cn-1040
USER_NAME=thomasgrnbk
TYPE=sRNAseq
SLAM=N
BASE_FOLDER=/faststorage/project/PAN_illumina/results/
FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2024-03-21-sRNAseq_HsBam_10Muniqnorm/
FOLDER_NAME=sRNAseq_HsBam_10Muniqnorm
RUNname=2024-03-21-sRNAseq_HsBam_10Muniqnorm
TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2024-03-21-sRNAseq_HsBam_10Muniqnorm/
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=r6.40
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=
FIRST=1
LAST=1000
INVERT=N
Ychrom=N
RANDOMmulti=N
MM=0
FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA
WIG=Y
WIG_FASTA=
spikeINnorm=N
noNORM=
EXTEND=0
COMPUTING=C
GRIDsystem=SLURM
keepTMP=N
SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2024-03-21-sRNAseq_HsBam_10Muniqnorm/script-files/
BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/
UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/
RELEASE=
VERSION=r6.40
UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/
nFILES=20
FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2024-03-21-sRNAseq_HsBam_10Muniqnorm/files.txt
FOLDER_NAME=sRNAseq_HsBam_10Muniqnorm
GENOME_VERSION=dm6
subCOLOR=0~0~0
FORCE=
SYSTEM=EXTERN
LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2024-03-21-sRNAseq_HsBam_10Muniqnorm/LOGs/
prepareREF=no
nSPLITS=1000000
SE=N
SE2nd=
maxCOUNT=1000000
demuxFASTA=N
autoViewLimits=
only5end=
PingPong=
DGE=
GEO=
noSTRANDED=
FORCEimport=
exportBAM=N
exportBAMuncollapsed=N
RATIOtracks=N
GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/
newCOLLECTION=N
2
/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2024-03-21-sRNAseq_HsBam_10Muniqnorm/
[1] "argmat"  "args"    "FILE"    "i"       "OUTdir"  "PLOTdir" "TMP"    
[1] "argmat"   "args"     "CATEGORY" "FOLDER"   "i"        "PLOTdir"  "TMP"     
 [1] length                                               
 [2] sRNAseq_HsBam_ControlKD_00hAHS_repA_283079_sRBC_CAGTG
 [3] sRNAseq_Ovaries_MTD_ControlKD_repE_283083_sRBC_ATGGA 
 [4] sRNAseq_HsBam_PiwiKD_00hAHS_repA_283079_sRBC_GGTAT   
 [5] sRNAseq_HsBam_ControlKD_68hAHS_repA_283079_sRBC_AGCAA
 [6] sRNAseq_HsBam_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT   
 [7] sRNAseq_Ovaries_MTD_PiwiKD_repE_283083_sRBC_ACGAG    
 [8] sRNAseq_HsBam_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
 [9] sRNAseq_Ovaries_MTD_PiwiKD_repF_283083_sRBC_CTGAT    
[10] sRNAseq_HsBam_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
[11] sRNAseq_Ovaries_MTD_ControlKD_repF_283083_sRBC_GAACG 
[12] sRNAseq_HsBam_PiwiKD_68hAHS_repC_283081_sRBC_TACCA   
[13] sRNAseq_HsBam_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA   
[14] sRNAseq_HsBam_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC   
[15] sRNAseq_HsBam_PiwiKD_68hAHS_repA_283079_sRBC_TACCA   
[16] sRNAseq_HsBam_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC   
[17] sRNAseq_HsBam_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
[18] sRNAseq_HsBam_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
[19] sRNAseq_HsBam_ControlKD_68hAHS_repD_283082_sRBC_TGACT
[20] sRNAseq_HsBam_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA   
[21] sRNAseq_HsBam_ControlKD_68hAHS_repB_283080_sRBC_TGACT
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[1] length   variable value   
<0 rows> (or 0-length row.names)
[1] "argmat"   "args"     "CATEGORY" "FOLDER"   "i"        "PLOTdir"  "TMP"     
 [1] length                                               
 [2] sRNAseq_HsBam_ControlKD_00hAHS_repA_283079_sRBC_CAGTG
 [3] sRNAseq_Ovaries_MTD_ControlKD_repE_283083_sRBC_ATGGA 
 [4] sRNAseq_HsBam_PiwiKD_00hAHS_repA_283079_sRBC_GGTAT   
 [5] sRNAseq_HsBam_ControlKD_68hAHS_repA_283079_sRBC_AGCAA
 [6] sRNAseq_HsBam_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT   
 [7] sRNAseq_Ovaries_MTD_PiwiKD_repE_283083_sRBC_ACGAG    
