* dDocentHPC v4.6 Forked by cbird@tamucc.edu * 


Running dDocentHPC mkBAM in OVERWRITE mode. \n          Sample names, file indexing, etc will be overwritten to clear errors...
 
Fri Dec 22 02:52:38 PM CET 2023 Files output to:  /UBT_genomics/Projekte/Baessler1/FK1/2_fastq_Ac/mkBAM

Fri Dec 22 02:52:38 PM CET 2023 Reading config file... 
 
Settings for dDocentHPC
#Made in notepad++, use for best viewing

These default settings assume ddRAD, no overlapping 151 bp reads

All		Number of Processors (Not Adjustable)
All		Free Memory (Not Adjustable)

----------trimFQ: Settings for Trimming FASTQ Files---------------------------------------------------------------
146		trimmomatic MINLEN (integer, mkREF only)						Drop the read if it is below a specified length. Set to the length of the Read1 reads.
75		trimmomatic MINLEN (integer, mkBAM only)						Drop the read if it is below a specified length. Set to the minimum frag length you want mapped to the reference.
20		trimmomatic LEADING:<quality> (integer, mkBAM only)				Specifies the minimum quality required to keep a base.
15		trimmomatic TRAILING:<quality> (integer, mkREF only)			Specifies the minimum quality required to keep a base.
20		trimmomatic TRAILING:<quality> (integer, mkBAM only)			Specifies the minimum quality required to keep a base.
TruSeq3-PE-2.fa	trimmomatic ILLUMINACLIP:<fasta> (0, fasta file name)			Specifies the trimmomatic adapter file to use. entering a 0 (zero) will turn off adapter trimming. Options are: TruSeq3-PE-2.fa, TruSeq3-PE.fa, TruSeq3-SE.fa, TruSeq2-PE.fa, TruSeq2-SE.fa, any other files included with trimmomatic.  Entering a custom path here will break the script. If you want a customized file, you have to put it where the default trimmomatic files are located on your computer.  If you have trouble finding this location, run dDocentHPC trimREF and it will be included in the output.
2		trimmomatic ILLUMINACLIP:<seed mismatches> (integer)			specifies the maximum mismatch count which will still allow a full match to be performed
30		trimmomatic ILLUMINACLIP:<palindrome clip thresh> (integer)		specifies how accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment
10		trimmomatic ILLUMINACLIP:<simple clip thresh> (integer)			specifies how accurate the match between any adapter etc. sequence must be against a read.
20		trimmomatic SLIDINGWINDOW:<windowSize> (integer)				specifies the number of bases to average across
20		trimmomatic SLIDINGWINDOW:<windowQuality> (integer)				specifies the average quality required.
0		trimmomatic CROP:<bp to keep> (integer, mkBAM only)    Trim read sequences down to this length. Enter 0 for no cropping
0		trimmomatic HEADCROP:<length> (integer, only Read1 for ezRAD)	The number of bases to remove from the start of the read. 0 for ddRAD, 5 for ezRAD
no		FixStacks (yes,no)   											Demultiplexing with stacks introduces anomolies.  This removes them.  
------------------------------------------------------------------------------------------------------------------

----------mkREF: Settings for de novo assembly of the reference genome--------------------------------------------
PE		Type of reads for assembly (PE, SE, OL, RPE)					PE=ddRAD & ezRAD pairedend, non-overlapping reads; SE=singleend reads; OL=ddRAD & ezRAD overlapping reads, miseq; RPE=oregonRAD, restriction site + random shear
0.9		cdhit Clustering_Similarity_Pct (0-1)							Use cdhit to cluster and collapse uniq reads by similarity threshold
2		Cutoff1 (integer)												Use unique reads that have at least this much coverage for making the reference	genome
2		Cutoff2 (integer)												Use unique reads that occur in at least this many individuals for making the reference genome
0.05	rainbow merge -r <percentile> (decimal 0-1)						Percentile-based minimum number of seqs to assemble in a precluster
0.95	rainbow merge -R <percentile> (decimal 0-1)						Percentile-based maximum number of seqs to assemble in a precluster
------------------------------------------------------------------------------------------------------------------

