├── chr5.net │ ├── chr6.net │ ├── chr7.net │ ├── chr8.net │ └── chr9.net └── PB ├── chain │ ├── chr10.chain │ ├── chr11.chain │ ├── chr12.chain │ ├── chr13.chain │ ├── chr14.chain │ ├── chr15.chain │ ├── chr16.chain │ ├── chr17.chain │ ├── chr18.chain │ ├── chr1.chain │ ├── chr2.chain │ ├── chr3.chain │ ├── chr4.chain │ ├── chr5.chain │ ├── chr6.chain │ ├── chr7.chain │ ├── chr8.chain │ └── chr9.chain └── net ├── chr10.net ├── chr11.net ├── chr12.net ├── chr13.net ├── chr14.net ├── chr15.net ├── chr16.net ├── chr17.net ├── chr18.net ├── chr1.net ├── chr2.net ├── chr3.net ├── chr4.net ├── chr5.net ├── chr6.net ├── chr7.net ├── chr8.net └── chr9.net — Reply to this email directly, view it on GitHub https://github.com/jkimlab/DESCHRAMBLER/issues/18#issuecomment-1800972633, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEU6PV7JISEABGHEYSWRJJDYDL7F3AVCNFSM6AAAAAA7CBODG6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBQHE3TENRTGM. You are receiving this because you commented.
HuTaoJiaZiAckerman
commented
7 months ago Thank you very much for your reply!
I seem to find my fault.
You must ensure that in your fa file, the chromosome name starts with chr. For instence,
>chr10
TGCCAGTTTGATCCCAGTGTGGGCAAAGGGCTAGATATGTCCATTCAGCA
GCTGAGGGGGGGGGGTGGGCTTAAGAtcgtcacagatgccgctcagattc
gatccctgagtcaggaatttccctatgccacaagtgtgactgaaaaagga
aaaggaaaaaaaaaatagggaaattctTTCTAAGCAAGAcataaaagaca
>chr11
TTATTCTTAGTCTTATCTGTGCAAATGTGTTCACAATCTGAAGAATGAGT
TTTTAACTCACTCATAAGGATATGGAATTCTTCTTTTATCCAGTCTGATA
ACAGAGAGCAAAAGGCTGCATTATTCCTTGAGGAATACTCTAATTCATTT
ACATATCTGCTCATTTTCTCCATGGATTTTTCTGATTACTCAGAAGATTG
TTTTTACTTACACTAtatctaatttaaaagaaatttcatggtgcacacac
aaaaagacaaaaaaaaataccatgttaaAGGATtatttatcaaaaagacaAnd repeat this tutorial
Hello, I meet a fault when I run the following code.
My file structure is following: (this is only small part)
I use
Crossas a reference, andBMas a outgroup.I can't find anymore question. Could you help me. This is log: