[Cortexassembler-variation] error with wrapper

[astrid b. <ast...@un...>]

Dear Zam,
I am trying to run cortex and posted to the google group, however, my 
post does not go online and I am somewhat stuck with the program.
I ran the following on a compute cluster with cortex compiled for k31 
and 11 colors.
module load cortex_var/1.0.5.21-goolf-1.7.20_31_c11
module load VCFtools/0.1.14-goolf-1.4.10-Perl-5.16.3
module load Stampy/1.0.23-goolf-1.4.10

cd $EBROOTCORTEX_VAR/scripts/calling
./run_calls.pl \
--first_kmer 31 \
--auto_cleaning yes \
--bc yes \
--pd no \
--outdir $HOME/Ambizione/Pseudocrenilabrus/cortex_var \
--outvcf Pseudocrenilabrus \
--logfile $HOME/Ambizione/Pseudocrenilabrus/cortex_var/logfile_Pseudocren \
--ref Absent \
--ploidy 2 \
--fastaq_index 
$HOME/Ambizione/Pseudocrenilabrus/cortex_var/Pseudocren_Index \
--mem_height 25 \
--mem_width 70 \
--vcftools_dir $EBROOTVCFTOOLS \
--genome_size 1000000000 \
--do_union yes \
--workflow joint \
--squeeze_mem

I get this error
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 1.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 1.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 1.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 1.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 1.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 1.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 1.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 1.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 1.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 2.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 2.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 2.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 2.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 2.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 2.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 2.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 2.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 2.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 3.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 3.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 3.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 3.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 3.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 3.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 3.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 3.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 3.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 4.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 4.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 4.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 4.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 4.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 4.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 4.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 4.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 4.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 5.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 5.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 5.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 5.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 5.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 5.
Use of uninitialized value $file in string eq at ./run_calls.pl line 
1976, <SAM> line 5.
Use of uninitialized value $file in concatenation (.) or string at 
./run_calls.pl line 1982, <SAM> line 5.
Use of uninitialized value $file in regexp compilation at ./run_calls.pl 
line 1984, <SAM> line 5.
Abort - please go and compile 
/scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11//bin/cortex_var_31_c1

Any help would be appreciated
Best
Astrid

-- 
Astrid Böhne
Universität Basel
Zoologisches Institut
Evolutionsbiologie
Vesalgasse 1
CH-4051 Basel
Switzerland
Phone +41 (0)61 207 03 05
Fax +41 (0) 61 207 03 01