fst-sliding.pl errors

[GoogleCodeExporter]

What steps will reproduce the problem?
1. when running fst-sliding.pl with command line 'perl 
tools/popoolation2_1201/fst-sliding.pl --input H-J.sync --output 
analysis2/H-J.fst --suppress-noninformative --min-coverage 10 --max-coverage 2% 
--min-covered-fraction 1 --window-size 1 --step-size 1 --pool-size 60'

bwa 0.7.8, samtools 0.1.19, picard 1.123 (sort and markduplicates) were used to 
generate a mpileup file.

What is the expected output? What do you see instead?

I got these lines on screen:
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 5.
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 6.
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 6.
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 7.
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 7.
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 8.
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 8.
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 9.
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 9.
Use of uninitialized value in numeric gt (>) at 
/state/partition1/home/zhoucc/tools/popoolation2_1201/Modules/Synchronized.pm 
line 105, <$ifh> line 10.
...
these lines showed very fast and the output file was empty.

My sync file looks normal:
null
null
chr01   1000    N       0:0:1:0:0:0     0:0:1:0:0:0
chr01   1001    C       0:0:7:0:0:0     0:0:8:0:0:0
chr01   1002    T       0:13:0:0:0:0    0:13:0:0:0:0
chr01   1003    A       18:0:0:0:0:0    16:1:0:0:0:0
chr01   1004    A       24:0:0:0:0:0    20:0:0:0:0:0
chr01   1005    A       24:0:0:0:0:0    23:0:0:0:0:0
chr01   1006    C       0:0:28:0:0:0    0:0:27:0:0:0
chr01   1007    C       0:0:30:0:0:0    0:0:31:0:0:0
chr01   1008    C       0:0:30:0:0:0    0:0:32:0:0:0
chr01   1009    T       0:30:0:0:0:0    0:32:0:0:0:0
chr01   1010    A       30:0:0:0:0:0    35:1:0:0:0:0
chr01   1011    A       31:0:0:0:0:0    34:0:0:0:0:0
chr01   1012    A       31:0:0:0:0:0    33:0:0:0:0:0
chr01   1013    C       0:0:32:0:0:0    0:0:40:0:0:0
chr01   1014    C       0:0:33:0:0:0    0:0:42:0:0:0
chr01   1015    C       0:0:33:0:0:0    0:0:43:0:0:0
chr01   1016    T       0:33:0:0:0:0    0:41:0:0:0:0

What version of the product are you using? On what operating system?
I used popoolation2_1201 on CentOS release 5.9.

Thanks for your help!

Original issue reported on code.google.com by CCzhou1...@gmail.com on 3 Nov 2014 at 1:23

[GoogleCodeExporter]

the problem is your sync file, its not normal
there are the null entries inside
this means that you probably used the wrong quality encoding when creating the 
sync file,
you used illumina no? your file is probably sanger

Original comment by RoKof...@gmail.com on 24 Jan 2015 at 10:49