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