Hello,
I have a shell script like the one below but cannot get it working:
#!/bin/bash
#$ -cwd
CHR=$2
# directories
ROOT_DIR=./
RESULTS_DIR=${ROOT_DIR}results/
# executable
SHAPEIT_EXEC=${ROOT_DIR}shapeit.v2.r727.linux.x64/shapeit.v2.r727.linux.x64
# parameters
THREAT=5
EFFECTIVESIZE=11418
# reference data files
GENMAP_FILE=/home/whme1016/Imputation/genetic_map_b37/genetic_map_chr${CHR}_combined_b37.txt
# GWAS data files in PLINK BED format
GWASDATA_BED=${ROOT_DIR}chr${CHR}.unphased.bed
GWASDATA_BIM=${ROOT_DIR}chr${CHR}.unphased.bim
GWASDATA_FAM=${ROOT_DIR}chr${CHR}.unphased.fam
# problem SNP file
EXCLUDE_SNP=${ROOT_DIR}chr${CHR}.alignments.snp.strand.exclude
# main output file
OUTPUT_HAPS=${RESULTS_DIR}chr${CHR}.phased.haps
OUTPUT_SAMPLE=${RESULTS_DIR}chr${CHR}.phased.sample
OUTPUT_LOG=${RESULTS_DIR}chr${CHR}.phased.log
## phase GWAS genotypes
$SHAPEIT_EXEC \
--input-bed $GWASDATA_BED $GWASDATA_BIM $GWASDATA_FAM \
--input-map $GENMAP_FILE \
--exclude-snp $EXCLUDE_SNP \
--thread $THREAT \
--effective-size $EFFECTIVESIZE \
--output-max $OUTPUT_HAPS $OUTPUT_SAMPLE \
--output-log $OUTPUT_LOG
done
I am trying to run a program called SHAPEIT. When I run the shell script, I get the following error:
Segmented HAPlotype Estimation & Imputation Tool
* Authors : Joe BLOGGS
* Contact : someone@somewhere.com
* Webpage : http:://www.example.fr
* Version : v2.r727
ERROR: [./chr.alignments.snp.strand.exclude] is impossible to open, check file existence or reading permissions
I have the following files in my root directory for chromosome 2 with full permissions:
chr2.alignments.log
chr2.alignments.snp.strand
chr2.alignments.snp.strand.exclude
chr2.unphased.bed
chr2.unphased.bim
chr2.unphased.fam
chr2.unphased.log
My shell script is clearly reading the chr2.unphased.fam/bed/bim files, but not my chr2.alignments.snp.strand.exclude. Any ideas why this is? Thanks for any help.