codeml memory problem

40 views
Skip to first unread message

bilge

unread,
Feb 9, 2024, 5:07:29 AMFeb 9
to PAML discussion group

C:\Desktop\paml\bin\codeml.exe running...



AAML in paml version 4.9j, February 2020

ns = 5 ls = 715

Reading sequences, sequential format..

Reading seq # 1: Danio rerio MMQESANETISNSSMSQNGMSSL-SSQLDAGSRDGRSS-GETSSEVSAVELLHLQQQQALQAARQLLLQQPGSGLKSPKNNDK

Reading seq # 2: Bos taurus MMQESATETISNSSMNQNGMSTL-SSQLDAGSRDGRSS-GDTSSEVSTVELLHLQQQQALQAARQLLLQQQTSGLKSPKSSDKQ

Reading seq # 3: Takifugu rubripes MMQESATETISNSSMSQNGMSTLSSSQLEAGSRDGRSSAGDTSSEVSTVELLHLQQQQALQAARQLLLQQPGSGLKSP

Reading seq # 4: Latimeria chalumnae MMQESATETISNSSMNQNGMSAL-SSQLDAGSRDGRSS-GDTSSEVSTVELLHLQQQQALQAARQLLLQQQTSGLK

Reading seq # 5: Homo sapiens MMQESATETISNSSMNQNGMSTL-SSQLDAGSRDGRSS-GDTSSEVSTVELLHLQQQQALQAARQLLLQQQTSGLKSPKSSD


Sequences read..

Counting site patterns.. 0:01


Compressing, 658 patterns at 715 / 715 sites (100.0%), 0:01


Collecting fpatt[] & pose[], 658 patterns at 715 / 715 sites (100.0%), 0:01

Counting frequencies..

Counting site patterns again, for JC69.. 0:01


Compressing, 104 patterns at 658 / 658 sites (100.0%), 0:01


Collecting fpatt[] & pose[], 104 patterns at 658 / 658 sites (100.0%), 0:01


80 bytes for distance

33280 bytes for conP

31525592535924847 bytes for fhK

5000000 bytes for space


Species NP_001192498.1_forkhead_box_protein_P2_Bos_taurus?


C:\Desktop\paml\bin\codeml.exe -- killed

i get this error but i could not find a solution

Sandra AC

unread,
Feb 9, 2024, 11:48:44 AMFeb 9
to PAML discussion group
Hi there,

It is hard to tell what the problem is without the input files you are using. Nevertheless, I would guess that you are not using the same sequence names in the tree file and the sequence file. Make sure that the same sequence names (or "sequence IDs") are the same in both the input sequence file and the input tree file without spaces or special characters (e.g., avoid using "Danio rerio", instead use "Danio_rerio"). You have all the details regarding the format to follow for sequence names in the PAML Wiki, section "Data formatting".

If things keep failing after correcting the format of both input files, please send another message with your input data so it is easier to troubleshoot the problem.

Hope this helps!
S.

Ziheng

unread,
Feb 9, 2024, 2:25:14 PMFeb 9
to PAML discussion group

In this case you should insert at least two spaces between the name and the sequence.  Right now the first sequence name is read as
Danio rerio MMQESANETISNSSMSQNGMSSL-SSQLDAGSRDGRSS-GETSSEVSAVELLHLQQQQALQAARQLLLQQPGSGLKSPKNNDK”
Ziheng

bilge

unread,
Feb 9, 2024, 5:43:14 PMFeb 9
to PAML discussion group
this did not work, but i tried the upper answer and it worked, thank you both so much 

9 Şubat 2024 Cuma tarihinde saat 22:25:14 UTC+3 itibarıyla Ziheng şunları yazdı:
Reply all
Reply to author
Forward
0 new messages