ERROR: Bad base (.) at site 6 of sequence 2

[Yuen]

Hello. I've tried several times generating RAxML-HPC2 on XSEDE with 64 of my sequences but I could not get the RAxML_bipartitions or any output files as I named. Instead, I checked the stdout.txt file and they all gave the same error which was as follows. What should I do? 

CIPRES_THREADSPP=4
CIPRES_NP=6
running:
 raxmlHPC-HYBRID -T 4 -n result -s infile.txt -c 25 -m GTRCAT -p 12345 -f a -N 1000 -x 12345 -o HM240413.1 Paraboysidia tarutao voucher MOL 116412,HM240412.1 Paraboysidia tarutao voucher MOL 116411,HM240411.1 Paraboysidia tarutao voucher MOL 116385,HM240410.1 Gyliotrachela depressispira voucher MOL 116409,HM240409.1 Gyliotrachela frequens voucher MOL 116407,HM240408.1 Gyliotrachela salpinx voucher MOL 116372,HM240407.1 Gyliotrachela salpinx voucher MOL 116371,HM240406.1 Gyliotrachela transitans voucher MOL 116382,HM240405.1 Gyliotrachela transitans voucher MOL 116381
CIPRES_THREADSPP=4
CIPRES_NP=6
running:
 raxmlHPC-HYBRID -T 4 -n result -s infile.txt -c 25 -m GTRCAT -p 12345 -f a -N 1000 -x 12345 -o HM240413.1 Paraboysidia tarutao voucher MOL 116412,HM240412.1 Paraboysidia tarutao voucher MOL 116411,HM240411.1 Paraboysidia tarutao voucher MOL 116385,HM240410.1 Gyliotrachela depressispira voucher MOL 116409,HM240409.1 Gyliotrachela frequens voucher MOL 116407,HM240408.1 Gyliotrachela salpinx voucher MOL 116372,HM240407.1 Gyliotrachela salpinx voucher MOL 116371,HM240406.1 Gyliotrachela transitans voucher MOL 116382,HM240405.1 Gyliotrachela transitans voucher MOL 116381
CIPRES_THREADSPP=4
CIPRES_NP=6
running:
 raxmlHPC-HYBRID -T 4 -n result -s infile.txt -c 25 -m GTRCAT -p 12345 -f a -N 1000 -x 12345 -o HM240413.1 Paraboysidia tarutao voucher MOL 116412,HM240412.1 Paraboysidia tarutao voucher MOL 116411,HM240411.1 Paraboysidia tarutao voucher MOL 116385,HM240410.1 Gyliotrachela depressispira voucher MOL 116409,HM240409.1 Gyliotrachela frequens voucher MOL 116407,HM240408.1 Gyliotrachela salpinx voucher MOL 116372,HM240407.1 Gyliotrachela salpinx voucher MOL 116371,HM240406.1 Gyliotrachela transitans voucher MOL 116382,HM240405.1 Gyliotrachela transitans voucher MOL 116381
CIPRES_THREADSPP=4
CIPRES_NP=6
running:
 raxmlHPC-HYBRID -T 4 -n result -s infile.txt -c 25 -m GTRCAT -p 12345 -f a -N 1000 -x 12345 -o HM240413.1 Paraboysidia tarutao voucher MOL 116412,HM240412.1 Paraboysidia tarutao voucher MOL 116411,HM240411.1 Paraboysidia tarutao voucher MOL 116385,HM240410.1 Gyliotrachela depressispira voucher MOL 116409,HM240409.1 Gyliotrachela frequens voucher MOL 116407,HM240408.1 Gyliotrachela salpinx voucher MOL 116372,HM240407.1 Gyliotrachela salpinx voucher MOL 116371,HM240406.1 Gyliotrachela transitans voucher MOL 116382,HM240405.1 Gyliotrachela transitans voucher MOL 116381
CIPRES_THREADSPP=4
CIPRES_NP=6
running:
 raxmlHPC-HYBRID -T 4 -n result -s infile.txt -c 25 -m GTRCAT -p 12345 -f a -N 1000 -x 12345 -o HM240413.1 Paraboysidia tarutao voucher MOL 116412,HM240412.1 Paraboysidia tarutao voucher MOL 116411,HM240411.1 Paraboysidia tarutao voucher MOL 116385,HM240410.1 Gyliotrachela depressispira voucher MOL 116409,HM240409.1 Gyliotrachela frequens voucher MOL 116407,HM240408.1 Gyliotrachela salpinx voucher MOL 116372,HM240407.1 Gyliotrachela salpinx voucher MOL 116371,HM240406.1 Gyliotrachela transitans voucher MOL 116382,HM240405.1 Gyliotrachela transitans voucher MOL 116381
CIPRES_THREADSPP=4
CIPRES_NP=6
running:
 raxmlHPC-HYBRID -T 4 -n result -s infile.txt -c 25 -m GTRCAT -p 12345 -f a -N 1000 -x 12345 -o HM240413.1 Paraboysidia tarutao voucher MOL 116412,HM240412.1 Paraboysidia tarutao voucher MOL 116411,HM240411.1 Paraboysidia tarutao voucher MOL 116385,HM240410.1 Gyliotrachela depressispira voucher MOL 116409,HM240409.1 Gyliotrachela frequens voucher MOL 116407,HM240408.1 Gyliotrachela salpinx voucher MOL 116372,HM240407.1 Gyliotrachela salpinx voucher MOL 116371,HM240406.1 Gyliotrachela transitans voucher MOL 116382,HM240405.1 Gyliotrachela transitans voucher MOL 116381

This is RAxML MPI Process Number: 0

This is RAxML MPI Process Number: 1

This is RAxML MPI Process Number: 2

This is RAxML MPI Process Number: 3

This is RAxML MPI Process Number: 4

This is RAxML MPI Process Number: 5
ERROR: Bad base (.) at site 6 of sequence 2
Printing error context:

CT
142_Gyliot -----..... .......... ....

Problem reading alignment file 
ERROR: Bad base (.) at site 6 of sequence 2
Printing error context:

CT
142_Gyliot -----..... .......... ....

Problem reading alignment file 
ERROR: Bad base (.) at site 6 of sequence 2
Printing error context:

CT
142_Gyliot -----..... .......... ....

Problem reading alignment file 
ERROR: Bad base (.) at site 6 of sequence 2
Printing error context:

CT
142_Gyliot -----..... .......... ....

Problem reading alignment file 
ERROR: Bad base (.) at site 6 of sequence 2
Printing error context:

CT
142_Gyliot -----..... .......... ....

Problem reading alignment file 
ERROR: Bad base (.) at site 6 of sequence 2
Printing error context:

CT
142_Gyliot -----..... .......... ....

Problem reading alignment file 

[Alexandros Stamatakis]

replace . by N in your alignent file ...

alexis

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Gianmarco Virga]

I've got the same problem: "ERROR: Bad base <2> at site 47 of sequence 1"

printing error context:

 

 0 ? ? ? ? ? ? 0 0 2 ? 0

t1                   0 0 ? 0 ?

what should i do?

Thanks in advance

[Alexandros Stamatakis]

can you please send us the full alignment file such that we can check?

alexis