AutoMap_v1.2.sh: line 326: [: : integer expression expected

[tugcebb]

Hi,

I have installed all prerequisites with the latest versions and tried to use the command below:

(automap_analysis) tugcebozkurt@x86_64-apple-darwin13 AutoMap-master % bash AutoMap_v1.2.sh --vcf ../family_2311713/vcf/62524530_PASS_only.vcf --out 62524530 --genome hg19
# bcftools higher or equal to v1.9
# bedtools higher or equal to v2.24.0
# perl higher or equal to v5.22.0
# R higher or equal to v3.2.0
## Parameters used by default:
 -> No use of --DP option, value set as default: 8
 -> No use of --binomial option, value set as default: 0.000001
 -> No use of --percaltlow option, value set as default: 0.25
 -> No use of --percalthigh option, value set as default: 0.75
 -> No use of --window option, value set as default: 7
 -> No use of --windowthres option, value set as default: 5
 -> No use of --minsize option, value set as default: 1
 -> No use of --minvar option, value set as default: 25
 -> No use of --minperc option, value set as default: 88
 -> No use of --maxgap option, value set as default: 10
 -> chrX will NOT be included in the analysis and in the graphics.
 -> Homozygosity regions will be extended to nearest variant with maximum of 1 Mb.
AutoMap_v1.2.sh: line 326: [: : integer expression expected

1) Parsing of VCF file and variant filtering
 *  4186573 variants before filtering
 *  1842046 variants after filtering

2) Detection of ROHs with sliding window, trimming and extension
 * Treatment of the data
 * Printing of the homozygous regions

3) Filtering of regions found and output to text file
 *        0 regions before filtering
 *        0 regions after filtering with 0 Mb in total

4) Generating PDF

But, the output could not be generated and I don't know why. It may be related to line 326 as implied in the above (AutoMap_v1.2.sh: line 326: [: : integer expression expected). Btw, I got the same problem when I used the test data you provided. Then I tried to run the same code on a Windows computer then it worked without any problem.

Thank you in advance! Tugce

[mquinodo]

Dear Tugce, I apologise for the late answer. It seems the problem comes from the OS. AutoMap has only been tested on Linux and therefore the problem should come from the Mac OS you are using. Best, Mathieu

[tugcebb]

Thank you for your reply, Mathieu. I hope this issue will be solved in the future.