FID	IID	CLUSTER
HeliagrossG5_11_4	1	gross
HeliagrossG9_9_4	1	ang
HeliavertA5_11_7	1	vert
HeliavertE11_9_8	1	miss
HeliavertE12_9_5	1	miss
HeliavertG2_9_3	1	vert
HeliavertG3_9_7	1	vert
HeliavertG4_9_6	1	miss
HeliavertH12_11_3	1	miss

WRAPPER: Zipping advanced arguments onto basic ones

        -> angsd version: 0.911-44-g1c0ebb6 (htslib: 1.3.1-30-gbb03b02) build(Oct 31 2021 11:04:52)
        -> Reading fasta: /mnt/steelhead/remote/Sophie/Programs/angsd-wrapper/Example_Data/Sequences/Tripsacum_TDD39103.fa
        -> Reading fasta: /mnt/steelhead/remote/Sophie/Programs/angsd-wrapper/Example_Data/Sequences/Zea_mays.AGPv3.30.dna_sm.chromosome.10.fa
        -> (Using Filipe G Vieira modification of: abcSaf.cpp)
        -> Parsing 11 number of samples
        -> Region lookup 1/1

        -> We have now allocated approximately 10 Megabytes of raw nodes to the nodepool
        -> Printing at chr: 10 pos:17551496 chunknumber 1100
        -> We have now allocated approximately 20 Megabytes of raw nodes to the nodepool
        -> Printing at chr: 10 pos:19386992 chunknumber 2000 [emFrequency_F] caught nan will not exit
logLike (3*nInd). nInd=11
keepList (nInd)
used logLike (3*length(keep))=11
        -> Printing at chr: 10 pos:22395913 chunknumber 3200 [emFrequency_F] caught nan will not exit
logLike (3*nInd). nInd=11
keepList (nInd)
used logLike (3*length(keep))=10
[emFrequency_F] caught nan will not exit
logLike (3*nInd). nInd=11
keepList (nInd)
used logLike (3*length(keep))=10
[emFrequency_F] caught nan will not exit
logLike (3*nInd). nInd=11
keepList (nInd)
used logLike (3*length(keep))=10
        -> Printing at chr: 10 pos:24004662 chunknumber 3600 [emFrequency_F] caught nan will not exit
logLike (3*nInd). nInd=11
keepList (nInd)
used logLike (3*length(keep))=11
        -> Printing at chr: 10 pos:24908040 chunknumber 4000
        -> Done reading data waiting for calculations to finish
        -> Done waiting for threads

        -> npools:26 unfreed tnodes before clean:0
        -> Output filenames:
                ->"/mnt/steelhead/remote/Sophie/scratch/Maize/SFS/Maize_SFSOut.arg"
                ->"/mnt/steelhead/remote/Sophie/scratch/Maize/SFS/Maize_SFSOut.mafs.gz"
                ->"/mnt/steelhead/remote/Sophie/scratch/Maize/SFS/Maize_SFSOut.geno.gz"
                ->"/mnt/steelhead/remote/Sophie/scratch/Maize/SFS/Maize_SFSOut.saf.gz"
                ->"/mnt/steelhead/remote/Sophie/scratch/Maize/SFS/Maize_SFSOut.saf.pos.gz"
                ->"/mnt/steelhead/remote/Sophie/scratch/Maize/SFS/Maize_SFSOut.saf.idx"
        -> Sun Oct 31 12:08:56 2021
        -> Arguments and parameters for all analysis are located in .arg file
        [ALL done] cpu-time used =  199.08 sec
        [ALL done] walltime used =  130.00 sec
        -> Version of fname:/mnt/steelhead/remote/Sophie/scratch/Maize/SFS/Maize_SFSOut.saf.idx is:2
        -> Assuming .saf.gz file: /mnt/steelhead/remote/Sophie/scratch/Maize/SFS/Maize_SFSOut.saf.gz
        -> Assuming .saf.pos.gz: /mnt/steelhead/remote/Sophie/scratch/Maize/SFS/Maize_SFSOut.saf.pos.gz
        -> Problem opening file: '-fold'

