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License: GNU General Public License v3.0
Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array
License: GNU General Public License v3.0
Thanks for this great piece of software!
I have one bug report and one request
slaMEM
? It matters when testing builds with travis.slaMEM -l 17 refs.fa reads.fa -o outfolder/mems.txt
reads:
>read3
GTAATTACAGGACTTGTGGTTGGTTTTACGATAGCGACTGAACTGCCGAACTTTGTTTAATAATTACACGTTAATCTGGGACAAGCAAGCTGAAGACGCAGTAACAGTTGGTTCTTGCTGAAAGGACCAACCTATGACTTTCTGGTTTTGCCTGTTGTGAACAACGTTACAGTAAAAGGCGGCTTCGTGACTGCTGGTCGAAGAGCCAAATGGTCAACATTAGCATAGCTTGCTTCCTCTTTTTCGTTGCGGAGTTAGCAGGAGAACGTTATGTTTTTACCGAAGAAGGCGCAGTGTTTGCTTGACAATTTACCGTCGTGTCTTCGGTAACAGATATGCTTACCGCTATCCTAACCACCTCAATCACTGCCTTACGGACGTTAACCTAACGCAAATGCCACCAAATACATATGTAAGTCCTCTTAATGTTTGCATGCTTAATCTTTTGATTATTTCCTCTTTCTTTTCTATTTATTAATCCTGTGTCCTCGCCAACCGAATCAACATAAATACGTCAACGAATCAAATGTTGATCTCAAATATCTGTGTCCATGAAATTTCGATCGTAAAAACA
>read4
GGCCTCTAAATTCGGTATCAAGTATTTGCTTCTCCACCGCCAAGCGCACATAAATTCTTTGCGAGTGTTGTTTGGCCACTTTTGGTAGCTCCTGTTTCTTGGCAATTTTGGCTGACACGTTCAGTTTCTTTGCTCCAACTTCGTAAGCAGTTAGTGTAGGCGTGCGGAGGCGTGCGCTACTCGCTACATCGTTGGTTCTACCACCCATATGCCATGGCGTCCTGTAGGTTTGCGCCTAATTACTCGAAGCGCTTTCATTTCTACGAAACGTTTTGGAATAATGTCAACTTGGGCATTGTTGAAACTACGGCTTCCTTAATGCTGACAACCTTGTTTAGTTGTTGTTCTTCCCTTCTTCCAGCATTTAATAACCAGCTTGTTTTAACTCCTTCGCTTTTTCGACTTTCTCCTTCCAGCACCGCAACGTTCTTTTAAGCTACAACGCTTTCTTGAAATCTTCTCGTCATAAA
refs:
>1^1000^1484
AAAGTAATGCCTCTACGTCAGTCGGAACAATGTCGTCGTGTAACTCGACGATCTTAGGAGCTACTAAGGAGAGTCTGTAGGGAACCGACTGGGAAGGTGCCACAAGTTTTCTCTACTACTCCGTCTCCTAAAACAACTCCAAGTGGAAGGTCTGTGGGTTTTTGAGTATAGTCCGTATCTAGACCCAAAAGGGCTTACCTTCGCAATGAAAGAATATCCTTATAGACACGAACGGGAAGAACGGAATCGTTATTAATGACGTCGTACAACGTTTTCCAAGTTCTCCTCTTCCTCCGGATTCGGTTTGGGTTATCTCAACTAGTCCTTTCAAAGACATTGGAGAGTTTCACCTTCCCGTTAAGGTAGAACCCTCAGCATGTTTCACCCCCGGTGACCACTCAGTTACGGAATGTTTTTAAGCCACCTCAGCTAGTGTTCCGAGAGGTGACAGCGACGACGTCCACGTTTGGACTTGTTATCATAA
>1^6337^6813
CATCCTAACATGTTTAGGAACTTCCCCCGAACGTTCGACTCTGAGACACCCCAGGGACCGTACTCTAACTACCTACCTAGTACCCATAGAGAAGTCTTTTGACTTCCAGGCCCTACCACGAGAGGTCTAGTCGAACCTTTACAGGTACTAAAGGTATGTCTACTTTAACTTGTGGAACACCAACTTCTCAACCACTTCTTCTCCCTTCTCACAAACCTACGACATCTTTGATAGTAGTGTTGGTTCAGATATTCATCGTCTGCAGAGTCAGTAAAGTCCTTTGACCAAGGACCCAAACCTTTCCGTATGTGAGAGTAGTTGTTCTGAGAGTACCTTCGTCTACAGGTAATGTTCAGACATTCTCTTACCTTTCTTCACTAGGGTAGATTTCCCACAGACTACCGTCCCCCCTCTACGGTAGGAGTGATGTCACCATATAAGAAGTTACCCTAGTATGACTCAGGTCCCCCACTATC
Hi, using gcc 4.8.2 and after 24 hours I got a seg. fault
However in your paper you could index the human genome. I wonder which steps I have to make to reproduce your results.
./slaMEM -m ~/genomes/human.fa ~/genomes/chimpanzee_genome.fa
[ slaMEM v0.7.1 ]
Loading sequences from file </genomes/human.fa> ... (3157590979 bytes)
01 [human ](-1199289884 bp) OK
Loading sequences from file </genomes/chimpanzee_genome.fa> ... (2678898688 bytes)
02 [gi|114573996|ref|NW_001229892.1|Ptr1_WGA](-1653809352 bp) OK
1 reference and 1 query successfully loaded
Using options: minimum MEM length = 50
Processing reference sequence "human" ...
Collecting LMS positions .......... (798090407) OK
Sorting LMS suffixes .......... OK
Induced Sorting suffixes .......... OK
Collecting LF samples .......... OK
Collecting SA samples .......... OK
:: FM-Index size = 3482 MB
Building Sampled LCP Array Segmentation fault (core dumped)
Using "slaMEM" to find MEMs in human reference genome hg19 (3.2 Gigabytes). I executed the following command:
./slaMEM -l 17 -b -n ../bio_data/gnome/hg19/slamem/hg19.fna query.fna
query.fna contains a single sequence of 3119 bases. The program is "Building Sampled LCP Array" and not progressing for the last 10 hours or so. The program is executing for nearly 24 hours now.
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