----------mkBAM: Settings for mapping the reads to the reference genome-------------------------------------------
Make sure the cutoffs above match the reference*fasta!
1		bwa mem -A Mapping_Match_Value (integer) 						bwa mem default is 1
6		bwa mem -B Mapping_MisMatch_Value (integer) 					bwa mem default is 4
10		bwa mem -O Mapping_GapOpen_Penalty (integer) 					bwa mem default is 6
50		bwa mem -T Mapping_Minimum_Alignment_Score (integer) 			bwa mem default is 30. Remove reads that have an alignment score less than this. don't go lower than 1 or else the resulting file will be huge. NOTE! in fltrBAM settings (below) there is an alignment score filter that uses a threshold relative to read length.  This -T setting here affects which reads the relative alignment score threshold will be applied to.
30,5	bwa mem -L Mapping_Clipping_Penalty (integer,integer) 			bwa mem default is 5
------------------------------------------------------------------------------------------------------------------

----------fltrBAM: Settings for filtering mapping alignments in the *bam files---------------
20		samtools view -q 		Mapping_Min_Quality (integer)    									Remove reads with mapping qual less than this value
no		samtools view -F 4 		Remove_unmapped_reads? (yes,no)   									Since the reads aren't mapped, we generally don't need to filter them
yes		samtools view -F 8 		Remove_read_pair_if_one_is_unmapped? (yes,no)    					If either read in a pair does not map, then the other is also removed
yes		samtools view -F 256 	Remove_secondary_alignments? (yes,no)     							Secondary alignments are reads that also map to other contigs in the reference genome
no		samtools view -F 512 	Remove_reads_not_passing_platform_vendor_filters (yes,no)     		We generally don't see any of these
no		samtools view -F 1024 	Remove_PCR_or_optical_duplicates? (yes,no)     						You probably don't want to set this to yes
no		samtools view -F 2048 	Remove_supplementary_alignments? (yes,no)     						We generally don't see any of these
yes		samtools view -f 2 		Keep_only_properly_aligned_read_pairs? (yes,no)						Set to no if OL mode 
0		samtools view -F 		Custom_samtools_view_F_bit_value? (integer)     					performed separately from the above, consult samtools man
0		samtools view -f 		Custom_samtools_view_f_bit_value? (integer)     					performed separately from the above, consult samtools man
20								Remove_reads_with_excessive_soft_clipping? (no, integers)			minimum number of soft clipped bases in a read, summed between the beginning and end, that are unacceptable
50								Remove_reads_with_alignment_score_below_relative_threshold (integer)	Alignment score thresholds are calculated based on this value adjusted by a factor (actual read length relative the assumed read length value in next setting). RelativeThreshold = as_threshold * actual_read_length / assumed_read_length, where this setting controls as_threshold. NOTE! bwa mem -T affects which reads are mapped based on alignment score, and therefore this filter cannot save reads elimated by bwa mem -T, but if the -T setting is too low then the RAW bam files can be huge.
150								Read_length_assumed_by_relative_alignment_score_threshold (integer)	Alignment score thresholds are calculated based on the threshold in the previous setting adjusted by a factor (actual read length relative the assumed read length value here). RelativeThreshold= as_threshold * actual_read_length / assumed_read_length, where this setting controls assumed_read_length
yes								Remove_reads_orphaned_by_filters? (yes,no)
------------------------------------------------------------------------------------------------------------------

