uninitialized value $file

[astrid...@unibas.ch]

Hi
I encountered the following error with cortex_var compiled for 11 colours and K31
uninitialized value $file in several lines of run_calls.pl.
Here is how I ran the program. The output directories were created but are all empty. I post the full error message below. Sorry for double posting if this appears in double, I had some trouble with my google account.
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

Best
Astrid





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

[astrid...@unibas.ch]

Hi
is there any update on this?
I would still like to run cortex if it is possible
Best
Astrid

[Zamin Iqbal]

Hi Astrid

Sorry for the slow reply. You have compiled for 11 colours, but you need also to compile for 1 colour. The last line of the error message was meant to be informative but sadly did not help

"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"

Try that and let us know if it helps?

regards

Zam

[astrid boehne]

Hi Zam
We had it compiled for c11 and c1, we put both binaries together in one directory but I still get the same error.
And to me it looks like the major issue is an undefined variable in a perl script?
Maybe it is just the wrapper that does not work for us? Although I have to say using the wrapper would be ideal.
Thanks for getting back to me and any further help is appreciated. The error message remains as before
(See below for completeness)
Cheers

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

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

[Zamin Iqbal]

Astrid

That variable is undefined because the wrapper is failing to get the contents of your index file (listing samples and fastq-lists).

Is it possible the file has one line and no carriage-return? If yes, can you add a carriage return?  That was a bug, which has since been fixed on github

Z

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[astrid boehne]

Hi Zam
there was indeed an issue with the index file. Now it went a step further, telling from the log file
But then I get this error
Unable to build /scicore/home/salzburg/boehne/Ambizione/Pseudocrenilabrus/cortex_var/binaries/uncleaned/31/MJC1.unclean.kmer31.ctx at /scicore/home/salzburg/boehne/applications/cortex/scripts/calling/run_calls.pl line 2139.
Would it better not to use the wrapper?
Thanks for your continued help.
Best
Astrid

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