Entering edit mode
7.4 years ago
Niek De Klein
★
2.6k
I am trying to run Shapeit -call function. However, it gives me the error chr_1.haps.gz is impossible to open, check file existence or reading permissions
. I have set the file permissions completely open and checked that the file exists: ll chr_1.haps.gz
-rwxrwxrwx 1 ndeklein group 8694707 Nov 24 10:40 chr_1.haps.gz
. I also tried using the unzipped version of the file, but this gives the same error.
What am I doing wrong in the below command that it isn't able to open an existing file with full permissions?
shapeit -call \
--input-gen genotype.beagle.genotype.probs.gg.gen.gz \
genotype.chr1.beagle.genotype.probs.gg.gen.sample
--input-init hap.chr1.beagle.genotype.probs.gg.hap.gz \
sample.chr1.beagle.genotype.probs.gg.hap.sample \
--input-map genetic_map_chr1_combined_b37.txt \
--input-scaffold chr_1.haps.gz \
chr1.sample \
--input-thr 1.0 \
--thread 8 \
--window 0.1 \
--states 400 \
--states-random 200 \
--burn 0 \
--run 12 \
--prune 4 \
--main 20 \
--output-max hap.chr1_1_10500000.shapeit.phased.hap.gz \
sample.chr1_1_10500000.shapeit.phased.hap.gz.sample \
--output-log log.chr1_1_10500000.shapeit.phased.log \
--input-from 1 \
--input-to 10500000