----------mkVCF: Settings for variant calling/ genotyping---------------------------------------------------------
no		freebayes -J --pooled-discrete (yes|no) 						If yes, a pool of individuals is assumed to be the statistical unit of observation. 
no		freebayes -A --cnv-map (filename.bed or no)						If the pools have different numbers of individuals, then you should provide a copy number variation (cnv) *.bed file with the "ploidy" of each pool. the bed file should be in the working directory and formatted as follows: popmap_column_1 ploidy_of_pool.  If that doesn't work, try the basenames of the files in popmap column 1.
2		freebayes -p --ploidy (integer)									Whether pooled or not, if no cnv-map file is provided, then what is the ploidy of the samples? for pools, this number should be the number of individuals * ploidy
no		freebayes -r --region (filename.bed or no)						Limit analysis to specified region.  Bed file format: <chrom>:<start_position>-<end_position>
0		only genotype read 1 (integer)									Limit analysis to only Read 1 positions, integer is maximum Read1 bp position
2		Minimum Mean Depth of Coverage Per Individual					Limit analysis to contigs with at least the specified mean depth of coverage per individual
0		freebayes -n --use-best-n-alleles (integer)						reduce the number of alleles considered to n, zero means all, set to 2 or more if you run out of memory
30		freebayes -m --min-mapping-quality (integer) 
20		freebayes -q --min-base-quality (integer) 
-1		freebayes -E --haplotype-length (-1, 3, or integer)    			Set to -1 to avoid multi nucleotide polymorphisms and force calling MNPs as SNPs.  Can be set up to half the read length, or more.
0		freebayes    --min-repeat-entropy (0, 1, or integer) 			Set to 0 to avoid multi nucleotide polymorphisms and force calling MNPs as SNPs. To detect interrupted repeats, build across sequence until it has entropy > N bits per bp. 
10		freebayes    --min-coverage (integer)       					Require at least this coverage to process a site
0.375	freebayes -F --min-alternate-fraction (decimal 0-1)   			There must be at least 1 individual with this fraction of alt reads to evaluate the position. If your individuals are barcoded, then use 0.2. If your data is pooled, then set based upon ~ 1/(numIndivids * ploidy) and average depth of coverage
20		freebayes -C --min-alternate-count (integer)					Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position.  default: 2
20		freebayes -G --min-alternate-total (integer)					Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis.  default: 1
0.33	freebayes -z --read-max-mismatch-fraction (decimal 0-1)			Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold default: 1.0
20		freebayes -Q --mismatch-base-quality-threshold (integer)		Count mismatches toward --read-mismatch-limit if the base quality of the mismatch is >= Q.  default: 10
30		freebayes -U --read-mismatch-limit (integer)					Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold. default: ~unbounded
30		freebayes ~3 ~~min-alternate-qsum (integer)						This value is the mean base quality score for alternate reads and will be multiplied by -C to set -3. Description of -3: Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position.  default: 2	
30		freebayes -$ --read-snp-limit (integer)							Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold. default: ~unbounded
20		freebayes -e --read-indel-limit	(integer)						Exclude reads with more than N separate gaps. default: ~unbounded
no		freebayes -w --hwe-priors-off (no|yes)							Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency.
no		freebayes -V --binomial-obs-priors-off (no|yes)					Disable incorporation of prior expectations about observations. Uses read placement probability, strand balance probability, and read position (5'-3') probability.
no		freebayes -a --allele-balance-priors-off (no|yes)				Disable use of aggregate probability of observation balance between alleles as a component of the priors.
no		freebayes    --no-partial-observations (no|yes)					Exclude observations which do not fully span the dynamically-determined detection window.  (default, use all observations, dividing partial support across matching haplotypes when generating haplotypes.)
no		freebayes    --report-monomorphic (no|yes)						Report even loci which appear to be monomorphic, and report allconsidered alleles, even those which are not in called genotypes. Loci which do not have any potential alternates have '.' for ALT.

------------------------------------------------------------------------------------------------------------------


Email
user@tamucc.edu


Fri Dec 22 02:52:38 PM CET 2023 Reading in variables from config file...

Fri Dec 22 02:52:38 PM CET 2023 Checking for all required dDocent software...

 Running CheckDependencies Function...

  The dependency trimmomatic is installed!

  The dependency freebayes is installed!

  The dependency mawk is installed!

  The dependency bwa is installed!

  The dependency samtools is installed!

  The dependency vcftools is installed!

  The dependency rainbow is installed!

  The dependency gnuplot is installed!

  The dependency gawk is installed!

  The dependency seqtk is installed!

  The dependency cd-hit-est is installed!

  The dependency bamToBed is installed!

  The dependency bedtools is installed!

  The dependency coverageBed is installed!

