cn-1060
USER_NAME=thomasgrnbk
TYPE=RNAseq
SLAM=N
BASE_FOLDER=/faststorage/project/PAN_illumina/results/
FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/
FOLDER_NAME=MTD_vs_TOsK_RNAseq
RUNname=2025-10-21-MTD_vs_TOsK_RNAseq
TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/
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=
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/2025-10-21-MTD_vs_TOsK_RNAseq/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=20
FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/files.txt
FOLDER_NAME=MTD_vs_TOsK_RNAseq
GENOME_VERSION=dm6
subCOLOR=0~128~0
FORCE=
SYSTEM=EXTERN
LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/LOGs/
prepareREF=no
nSPLITS=1000000
SE=N
SE2nd=
maxCOUNT=1000000
demuxFASTA=N
autoViewLimits=
only5end=
PingPong=
DGE=N
GEO=
noSTRANDED=
FORCEimport=
exportBAM=N
exportBAMuncollapsed=N
RATIOtracks=N
GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/
newCOLLECTION=N
prepANNOTATIONgff=
prepGENOMEfasta=
prepTRANSCRIPTOMEfasta=
prepCDSfasta=
prepNCRNAfasta=
refGENO=none
GENO=none
Nexec=1
2
[1] "argmat"  "args"    "DGE"     "FOLDER"  "GENO"    "i"       "Nexec"  
[8] "refGENO" "TMP"    
 [1] 0.9801075 1.0087336 1.0233773 1.0036011 1.0140933 0.9906142 0.9881738
 [8] 0.9555123 0.9954556 0.9750399 1.0448928 1.0085358 1.0021332 0.9805619
[15] 1.0000554 1.0105668 0.9919163 1.0320495 0.9908946 1.0076296
1.03333