Issues with pipeline taking cfg file

[remyakoshy]

I have made a cfg file specifying my system paths and requirements, the error shows is

2016-11-21 03:19:33,081 ancestral_allele path = not locatable path or in the directory specified in your config
2016-11-21 03:19:33,082 ancestral_allele_script not found check config file

Attaching the cfg file

sam.txt

Please consider this query asap,
Thanks in advance

[murraycadzow]

Hi @remyakoshy,

could you provide the result of running "ls /home/sam.k/archive/tools_rem/selectionTools-master/referencefiles/ancestral_ref/" in your terminal

thanks
Murray

[remyakoshy]

Thanks for the response, please find the list

ANCESTRAL.rst human_ancestor_18.bed human_ancestor_4.fa
human_ancestor_10.bed human_ancestor_18.fa human_ancestor_4.fa.flat
human_ancestor_10.fa human_ancestor_18.fa.flat human_ancestor_4.fa.gdx
human_ancestor_10.fa.flat human_ancestor_18.fa.gdx human_ancestor_5.bed
human_ancestor_10.fa.gdx human_ancestor_19.bed human_ancestor_5.fa
human_ancestor_11.bed human_ancestor_19.fa human_ancestor_5.fa.flat
human_ancestor_11.fa human_ancestor_19.fa.flat human_ancestor_5.fa.gdx
human_ancestor_11.fa.flat human_ancestor_19.fa.gdx human_ancestor_6.bed
human_ancestor_11.fa.gdx human_ancestor_1.bed human_ancestor_6.fa
human_ancestor_12.bed human_ancestor_1.fa human_ancestor_6.fa.flat
human_ancestor_12.fa human_ancestor_1.fa.flat human_ancestor_6.fa.gdx
human_ancestor_12.fa.flat human_ancestor_1.fa.gdx human_ancestor_7.bed
human_ancestor_12.fa.gdx human_ancestor_20.bed human_ancestor_7.fa
human_ancestor_13.bed human_ancestor_20.fa human_ancestor_7.fa.flat
human_ancestor_13.fa human_ancestor_20.fa.flat human_ancestor_7.fa.gdx
human_ancestor_13.fa.flat human_ancestor_20.fa.gdx human_ancestor_8.bed
human_ancestor_13.fa.gdx human_ancestor_21.bed human_ancestor_8.fa
human_ancestor_14.bed human_ancestor_21.fa human_ancestor_8.fa.flat
human_ancestor_14.fa human_ancestor_21.fa.flat human_ancestor_8.fa.gdx
human_ancestor_14.fa.flat human_ancestor_21.fa.gdx human_ancestor_9.bed
human_ancestor_14.fa.gdx human_ancestor_22.bed human_ancestor_9.fa
human_ancestor_15.bed human_ancestor_22.fa human_ancestor_9.fa.flat
human_ancestor_15.fa human_ancestor_22.fa.flat human_ancestor_9.fa.gdx
human_ancestor_15.fa.flat human_ancestor_22.fa.gdx human_ancestor_all.fa
human_ancestor_15.fa.gdx human_ancestor_2.bed human_ancestor_X.bed
human_ancestor_16.bed human_ancestor_2.fa human_ancestor_X.fa
human_ancestor_16.fa human_ancestor_2.fa.flat human_ancestor_Y.bed
human_ancestor_16.fa.flat human_ancestor_2.fa.gdx human_ancestor_Y.fa
human_ancestor_16.fa.gdx human_ancestor_3.bed README
human_ancestor_17.bed human_ancestor_3.fa README.txt
human_ancestor_17.fa human_ancestor_3.fa.flat summary.txt
human_ancestor_17.fa.flat human_ancestor_3.fa.gdx
human_ancestor_17.fa.gdx human_ancestor_4.bed

[murraycadzow]

The first thing I can think of would be to try removing the / from the end of the ancestral_fasta_dir and seeing if that helps - it's the only clear difference I can spot when comparing with my own config file

Murray

[remyakoshy]

Didnt help.. ANCESTRAL.rst is 0b, does that matter?

[murraycadzow]

ANCESTRAL.rst is a file that we create as a placeholder to indicate where files should go and doesn't affect anything.

Could you paste the command you used to run the pipeline?

[remyakoshy]

./selection_pipeline -i input.vcf --population pop --config-file /home/sam.k/archive/tools_rem/selectionTools-master/sam.cfg --cores 1 --no-gmap

[remyakoshy]

one more doubt, if it is already spitted vcf file(by chromosome), then it has to be written TRUE or FALSE in cfg file

[murraycadzow]

can you try run with an added "-c <chr>" where <chr> is the chromosome number. The -c argument is required.

The split by chromosome is true if you have separate ancestral files for each chromosome as you do. It's false if you have a single fasta containing all chromosomes

Murray

[remyakoshy]

Sure

[remyakoshy]

but if its not splitted then, how will we give -c argument

[murraycadzow]

Your input vcf file needs to be split by chromosome
so after splitting your input vcf file (you can use plink2, vcftools, or bcftools or some other method)
your command would look like for example on chr 1:
./selection_pipeline -i input_chr1.vcf --population pop --config-file /home/sam.k/archive/tools_rem/selectionTools-master/sam.cfg --cores 1 -c 1 --no-gmap

[remyakoshy]

okay. I will try this and get back to you.
Thanks

[remyakoshy]

./selection_pipeline -i ../tools_rem/selectionTools-master/natives_chr1.vcf --population hape --config-file /home/sam.k/archive/tools_rem/selectionTools-master/sam.cfg --cores 1 -c 1 --no-gmap -l hape.log

Same error sir

[murraycadzow]

When you install the pipeline it should automatically create a file called defaults.cfg
Is there a defaults.cfg in your selectionTools-master directory? if so can you attach it please?