  The dependency parallel is installed!

  The dependency vcfcombine is installed!

  The dependency bamtools is installed!

  The dependency pearRM is installed!

 All dependencies are installed and up to date!


Fri Dec 22 02:52:38 PM CET 2023  Begin main ddocent function

 The HPC version of dDocent will only digest files with particular extensions for particular tasks
  untouched files for trimming must be *.F.fq.gz and *.R.fq.gz
  files trimmed for assembly (mkREF) must be *r1.fq.gz *r2.fq.gz
  files trimmed for mapping (mkBAM) must be *R1.fq.gz *R2.fq.gz

  extensions selected: *.R1.fq.gz *.R2.fq.gz
 
 The samples being processed are:
  AT_AT1Ac
  AT_AT2Ac
  AT_AT3Ac
  CZ_CZ14Ac
  CZ_CZ15Ac
  CZ_CZ16Ac
  CZ_CZ17Ac
  CZ_CZ18Ac
  CZ_CZ19Ac
  CZ_CZ1Ac
  CZ_CZ20Ac
  CZ_CZ21Ac
  CZ_CZ22Ac
  CZ_CZ23Ac
  CZ_CZ24Ac
  CZ_CZ2Ac
  CZ_CZ3Ac
  CZ_CZ4Ac
  CZ_CZ5Ac
  CZ_CZ6Ac
  CZ_CZ7Ac
  CZ_CZ8Ac
  CZ_CZ9Ac
  DE_DE10Ac
  DE_DE11Ac
  DE_DE12Ac
  DE_DE13Ac
  DE_DE1Ac
  DE_DE2Ac
  DE_DE3Ac
  DE_DE4Ac
  DE_DE5Ac
  DE_DE6Ac
  DE_DE7Ac
  DE_DE8Ac
  DE_DE9Ac
  EE_EE1Ac
  EE_EE2Ac
  EE_EE3Ac
  EE_EE4Ac
  EE_EE5Ac
  FI_FI10Ac
  FI_FI11Ac
  FI_FI12Ac
  FI_FI13Ac
  FI_FI14Ac
  FI_FI15Ac
  FI_FI16Ac
  FI_FI17Ac
  FI_FI19Ac
  FI_FI1Ac
  FI_FI20Ac
  FI_FI21Ac
  FI_FI22Ac
  FI_FI23Ac
  FI_FI24Ac
  FI_FI25Ac
  FI_FI26Ac
  FI_FI27Ac
  FI_FI2Ac
  FI_FI3Ac
  FI_FI4Ac
  FI_FI5Ac
  FI_FI6Ac
  FI_FI7Ac
  FI_FI8Ac
  FI_FI9Ac
  GR_GR1Ac
  HR_HR12Ac
  HR_HR1Ac
  HR_HR4Ac
  HR_HR5Ac
  HR_HR6Ac
  HR_HR7Ac
  HR_HR9Ac
  LT_LT1Ac
  LT_LT2Ac
  LT_LT3Ac
  LT_LT4Ac
  LT_LT5Ac
  LT_LT6Ac
  NO_NO10Ac
  NO_NO11Ac
  NO_NO12Ac
  NO_NO13Ac
  NO_NO14Ac
  NO_NO15Ac
  NO_NO16Ac
  NO_NO17Ac
  NO_NO18Ac
  NO_NO19Ac
  NO_NO1Ac
  NO_NO20Ac
  NO_NO21Ac
  NO_NO22Ac
  NO_NO23Ac
  NO_NO24Ac
  NO_NO25Ac
  NO_NO27Ac
  NO_NO28Ac
  NO_NO29Ac
  NO_NO2Ac
  NO_NO30Ac
  NO_NO31Ac
  NO_NO32Ac
  NO_NO33Ac
  NO_NO34Ac
  NO_NO35Ac
  NO_NO3Ac
  NO_NO4Ac
  NO_NO5Ac
  NO_NO6Ac
  NO_NO7Ac
  NO_NO8Ac
  NO_NO9Ac
  PL_PL1Ac
  PL_PL2Ac
  PL_PL3Ac
  RU_RU1Ac
  RU_RU2Ac
  RU_RU3Ac
  RU_RU4Ac
  RU_RU5Ac
  RU_RU6Ac
  SK_SK1Ac
  SK_SK2Ac
  SK_SK3Ac
  SK_SK4Ac
  SK_SK5Ac
  US_US1Ac

 
Fri Dec 22 02:52:40 PM CET 2023  Checking files for mapping...
 
