smoothxg::(1-3)::smooth_and_lace

[guo23e]

Hello, may I ask if this is normal? This step has been running for almost a month.
[smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.84e+04 bp/s elapsed: 00:00:00:00 remain: 00:07:53:40
[smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 3.19e+03 bp/s elapsed: 00:00:00:00 remain: 01:21:27:00
[smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.94e+03 bp/s elapsed: 00:00:00:01 remain: 03:02:55:55
[smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.54e+03 bp/s elapsed: 00:00:00:01 remain: 03:22:15:43
[smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.25e+03 bp/s elapsed: 00:00:00:02 remain: 04:19:49:34
[smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.04e+03 bp/s elapsed: 00:00:00:02 remain: 05:19:11:17
。。。。
[smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 74.16% @ 1.52e+02 bp/s elapsed: 29:10:53:03 remain: 10:06:18:33

[AndreaGuarracino]

I sometimes encounter this type of problem in particularly repetitive regions of the genome. Increasing -k (and a little bit -p if necessary) helps reduce the complexity of the problem.

…

________________________________ From: guo23e ***@***.***> Sent: Thursday, September 25, 2025 10:18 To: pangenome/pggb ***@***.***> Cc: Subscribed ***@***.***> Subject: [pangenome/pggb] smoothxg::(1-3)::smooth_and_lace (Issue #471) [https://avatars.githubusercontent.com/u/202928813?s=20&v=4]guo23e created an issue (pangenome/pggb#471)<#471> Hello, may I ask if this is normal? This step has been running for almost a month. [smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.84e+04 bp/s elapsed: 00:00:00:00 remain: 00:07:53:40 [smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 3.19e+03 bp/s elapsed: 00:00:00:00 remain: 01:21:27:00 [smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.94e+03 bp/s elapsed: 00:00:00:01 remain: 03:02:55:55 [smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.54e+03 bp/s elapsed: 00:00:00:01 remain: 03:22:15:43 [smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.25e+03 bp/s elapsed: 00:00:00:02 remain: 04:19:49:34 [smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 0.00% @ 1.04e+03 bp/s elapsed: 00:00:00:02 remain: 05:19:11:17 。。。。 [smoothxg::(1-3)::smooth_and_lace] embedding 522278373 path fragments: 74.16% @ 1.52e+02 bp/s elapsed: 29:10:53:03 remain: 10:06:18:33 — Reply to this email directly, view it on GitHub<#471>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AO26XHXVAT27SSPLMU6BIEL3UOQMTAVCNFSM6AAAAACHOUO2B6VHI2DSMVQWIX3LMV43ASLTON2WKOZTGQ2TENBZGYZDCMQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[guo23e]

I sometimes encounter this type of problem in particularly repetitive regions of the genome. Increasing -k (and a little bit -p if necessary) helps reduce the complexity of the problem.
…

Thank you very much for your reply. I indeed have individuals with 10 different traits of the same species, which were then split into haploids, resulting in a total of twenty sets of genomes. Below are my general operational steps.
I am running this command to partition, each community will be about 2.5G after partitioning.
partition-before-pggb -i merged.fa -o out -n 20 -p 90 -s 5k -V '173_A#1#:1000'
So the command given is submitted, do you mean I should try adding a bit of -k and -p? How much adjustment do you recommend?

pggb -i out/merged.fa.bf3285f.community.0.fa
-o out/merged.fa.bf3285f.community.0.fa.out
-s 5000 -l 25000 -p 90 -c 1 -K 19 -F 0.001 -g 30
-k 23 -f 0 -B 10M
-n 20 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_
-Y "#" -V 173_A#1#:1000 --threads 80 --poa-threads 80

I am looking forward to your feedback.

[AndreaGuarracino]

Try -k above 200 and, if the problem persists, -p 95 Sent from Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: guo23e ***@***.***> Sent: Thursday, September 25, 2025 11:46:16 AM To: pangenome/pggb ***@***.***> Cc: Andrea Guarracino ***@***.***>; Comment ***@***.***> Subject: Re: [pangenome/pggb] smoothxg::(1-3)::smooth_and_lace (Issue #471) [https://avatars.githubusercontent.com/u/202928813?s=20&v=4]guo23e left a comment (pangenome/pggb#471)<#471 (comment)> I sometimes encounter this type of problem in particularly repetitive regions of the genome. Increasing -k (and a little bit -p if necessary) helps reduce the complexity of the problem. … Thank you very much for your reply. I indeed have individuals with 10 different traits of the same species, which were then split into haploids, resulting in a total of twenty sets of genomes. Below are my general operational steps. I am running this command to partition, each community will be about 2.5G after partitioning. partition-before-pggb -i merged.fa -o out -n 20 -p 90 -s 5k -V '173_A#1#:1000' So the command given is submitted, do you mean I should try adding a bit of -k and -p? How much adjustment do you recommend? pggb -i out/merged.fa.bf3285f.community.0.fa -o out/merged.fa.bf3285f.community.0.fa.out -s 5000 -l 25000 -p 90 -c 1 -K 19 -F 0.001 -g 30 -k 23 -f 0 -B 10M -n 20 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ -Y "#" -V 173_A#1#:1000 --threads 80 --poa-threads 80 I am looking forward to your feedback. — Reply to this email directly, view it on GitHub<#471 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AO26XHUMYWH56G6UC6HRR4L3UO2WRAVCNFSM6AAAAACHOUO2B6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTGMZTGE2TAMZRGA>. You are receiving this because you commented.Message ID: ***@***.***>

[guo23e]

尝试 -k 高于 200，如果问题仍然存在，则尝试 -p 95

从 Outlook for Android< 发送 https://aka.ms/AAb9ysg>
…
Thank you very much for your suggestions, I will try again! Thank you.

[guo23e]

I sometimes encounter this type of problem in particularly repetitive regions of the genome. Increasing -k (and a little bit -p if necessary) helps reduce the complexity of the problem.
…

Hello, if I use a genome treated with EDTA to run pggb, would that be a good choice?