 [8] sRNAseq_HsBam_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
 [9] sRNAseq_Ovaries_MTD_PiwiKD_repF_283083_sRBC_CTGAT    
[10] sRNAseq_HsBam_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
[11] sRNAseq_Ovaries_MTD_ControlKD_repF_283083_sRBC_GAACG 
[12] sRNAseq_HsBam_PiwiKD_68hAHS_repC_283081_sRBC_TACCA   
[13] sRNAseq_HsBam_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA   
[14] sRNAseq_HsBam_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC   
[15] sRNAseq_HsBam_PiwiKD_68hAHS_repA_283079_sRBC_TACCA   
[16] sRNAseq_HsBam_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC   
[17] sRNAseq_HsBam_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
[18] sRNAseq_HsBam_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
[19] sRNAseq_HsBam_ControlKD_68hAHS_repD_283082_sRBC_TGACT
[20] sRNAseq_HsBam_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA   
[21] sRNAseq_HsBam_ControlKD_68hAHS_repB_283080_sRBC_TGACT
<0 rows> (or 0-length row.names)
[1] length   variable value   
<0 rows> (or 0-length row.names)
[1] "argmat"   "args"     "CATEGORY" "FOLDER"   "i"        "PLOTdir"  "TMP"     
 [1] length                                               
 [2] sRNAseq_HsBam_ControlKD_00hAHS_repA_283079_sRBC_CAGTG
 [3] sRNAseq_Ovaries_MTD_ControlKD_repE_283083_sRBC_ATGGA 
 [4] sRNAseq_HsBam_PiwiKD_00hAHS_repA_283079_sRBC_GGTAT   
 [5] sRNAseq_HsBam_ControlKD_68hAHS_repA_283079_sRBC_AGCAA
 [6] sRNAseq_HsBam_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT   
 [7] sRNAseq_Ovaries_MTD_PiwiKD_repE_283083_sRBC_ACGAG    
 [8] sRNAseq_HsBam_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
 [9] sRNAseq_Ovaries_MTD_PiwiKD_repF_283083_sRBC_CTGAT    
[10] sRNAseq_HsBam_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
[11] sRNAseq_Ovaries_MTD_ControlKD_repF_283083_sRBC_GAACG 
[12] sRNAseq_HsBam_PiwiKD_68hAHS_repC_283081_sRBC_TACCA   
[13] sRNAseq_HsBam_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA   
[14] sRNAseq_HsBam_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC   
[15] sRNAseq_HsBam_PiwiKD_68hAHS_repA_283079_sRBC_TACCA   
[16] sRNAseq_HsBam_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC   
[17] sRNAseq_HsBam_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
[18] sRNAseq_HsBam_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
[19] sRNAseq_HsBam_ControlKD_68hAHS_repD_283082_sRBC_TGACT
[20] sRNAseq_HsBam_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA   
[21] sRNAseq_HsBam_ControlKD_68hAHS_repB_283080_sRBC_TGACT
<0 rows> (or 0-length row.names)
[1] length   variable value   
<0 rows> (or 0-length row.names)
[1] "argmat"   "args"     "CATEGORY" "FOLDER"   "i"        "PLOTdir"  "TMP"     
 [1] length                                               
 [2] sRNAseq_HsBam_ControlKD_00hAHS_repA_283079_sRBC_CAGTG
 [3] sRNAseq_Ovaries_MTD_ControlKD_repE_283083_sRBC_ATGGA 
 [4] sRNAseq_HsBam_PiwiKD_00hAHS_repA_283079_sRBC_GGTAT   
 [5] sRNAseq_HsBam_ControlKD_68hAHS_repA_283079_sRBC_AGCAA
 [6] sRNAseq_HsBam_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT   
 [7] sRNAseq_Ovaries_MTD_PiwiKD_repE_283083_sRBC_ACGAG    
 [8] sRNAseq_HsBam_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
 [9] sRNAseq_Ovaries_MTD_PiwiKD_repF_283083_sRBC_CTGAT    
[10] sRNAseq_HsBam_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
[11] sRNAseq_Ovaries_MTD_ControlKD_repF_283083_sRBC_GAACG 
[12] sRNAseq_HsBam_PiwiKD_68hAHS_repC_283081_sRBC_TACCA   
[13] sRNAseq_HsBam_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA   
[14] sRNAseq_HsBam_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC   
[15] sRNAseq_HsBam_PiwiKD_68hAHS_repA_283079_sRBC_TACCA   
[16] sRNAseq_HsBam_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC   
[17] sRNAseq_HsBam_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
[18] sRNAseq_HsBam_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