Fri Dec 22 02:52:40 PM CET 2023   Reference genome not found in working directory...
 
Fri Dec 22 02:52:40 PM CET 2023   Reference genome found in mkREF directory, creating a symbolic link here in the working directory...
 
Fri Dec 22 02:52:40 PM CET 2023   Indexing ref genome...
 
Fri Dec 22 02:52:40 PM CET 2023   Indexing for bwa-meme because there are 42701464 bytes of RAM avail...
 
Fri Dec 22 02:53:11 PM CET 2023   BWA-MEME training P-RMI...
[Info] build_rmis_dna script for BWA-MEME 1.0.5v
Generate 2^24 leaf-models: 16777216 models
Training top-level pwl24 model layer
Training second-level linear model layer (num models = 16777216)
[2nd layer]Computing lower bound stats...
[2nd layer]Fixing empty models...
Computing last level errors...
[INFO] Number of leaf and partial models: 16777216, leaf: 16777216, partial: 0, leaf models that have partial models:0
Model build time: 14415 ms
Average model error: 3.3777309755034066 (0.000005114968567549367%)
Average model log2 error: 2.2725027055780083
Max model log2 error on model 14380470: 8.67595703294175 (0.0006193572428650576%)

Fri Dec 22 02:53:33 PM CET 2023  was ref assembled by dDocent? No. BWA will estimate insert length stats

numPARALLEL=1
memPerPARALLEL=41279092
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memPerThreadPerPARALLEL=1031977
memSortPerThreadPerPARALLEL=1031977

Fri Dec 22 02:53:33 PM CET 2023  Run bwa mem 
FILE=AT_AT1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 02:53:33 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta AT_AT1Ac.R1.fq.gz AT_AT1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:AT_AT1ActSM:AT_AT1ActPL:Illumina 2> bwa.AT_AT1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > AT_AT1Ac.2.2-RAW.bam 2>samtools.sort.bam.AT_AT1Ac.2.2.log

Fri Dec 22 02:55:12 PM CET 2023  run samtools index AT_AT1Ac
FILE=AT_AT2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 02:55:15 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta AT_AT2Ac.R1.fq.gz AT_AT2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:AT_AT2ActSM:AT_AT2ActPL:Illumina 2> bwa.AT_AT2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > AT_AT2Ac.2.2-RAW.bam 2>samtools.sort.bam.AT_AT2Ac.2.2.log

Fri Dec 22 02:55:56 PM CET 2023  run samtools index AT_AT2Ac
FILE=AT_AT3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 02:55:57 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta AT_AT3Ac.R1.fq.gz AT_AT3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:AT_AT3ActSM:AT_AT3ActPL:Illumina 2> bwa.AT_AT3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > AT_AT3Ac.2.2-RAW.bam 2>samtools.sort.bam.AT_AT3Ac.2.2.log

Fri Dec 22 02:56:50 PM CET 2023  run samtools index AT_AT3Ac
FILE=CZ_CZ14Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 02:56:52 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ14Ac.R1.fq.gz CZ_CZ14Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ14ActSM:CZ_CZ14ActPL:Illumina 2> bwa.CZ_CZ14Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ14Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ14Ac.2.2.log

Fri Dec 22 02:58:15 PM CET 2023  run samtools index CZ_CZ14Ac
FILE=CZ_CZ15Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 02:58:18 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ15Ac.R1.fq.gz CZ_CZ15Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ15ActSM:CZ_CZ15ActPL:Illumina 2> bwa.CZ_CZ15Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ15Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ15Ac.2.2.log