#!/usr/bin/env bash

set -e
set -o pipefail

#   Load variables from supplied config file
source "$1"

#   Are we using Common_Config? If so, source it
if [[ -f "${COMMON}" ]]
then
    source "${COMMON}"
fi

#   Where is angsd-wrapper located?
SOURCE=$2

#   Where is ANGSD?
ANGSD_DIR=${SOURCE}/dependencies/angsd

#   Variables created from transforming other variables
#       The number of individuals in the taxon we are analyzing
N_IND=$(wc -l < "${SAMPLE_LIST}")
#       How many inbreeding coefficients are supplied?
N_F=$(wc -l < "${SAMPLE_INBREEDING}")
#       For ANGSD, the actual sample size is twice the number of individuals, since each individual has two chromosomes.
#       The individual inbreeding coefficents take care of the mismatch between these two numbers

#   Perform a check to see if number of individuals matches number of inbreeding coefficients
if [ "${N_IND}" -ne "${N_F}" ]
then
    echo "Mismatch between number of samples in ${SAMPLE_LIST} and ${SAMPLE_INBREEDING}"
    exit 1
fi

#   Check to see if ancestral state is supplied: If not, polarize samples using
#   the reference sequence and generate folded saf.
if [ ! -f "${ANC_SEQ}" ]
then
    echo "Ancestral state data not found, using reference sequence to polarize alignment data. BAQ will likewise not be calculated."
    if [ ! -f "${REF_SEQ}" ]
    then
        echo "No reference sequence supplied, unable to perform calculations."
        exit 2
    else
        ANC_SEQ=$REF_SEQ
        REF_SEQ=
        BAQ=0
        FOLD=1
    fi
else
    FOLD=0
fi

#   Create outdirectory
OUT="${SCRATCH}"/"${PROJECT}"/SFS
mkdir -p "${OUT}"

#   Now we actually run the command, this creates a binary file that contains the prior SFS
if [[ -f "${OUT}"/"${PROJECT}"_SFSOut.mafs.gz ]] && [ "$OVERRIDE" = "false" ]
then
    echo "WRAPPER:maf already exists and OVERRIDE=false, skipping angsd -bam..."
else
    #   Do we have a regions file?
    if [[ -f "${REGIONS}" ]]
    then
	WRAPPER_ARGS=$(echo -bam "${SAMPLE_LIST}" \
            -out "${OUT}"/"${PROJECT}"_SFSOut \
            -indF "${SAMPLE_INBREEDING}" \
            -doSaf "${DO_SAF}" \
            -uniqueOnly "${UNIQUE_ONLY}" \
            -anc "${ANC_SEQ}" \
            -minMapQ "${MIN_MAPQ}" \
            -minQ "${MIN_BASEQUAL}" \
            -nInd "${N_IND}" \
            -minInd "${MIN_IND}"\
            -baq "${BAQ}" \
            -ref "${REF_SEQ}" \
            -GL "${GT_LIKELIHOOD}" \
            -P "${N_CORES}" \
            -doMajorMinor "${DO_MAJORMINOR}" \
            -doMaf "${DO_MAF}" \
            -doGeno "${DO_GENO}" \
            -rf "${REGIONS}" \
            -doPost "${DO_POST}")
    #   Are we missing a definiton for regions?
    elif [[ -z "${REGIONS}" ]]
    then
	WRAPPER_ARGS=$(echo -bam "${SAMPLE_LIST}" \
            -out "${OUT}"/"${PROJECT}"_SFSOut \
            -indF "${SAMPLE_INBREEDING}" \
            -doSaf "${DO_SAF}" \
            -uniqueOnly "${UNIQUE_ONLY}" \
            -anc "${ANC_SEQ}" \
            -minMapQ "${MIN_MAPQ}" \
            -minQ "${MIN_BASEQUAL}" \
            -nInd "${N_IND}" \
            -minInd "${MIN_IND}"\
            -baq "${BAQ}" \
            -ref "${REF_SEQ}" \
            -GL "${GT_LIKELIHOOD}" \
            -P "${N_CORES}" \
            -doMajorMinor "${DO_MAJORMINOR}" \
            -doMaf "${DO_MAF}" \
            -doGeno "${DO_GENO}" \
            -doPost "${DO_POST}")
    #   Assuming a single region was defined in config file
    else
	WRAPPER_ARGS=$(echo -bam "${SAMPLE_LIST}" \
            -out "${OUT}"/"${PROJECT}"_SFSOut \
            -indF "${SAMPLE_INBREEDING}" \
            -doSaf "${DO_SAF}" \
            -uniqueOnly "${UNIQUE_ONLY}" \
            -anc "${ANC_SEQ}" \
            -folded "${FOLD}" \
            -minMapQ "${MIN_MAPQ}" \
            -minQ "${MIN_BASEQUAL}" \
            -nInd "${N_IND}" \
            -minInd "${MIN_IND}" \
            -baq "${BAQ}" \
            -ref "${REF_SEQ}" \
            -GL "${GT_LIKELIHOOD}" \
            -P "${N_CORES}" \
            -doMajorMinor "${DO_MAJORMINOR}" \
            -doMaf "${DO_MAF}" \
            -doGeno "${DO_GENO}" \
            -doPost "${DO_POST}" \
            -r "${REGIONS}")
    fi
fi
# Check for advanced arguments, and overwrite any overlapping definitions
FINAL_ARGS=($(source "${SOURCE}/Wrappers/Arg_Zipper.sh" "${WRAPPER_ARGS}" "${ADVANCED_ARGS}"))
# DEBUGGING
# echo "Wrapper arguments: ${WRAPPER_ARGS}" 1<&2
# echo -e "Final arguments:" ${FINAL_ARGS} 1<&2

