cn-1046
USER_NAME=thomasgrnbk
TYPE=RNAseq
SLAM=N
BASE_FOLDER=/faststorage/project/PAN_illumina/results/
FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-R17585_dKD_TOsK_piwiaub_GEO/
FOLDER_NAME=R17585_dKD_TOsK_piwiaub_GEO
RUNname=2026-03-18-R17585_dKD_TOsK_piwiaub_GEO
TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-R17585_dKD_TOsK_piwiaub_GEO/
LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/
SINGULARITYdir=/home/thomasgrnbk/AP_singu/
downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/
DEBUG=N
VERSION=r6.63
asmHUBpath=
ASMdir=
ASMname=
DEMUXonly=N
BAM=N
fwADAPTOR=
rvADAPTOR=
N_TRIMM=
rawPAIRED=N
onlyPAIRED=N
FASTQout=N
FASTQoutRAW=N
SUBSAMPLE=
MIN_LENGTH=18
MAX_LENGTH=1000
RAW=
TRIMM=Y
FIRST=6
LAST=200
INVERT=N
Ychrom=N
RANDOMmulti=N
MM=2
FILTERING_INPUT=rRNA:tRNA:mito
WIG=Y
WIG_FASTA=
spikeINnorm=N
noNORM=
EXTEND=0
COMPUTING=C
GRIDsystem=SLURM
keepTMP=N
SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-R17585_dKD_TOsK_piwiaub_GEO/script-files/
BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/
UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/
RELEASE=
VERSION=r6.63
UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/
nFILES=4
FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-R17585_dKD_TOsK_piwiaub_GEO/files.txt
FOLDER_NAME=R17585_dKD_TOsK_piwiaub_GEO
GENOME_VERSION=dm6
subCOLOR=0~128~0
FORCE=
SYSTEM=EXTERN
LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-R17585_dKD_TOsK_piwiaub_GEO/LOGs/
prepareREF=no
nSPLITS=1000000
SE=N
SE2nd=
maxCOUNT=1000000
demuxFASTA=N
autoViewLimits=
only5end=
PingPong=
DGE=N
GEO=
noSTRANDED=
FORCEimport=
exportBAM=N
exportBAMuncollapsed=N
exportSalmon=N
RATIOtracks=N
GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/
newCOLLECTION=N
prepANNOTATIONgff=
prepGENOMEfasta=
prepTRANSCRIPTOMEfasta=
prepCDSfasta=
prepNCRNAfasta=
extraSEQ=
FORCEquant_unstranded=N
refGENO=none
GENO=none
Nexec=1
2
[1] "argmat"  "args"    "DGE"     "FOLDER"  "GENO"    "i"       "Nexec"  
[8] "refGENO" "TMP"    
[1] 1.0229662 1.0092751 0.9735939 0.9948356
0.216667