I'm trying to generate the mappability files for the zebrafish (danRer7) and chicken (galGal4) genomes. I have downloaded the genome from UCSC genome browser and split it into individual files for each chromosome/scaffold using a python script, such that each file contains a fasta header and the sequence and the name of the header is in the filename. I then ran make which generated the three executables: chr2hash, oligoFindPLFFile and mergeOligoCounts and then added their location to my path. However, when I run compile.py . I get 'Segmentation fault' error messages with the last script:
oligoFindPLFFile chr1.fa chr1.fa . 0 0 1 1 > chr1xchr1.out
/bin/sh: line 1: 14190 Segmentation fault oligoFindPLFFile chr1.fa chr1.fa . 0 0 1 1 > chr1xchr1.out
Could you please let me know whether I'm doing something wrong?