I'm trying to create a reference database for deconseq. I've done this several times in the past and have had no issues. I went back and tried to re-create databases I've made in the past and get the same error. Not sure what is going. $ free -m shows no memory issues...although this cuts out within seconds. There's 64gb of memory on this box.
bwa index -p ZM4 -a bwtsw ZM4.fasta >bwa.log 2>&1
[bwa_index] Pack FASTA... 0.02 sec
[bwa_index] Reverse the packed sequence... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
BWTIncConstruct() : Not enough memory allocated!
[BWTIncConstructFromPacked] 10 iterations done. 500507 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 871915 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 1161035 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 1385275 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 1558331 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 1690987 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 1791803 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 1867467 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 1923339 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 1963579 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1991451 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 2009611 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 2020075 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 2024491 characters processed.
bwa index -p ZM4 -a bwtsw ZM4.fasta >bwa.log 2>&1
[bwa_index] Pack FASTA... 0.02 sec
[bwa_index] Reverse the packed sequence... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
BWTIncConstruct() : Not enough memory allocated!
[BWTIncConstructFromPacked] 10 iterations done. 500507 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 871915 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 1161035 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 1385275 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 1558331 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 1690987 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 1791803 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 1867467 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 1923339 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 1963579 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1991451 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 2009611 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 2020075 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 2024491 characters processed.
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