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unable to custom DB

Open juejun14 opened this issue 1 year ago • 4 comments

Hello, thank you for creating this amazing tool! I'm trying to custom a uniref90 DB from the uniref90.fsa file. I have made the file has a format like

1_1572043 MEEITQIKKRLSQTVRLEGKEDLLSKKDSITNLKTEEHVSVKKMVISEPKPEKKEDIQLK

and then I run the command with my protein faa file:

kaiju-mkbwt -n 32 -a ACDEFGHIKLMNPQRSTVWY -o uniref90 uniref90.fsa
kaiju-mkfmi proteins

But each time the process will be killed and I can't find the reason, here is the msg on terminal:

# infilename= databases/uniref90/uniref90.fsa
# outfilename= databases/uniref90/uniref90
# Alphabet= ACDEFGHIKLMNPQRSTVWY
# nThreads= 32
# length= 0.000000
# checkpoint= 5
# caseSens=OFF
# revComp=OFF
# term= *
# revsort=OFF
# help=OFF
Sequences read time = 397.070000s
SLEN 39118962811
NSEQ 113461890
ALPH *ACDEFGHIKLMNPQRSTVWY
/var/spool/slurm/slurmd/job31805075/slurm_script: line 24: 20773 Killed                  kaiju-mkbwt -n 32 -a ACDEFGHIKLMNPQRSTVWY -o databases/uniref90/uniref90 databases/uniref90/uniref90.fsa

I have tested it with a smaller size file which has only 50000 lines of my faa file. It can run successfully until the end. I can not find out where is the problem, can anyone help me pls?

Thanks, juejun

juejun14 avatar Feb 08 '23 09:02 juejun14