Fri Dec 22 03:00:21 PM CET 2023  run samtools index CZ_CZ15Ac
FILE=CZ_CZ16Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:00:25 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ16Ac.R1.fq.gz CZ_CZ16Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ16ActSM:CZ_CZ16ActPL:Illumina 2> bwa.CZ_CZ16Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ16Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ16Ac.2.2.log

Fri Dec 22 03:01:33 PM CET 2023  run samtools index CZ_CZ16Ac
FILE=CZ_CZ17Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:01:35 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ17Ac.R1.fq.gz CZ_CZ17Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ17ActSM:CZ_CZ17ActPL:Illumina 2> bwa.CZ_CZ17Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ17Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ17Ac.2.2.log

Fri Dec 22 03:02:40 PM CET 2023  run samtools index CZ_CZ17Ac
FILE=CZ_CZ18Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:02:43 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ18Ac.R1.fq.gz CZ_CZ18Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ18ActSM:CZ_CZ18ActPL:Illumina 2> bwa.CZ_CZ18Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ18Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ18Ac.2.2.log

Fri Dec 22 03:03:25 PM CET 2023  run samtools index CZ_CZ18Ac
FILE=CZ_CZ19Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:03:26 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ19Ac.R1.fq.gz CZ_CZ19Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ19ActSM:CZ_CZ19ActPL:Illumina 2> bwa.CZ_CZ19Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ19Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ19Ac.2.2.log

Fri Dec 22 03:05:00 PM CET 2023  run samtools index CZ_CZ19Ac
FILE=CZ_CZ1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:05:03 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ1Ac.R1.fq.gz CZ_CZ1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ1ActSM:CZ_CZ1ActPL:Illumina 2> bwa.CZ_CZ1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ1Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ1Ac.2.2.log

Fri Dec 22 03:06:20 PM CET 2023  run samtools index CZ_CZ1Ac
FILE=CZ_CZ20Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:06:22 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ20Ac.R1.fq.gz CZ_CZ20Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ20ActSM:CZ_CZ20ActPL:Illumina 2> bwa.CZ_CZ20Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ20Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ20Ac.2.2.log

Fri Dec 22 03:07:43 PM CET 2023  run samtools index CZ_CZ20Ac
FILE=CZ_CZ21Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:07:46 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ21Ac.R1.fq.gz CZ_CZ21Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ21ActSM:CZ_CZ21ActPL:Illumina 2> bwa.CZ_CZ21Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ21Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ21Ac.2.2.log

Fri Dec 22 03:09:00 PM CET 2023  run samtools index CZ_CZ21Ac
FILE=CZ_CZ22Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:09:03 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ22Ac.R1.fq.gz CZ_CZ22Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ22ActSM:CZ_CZ22ActPL:Illumina 2> bwa.CZ_CZ22Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ22Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ22Ac.2.2.log

Fri Dec 22 03:10:42 PM CET 2023  run samtools index CZ_CZ22Ac
FILE=CZ_CZ23Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:10:45 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ23Ac.R1.fq.gz CZ_CZ23Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ23ActSM:CZ_CZ23ActPL:Illumina 2> bwa.CZ_CZ23Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ23Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ23Ac.2.2.log

Fri Dec 22 03:12:34 PM CET 2023  run samtools index CZ_CZ23Ac
FILE=CZ_CZ24Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:12:38 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ24Ac.R1.fq.gz CZ_CZ24Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ24ActSM:CZ_CZ24ActPL:Illumina 2> bwa.CZ_CZ24Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ24Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ24Ac.2.2.log

Fri Dec 22 03:13:38 PM CET 2023  run samtools index CZ_CZ24Ac
FILE=CZ_CZ2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:13:40 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ2Ac.R1.fq.gz CZ_CZ2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ2ActSM:CZ_CZ2ActPL:Illumina 2> bwa.CZ_CZ2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ2Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ2Ac.2.2.log

Fri Dec 22 03:14:51 PM CET 2023  run samtools index CZ_CZ2Ac
FILE=CZ_CZ3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:14:54 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ3Ac.R1.fq.gz CZ_CZ3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ3ActSM:CZ_CZ3ActPL:Illumina 2> bwa.CZ_CZ3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ3Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ3Ac.2.2.log

Fri Dec 22 03:16:28 PM CET 2023  run samtools index CZ_CZ3Ac
FILE=CZ_CZ4Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:16:31 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ4Ac.R1.fq.gz CZ_CZ4Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ4ActSM:CZ_CZ4ActPL:Illumina 2> bwa.CZ_CZ4Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ4Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ4Ac.2.2.log

