problem with run_calls.pl Use of uninitialized value $file

[astrid...@unibas.ch]

Hi
I compiled cortex for K31 and 11 colours which worked fine
Using the following command however

perl $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 \
--ref Absent \
--ploidy 2 \
--fastaq_index Pseudocren_Index \
--mem_height 25 \
--mem_width 70 \
--vcftools_dir $EBROOTVCFTOOLS \
--genome_size 1000000000 \
--do_union yes \
--workflow joint \
--squeeze_mem

The output directories binaries calls and vcfs are created but all empty and
I get the following error messages. Any advice on what I might have overlooked here is appreciated. I used version 1.05.21
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 1.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 1.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 1.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 1.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 1.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 1.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 1.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 1.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 1.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 2.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 2.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 2.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 2.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 2.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 2.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 2.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 2.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 2.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 3.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 3.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 3.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 3.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 3.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 3.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 3.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 3.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 3.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 4.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 4.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 4.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 4.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 4.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 4.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 4.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 4.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 4.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 5.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 5.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 5.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 5.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 5.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 5.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 5.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 5.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 5.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 6.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 6.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 6.
Use of uninitialized value $name in hash element at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1947, <SAM> line 6.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 6.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 6.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 6.
Use of uninitialized value $file in string eq at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1976, <SAM> line 6.
Use of uninitialized value $file in concatenation (.) or string at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1982, <SAM> line 6.
Use of uninitialized value $file in regexp compilation at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1984, <SAM> line 6.
Use of uninitialized value $name in hash element at /scicore/soft/apps/cortex_var/1.0.5.21-goolf-1.7.20_31_c11/scripts/calling/run_calls.pl line 1967, <SAM> line 6.
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