[19] sRNAseq_HsBam_ControlKD_68hAHS_repD_283082_sRBC_TGACT
[20] sRNAseq_HsBam_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA   
[21] sRNAseq_HsBam_ControlKD_68hAHS_repB_283080_sRBC_TGACT
<0 rows> (or 0-length row.names)
[1] length   variable value   
<0 rows> (or 0-length row.names)
[1] "argmat"   "args"     "CATEGORY" "FOLDER"   "i"        "PLOTdir"  "TMP"     
 [1] length                                               
 [2] sRNAseq_HsBam_ControlKD_00hAHS_repA_283079_sRBC_CAGTG
 [3] sRNAseq_Ovaries_MTD_ControlKD_repE_283083_sRBC_ATGGA 
 [4] sRNAseq_HsBam_PiwiKD_00hAHS_repA_283079_sRBC_GGTAT   
 [5] sRNAseq_HsBam_ControlKD_68hAHS_repA_283079_sRBC_AGCAA
 [6] sRNAseq_HsBam_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT   
 [7] sRNAseq_Ovaries_MTD_PiwiKD_repE_283083_sRBC_ACGAG    
 [8] sRNAseq_HsBam_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
 [9] sRNAseq_Ovaries_MTD_PiwiKD_repF_283083_sRBC_CTGAT    
[10] sRNAseq_HsBam_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
[11] sRNAseq_Ovaries_MTD_ControlKD_repF_283083_sRBC_GAACG 
[12] sRNAseq_HsBam_PiwiKD_68hAHS_repC_283081_sRBC_TACCA   
[13] sRNAseq_HsBam_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA   
[14] sRNAseq_HsBam_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC   
[15] sRNAseq_HsBam_PiwiKD_68hAHS_repA_283079_sRBC_TACCA   
[16] sRNAseq_HsBam_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC   
[17] sRNAseq_HsBam_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
[18] sRNAseq_HsBam_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
[19] sRNAseq_HsBam_ControlKD_68hAHS_repD_283082_sRBC_TGACT
[20] sRNAseq_HsBam_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA   
[21] sRNAseq_HsBam_ControlKD_68hAHS_repB_283080_sRBC_TGACT
<0 rows> (or 0-length row.names)
[1] length   variable value   
<0 rows> (or 0-length row.names)
/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2024-03-21-sRNAseq_HsBam_10Muniqnorm/TMP/
/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2024-03-21-sRNAseq_HsBam_10Muniqnorm/TMP/
[1] "argmat"      "args"        "i"           "inALL"       "inANTISENSE"
[6] "inSENSE"     "OPENdir"     "TYPE"       
[1] "1360"
[1] "17.6"
[1] "1731"
[1] "297"
[1] "3S18"
[1] "412"
[1] "BS"
[1] "BS3"
[1] "BS4"
[1] "Bari1"
[1] "Bari2"
[1] "Burdock"
[1] "Circe"
[1] "Copia1"
[1] "Cr1a"
[1] "Dm88"
[1] "Doc"
[1] "Doc3-element"
[1] "Doc4-element"
[1] "Dsim_ninja"
[1] "F-element"
[1] "Fw2"
[1] "Fw3"
[1] "G-element"
[1] "G2"
[1] "G3"
[1] "G4"
[1] "G5"
[1] "G5A"
[1] "G6"
[1] "G7"
[1] "GATE"
[1] "HMS-Beagle"
[1] "HMS-Beagle2"
[1] "HeT-A"
[1] "Helena"
[1] "Helitron"
[1] "I-element_new"
[1] "INE-1"
[1] "Idefix"
[1] "Ivk"
[1] "Juan"
[1] "Max-element"
[1] "McClintock"
[1] "NOF"
[1] "Osvaldo"
[1] "P-element"
[1] "Quasimodo"
[1] "R1-2"
[1] "R1A1-element"
[1] "R2-element"
[1] "Repbase_Bica"
[1] "Repbase_Chimpo"
[1] "Repbase_Chouto"
[1] "Repbase_DNAREP1"
[1] "Repbase_FB4"
[1] "Repbase_Rt1a"
[1] "Repbase_Rt1b"
[1] "Repbase_Transib1"
[1] "Rt1c"
[1] "S-element"
[1] "S2"
[1] "Stalker"
[1] "Stalker2"
[1] "TAHRE"
[1] "TART-A"
[1] "Tabor"
[1] "Tc1"
[1] "Tc1-2"
[1] "Tc3"
[1] "Tirant"
[1] "Transib5"
[1] "Transpac"
[1] "X-element"
[1] "ZAM"
[1] "accord"
[1] "accord2_new"
[1] "baggins"
[1] "blood"
[1] "copia"
[1] "diver"
[1] "diver2"
[1] "flea"
[1] "frogger"
[1] "gtwin"
[1] "gypsy"
[1] "gypsy10_new"
[1] "gypsy11"
[1] "gypsy12"
[1] "gypsy2_new"
[1] "gypsy3_new"
[1] "gypsy4"
[1] "gypsy5"
[1] "gypsy6_new"
[1] "gypsy7_new"
[1] "gypsy8"
[1] "gypsy9_new"
[1] "hobo"
[1] "hopper"
[1] "hopper2"
[1] "invader1"
[1] "invader2"
[1] "invader3"
[1] "invader4"
[1] "invader5"
[1] "invader6"
[1] "jockey"
[1] "jockey2"
[1] "looper1"
[1] "mariner2"
[1] "mdg1"
[1] "mdg3"
[1] "micropia"
[1] "opus"
[1] "pogo"
[1] "roo"
[1] "rooA"
[1] "rover"
[1] "springer"
[1] "transib2"
[1] "transib3"
[1] "transib4"