cn-1040
USER_NAME=thomasgrnbk
TYPE=RNAseq
SLAM=N
BASE_FOLDER=/faststorage/project/PAN_illumina/results/
FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-09-19-RNAseq_Thomas_PolyA_HsBam_ov/
FOLDER_NAME=RNAseq_Thomas_PolyA_HsBam_ov
RUNname=2025-09-19-RNAseq_Thomas_PolyA_HsBam_ov
TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-09-19-RNAseq_Thomas_PolyA_HsBam_ov/
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/2025-09-19-RNAseq_Thomas_PolyA_HsBam_ov/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=23
FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-09-19-RNAseq_Thomas_PolyA_HsBam_ov/files.txt
FOLDER_NAME=RNAseq_Thomas_PolyA_HsBam_ov
GENOME_VERSION=dm6
subCOLOR=0~128~0
FORCE=
SYSTEM=EXTERN
LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-09-19-RNAseq_Thomas_PolyA_HsBam_ov/LOGs/
prepareREF=no
nSPLITS=1000000
SE=N
SE2nd=
maxCOUNT=1000000
demuxFASTA=N
autoViewLimits=
only5end=
PingPong=
DGE=Y
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=w_KD_Ov
GENO=w_KD_0h~m_KD_0h~m_KD_42h~m_KD_68h~p_KD_0h~p_KD_42h~p_KD_68h~p_KD_OV~w_KD_42h~w_KD_68h~w_KD_Ov
Nexec=1
2
[1] "argmat"  "args"    "DGE"     "FOLDER"  "GENO"    "i"       "Nexec"  
[8] "refGENO" "TMP"    
 [1] 1.0184332 1.0393174 0.9441003 1.0158363 1.0182714 0.9753030 0.9733505
 [8] 1.0551248 1.0725111 1.0318731 1.0059426 1.0584663 1.0650409 1.0388977
[15] 1.0480478 0.9815782 0.9755175 0.9981388 1.0013235 0.9530990 0.9107750
[22] 0.9320176 0.9128602
[1] "w_KD_0h" "m_KD_0h"
[1] "w_KD_0h"  "m_KD_42h"
[1] "w_KD_0h"  "m_KD_68h"
[1] "w_KD_0h" "p_KD_0h"
[1] "w_KD_0h"  "p_KD_42h"
[1] "w_KD_0h"  "p_KD_68h"
[1] "w_KD_0h" "p_KD_OV"
[1] "w_KD_0h"  "w_KD_42h"
[1] "w_KD_0h"  "w_KD_68h"
[1] "w_KD_0h" "w_KD_Ov"
[1] "m_KD_0h"  "m_KD_42h"
[1] "m_KD_0h"  "m_KD_68h"
[1] "m_KD_0h" "p_KD_0h"
[1] "m_KD_0h"  "p_KD_42h"
[1] "m_KD_0h"  "p_KD_68h"
[1] "m_KD_0h" "p_KD_OV"
[1] "m_KD_0h"  "w_KD_42h"
[1] "m_KD_0h"  "w_KD_68h"
[1] "m_KD_0h" "w_KD_Ov"
[1] "m_KD_42h" "m_KD_68h"
[1] "m_KD_42h" "p_KD_0h" 
[1] "m_KD_42h" "p_KD_42h"
[1] "m_KD_42h" "p_KD_68h"
[1] "m_KD_42h" "p_KD_OV" 
[1] "m_KD_42h" "w_KD_42h"
[1] "m_KD_42h" "w_KD_68h"
[1] "m_KD_42h" "w_KD_Ov" 
[1] "m_KD_68h" "p_KD_0h" 
[1] "m_KD_68h" "p_KD_42h"
[1] "m_KD_68h" "p_KD_68h"
[1] "m_KD_68h" "p_KD_OV" 
[1] "m_KD_68h" "w_KD_42h"
[1] "m_KD_68h" "w_KD_68h"
[1] "m_KD_68h" "w_KD_Ov" 
[1] "p_KD_0h"  "p_KD_42h"
[1] "p_KD_0h"  "p_KD_68h"
[1] "p_KD_0h" "p_KD_OV"
[1] "p_KD_0h"  "w_KD_42h"
[1] "p_KD_0h"  "w_KD_68h"
[1] "p_KD_0h" "w_KD_Ov"
[1] "p_KD_42h" "p_KD_68h"
[1] "p_KD_42h" "p_KD_OV" 
[1] "p_KD_42h" "w_KD_42h"
[1] "p_KD_42h" "w_KD_68h"
[1] "p_KD_42h" "w_KD_Ov" 
[1] "p_KD_68h" "p_KD_OV" 
[1] "p_KD_68h" "w_KD_42h"
[1] "p_KD_68h" "w_KD_68h"
[1] "p_KD_68h" "w_KD_Ov" 
[1] "p_KD_OV"  "w_KD_42h"
[1] "p_KD_OV"  "w_KD_68h"
[1] "p_KD_OV" "w_KD_Ov"
[1] "w_KD_42h" "w_KD_68h"
[1] "w_KD_42h" "w_KD_Ov" 
[1] "w_KD_68h" "w_KD_Ov" 
7.43333