Fri Dec 22 03:16:38 PM CET 2023  run samtools index CZ_CZ4Ac
FILE=CZ_CZ5Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:16:39 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ5Ac.R1.fq.gz CZ_CZ5Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ5ActSM:CZ_CZ5ActPL:Illumina 2> bwa.CZ_CZ5Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ5Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ5Ac.2.2.log

Fri Dec 22 03:18:00 PM CET 2023  run samtools index CZ_CZ5Ac
FILE=CZ_CZ6Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:18:03 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ6Ac.R1.fq.gz CZ_CZ6Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ6ActSM:CZ_CZ6ActPL:Illumina 2> bwa.CZ_CZ6Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ6Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ6Ac.2.2.log

Fri Dec 22 03:19:13 PM CET 2023  run samtools index CZ_CZ6Ac
FILE=CZ_CZ7Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:19:16 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ7Ac.R1.fq.gz CZ_CZ7Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ7ActSM:CZ_CZ7ActPL:Illumina 2> bwa.CZ_CZ7Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ7Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ7Ac.2.2.log

Fri Dec 22 03:20:23 PM CET 2023  run samtools index CZ_CZ7Ac
FILE=CZ_CZ8Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:20:25 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ8Ac.R1.fq.gz CZ_CZ8Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ8ActSM:CZ_CZ8ActPL:Illumina 2> bwa.CZ_CZ8Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ8Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ8Ac.2.2.log

Fri Dec 22 03:21:24 PM CET 2023  run samtools index CZ_CZ8Ac
FILE=CZ_CZ9Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:21:26 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta CZ_CZ9Ac.R1.fq.gz CZ_CZ9Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:CZ_CZ9ActSM:CZ_CZ9ActPL:Illumina 2> bwa.CZ_CZ9Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > CZ_CZ9Ac.2.2-RAW.bam 2>samtools.sort.bam.CZ_CZ9Ac.2.2.log

Fri Dec 22 03:22:55 PM CET 2023  run samtools index CZ_CZ9Ac
FILE=DE_DE10Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:22:58 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE10Ac.R1.fq.gz DE_DE10Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE10ActSM:DE_DE10ActPL:Illumina 2> bwa.DE_DE10Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE10Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE10Ac.2.2.log

Fri Dec 22 03:25:08 PM CET 2023  run samtools index DE_DE10Ac
FILE=DE_DE11Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:25:12 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE11Ac.R1.fq.gz DE_DE11Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE11ActSM:DE_DE11ActPL:Illumina 2> bwa.DE_DE11Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE11Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE11Ac.2.2.log

Fri Dec 22 03:26:36 PM CET 2023  run samtools index DE_DE11Ac
FILE=DE_DE12Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:26:39 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE12Ac.R1.fq.gz DE_DE12Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE12ActSM:DE_DE12ActPL:Illumina 2> bwa.DE_DE12Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE12Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE12Ac.2.2.log

Fri Dec 22 03:28:03 PM CET 2023  run samtools index DE_DE12Ac
FILE=DE_DE13Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:28:05 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE13Ac.R1.fq.gz DE_DE13Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE13ActSM:DE_DE13ActPL:Illumina 2> bwa.DE_DE13Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE13Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE13Ac.2.2.log

Fri Dec 22 03:29:51 PM CET 2023  run samtools index DE_DE13Ac
FILE=DE_DE1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:29:55 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE1Ac.R1.fq.gz DE_DE1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE1ActSM:DE_DE1ActPL:Illumina 2> bwa.DE_DE1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE1Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE1Ac.2.2.log

Fri Dec 22 03:30:58 PM CET 2023  run samtools index DE_DE1Ac
FILE=DE_DE2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:31:00 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE2Ac.R1.fq.gz DE_DE2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE2ActSM:DE_DE2ActPL:Illumina 2> bwa.DE_DE2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE2Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE2Ac.2.2.log

Fri Dec 22 03:31:53 PM CET 2023  run samtools index DE_DE2Ac
FILE=DE_DE3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:31:55 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE3Ac.R1.fq.gz DE_DE3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE3ActSM:DE_DE3ActPL:Illumina 2> bwa.DE_DE3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE3Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE3Ac.2.2.log