"${ANGSD_DIR}"/angsd "${FINAL_ARGS[@]}"

"${ANGSD_DIR}"/misc/realSFS \
    "${OUT}"/"${PROJECT}"_SFSOut.saf.idx \
    -P "${N_CORES}" \
    -fold "${FOLD}" \
    > "${OUT}"/"${PROJECT}"_DerivedSFS.graph.me`

format.pval, units

zoom

dataTableOutput, renderDataTable

abcHWE.cpp: In member function ‘void abcHWE::HWE_EM(double*, double*, int)’:
abcHWE.cpp:272:8: error: ‘isnan’ was not declared in this scope
     if(isnan(newFreq1*0.5 + newFreq2)){
        ^~~~~
abcHWE.cpp:272:8: note: suggested alternative:
In file included from analysisFunction.h:6:0,
                 from abc.h:8,
                 from abcFreq.h:2,
                 from abcHWE.cpp:17:
/usr/include/c++/7/cmath:639:5: note:   ‘std::isnan’
     isnan(_Tp __x)
     ^~~~~
Makefile:47: recipe for target 'abcHWE.o' failed
make: *** [abcHWE.o] Error 1

stelo@H4:~/sw/angsd-wrapper$ sudo apt install libgeos-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libgeos-dev is already the newest version (3.6.2-1build2).

~/Desktop/programs/angsd-wrapper$ ./angsd-wrapper shiny graphing
angsd-wrapper running from /home/carlos/Desktop/programs/angsd-wrapper

Loading required package: methods
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:

    format.pval, units

Error: package or namespace load failed for ‘ape’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/carlos/Desktop/programs/angsd-wrapper/.RLibs/ape/libs/ape.so':
  libRlapack.so: cannot open shared object file: No such file or directory
Execution halted

~/Desktop/programs/angsd-wrapper$ ls /home/carlos/Desktop/programs/angsd-wrapper/.RLibs/ape/libs
ape.so

> install.packages('ape')
Installing package into ‘/home/carlos/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
...
* DONE (ape)

The downloaded source packages are in
	‘/tmp/RtmpgvgvS3/downloaded_packages’

export PATH="/home/carlos/R/x86_64-pc-linux-gnu-library/3.4/:$PATH"
export LD_LIBRARY_PATH=/home/carlos/Desktop/programs/angsd-wrapper/.RLibs/ape/libs/ape.so:${LD_LIBRARY_PATH}