codeML v.4.10.7 segmentation fault (core dumped)

Vinciane Mossion

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Sep 13, 2023, 10:13:32 AM9/13/23

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Hi there,

I got a Segmentation Fault error when I ran codeml on genes with a length of a few thousands bp.

CODONML in paml version 4.10.7, June 2023

ns = 26 ls = 8031
Reading sequences, sequential format..
Reading seq #26: STRI_M07
Sequences read..
Counting site patterns.. 0:00
Compressing, 666 patterns at 2677 / 2677 sites (100.0%), 0:00
Collecting fpatt[] & pose[], 666 patterns at 2677 / 2677 sites (100.0%), 0:00
132 ambiguous codons are seen in the data:
--- AAR ACN ANC ANG ATR CAN CAR CCN CRC CRT CTN CTY GAR GCR GGN GGY GNA GNC GTN GYA GYC NCA NCC NGC NGG NGT NNN RAG RAT RCC RGA RGC RGG RGT RTA RTC RTG TAY TCN TCR TGR TNC TNG TNT TTN TYT YCA YCT YGC YGG YTC YTG YTT AAN AAY ATY CGN GTY GAN NGA RTT TGY AYG ANA CCR CNG ARA ARC ATN YGA CNT GCN RCT GCY TTY NTT NAC NAG RCA YAC TCY TTR YAA NTG GYG GTR ARG GNT NCT ANT CYT CRG CNC NTC GRC GYT YGT YCC YAT ACY NAT TRT RAC CAY CYA CYG RYT GGR NTA YNC ACR CNA GAY CTR TAN RAA GRT YCG TYC AYC YRT AGR RNT NTY TNA TYG AYA AGN AYT CGR TYA
Counting codons..
Segmentation fault (core dumped)

Here attached are the tree, alignment and ctrl files I used. Could you please help me to resolve this issue?

Best wishes,

Vinciane

g58.phyta

pruned-species-tree.tre

nullmodel.ctl

Sishuo Wang

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Sep 15, 2023, 4:45:37 AM9/15/23

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Dear vinciane,

i see no error msg w paml 4.10.0 on ur data if u don't mind i can send you the resulting files. See also the following screenshot.

sishuo

vancine.png

Vinciane Mossion

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Sep 15, 2023, 5:02:18 AM9/15/23

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Dear Sishuo,

Thank you for looking into this. Sure, please send me the results. Unfortunately, it does not really solve my problem as I have many more genes to analyses. I gave it another try and got the same error while running on our cluster. I also tried with PAML v.4.9 and had the same problem. Is there a way to specify the memory that codeML might use inside the codeML command line? May I ask which command line you used?

Best wishes,

Vinciane

Sishuo Wang

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Sep 15, 2023, 10:38:40 PM9/15/23

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Dear vinciane,

here u r, perhaps try not using clstr or 4.10.0 which i used? as to memory limit i am unsure if that's possible.