Fri Dec 22 03:32:50 PM CET 2023  run samtools index DE_DE3Ac
FILE=DE_DE4Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:32:52 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE4Ac.R1.fq.gz DE_DE4Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE4ActSM:DE_DE4ActPL:Illumina 2> bwa.DE_DE4Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE4Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE4Ac.2.2.log

Fri Dec 22 03:33:58 PM CET 2023  run samtools index DE_DE4Ac
FILE=DE_DE5Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:34:00 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE5Ac.R1.fq.gz DE_DE5Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE5ActSM:DE_DE5ActPL:Illumina 2> bwa.DE_DE5Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE5Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE5Ac.2.2.log

Fri Dec 22 03:35:11 PM CET 2023  run samtools index DE_DE5Ac
FILE=DE_DE6Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:35:14 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE6Ac.R1.fq.gz DE_DE6Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE6ActSM:DE_DE6ActPL:Illumina 2> bwa.DE_DE6Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE6Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE6Ac.2.2.log

Fri Dec 22 03:36:28 PM CET 2023  run samtools index DE_DE6Ac
FILE=DE_DE7Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:36:31 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE7Ac.R1.fq.gz DE_DE7Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE7ActSM:DE_DE7ActPL:Illumina 2> bwa.DE_DE7Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE7Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE7Ac.2.2.log

Fri Dec 22 03:37:51 PM CET 2023  run samtools index DE_DE7Ac
FILE=DE_DE8Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:37:53 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE8Ac.R1.fq.gz DE_DE8Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE8ActSM:DE_DE8ActPL:Illumina 2> bwa.DE_DE8Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE8Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE8Ac.2.2.log

Fri Dec 22 03:38:53 PM CET 2023  run samtools index DE_DE8Ac
FILE=DE_DE9Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:38:55 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta DE_DE9Ac.R1.fq.gz DE_DE9Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:DE_DE9ActSM:DE_DE9ActPL:Illumina 2> bwa.DE_DE9Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > DE_DE9Ac.2.2-RAW.bam 2>samtools.sort.bam.DE_DE9Ac.2.2.log

Fri Dec 22 03:40:42 PM CET 2023  run samtools index DE_DE9Ac
FILE=EE_EE1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:40:45 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta EE_EE1Ac.R1.fq.gz EE_EE1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:EE_EE1ActSM:EE_EE1ActPL:Illumina 2> bwa.EE_EE1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > EE_EE1Ac.2.2-RAW.bam 2>samtools.sort.bam.EE_EE1Ac.2.2.log

Fri Dec 22 03:41:57 PM CET 2023  run samtools index EE_EE1Ac
FILE=EE_EE2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:41:59 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta EE_EE2Ac.R1.fq.gz EE_EE2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:EE_EE2ActSM:EE_EE2ActPL:Illumina 2> bwa.EE_EE2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > EE_EE2Ac.2.2-RAW.bam 2>samtools.sort.bam.EE_EE2Ac.2.2.log

Fri Dec 22 03:42:55 PM CET 2023  run samtools index EE_EE2Ac
FILE=EE_EE3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:42:57 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta EE_EE3Ac.R1.fq.gz EE_EE3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:EE_EE3ActSM:EE_EE3ActPL:Illumina 2> bwa.EE_EE3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > EE_EE3Ac.2.2-RAW.bam 2>samtools.sort.bam.EE_EE3Ac.2.2.log

Fri Dec 22 03:43:58 PM CET 2023  run samtools index EE_EE3Ac
FILE=EE_EE4Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:44:00 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta EE_EE4Ac.R1.fq.gz EE_EE4Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:EE_EE4ActSM:EE_EE4ActPL:Illumina 2> bwa.EE_EE4Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > EE_EE4Ac.2.2-RAW.bam 2>samtools.sort.bam.EE_EE4Ac.2.2.log

Fri Dec 22 03:45:31 PM CET 2023  run samtools index EE_EE4Ac
FILE=EE_EE5Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:45:34 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta EE_EE5Ac.R1.fq.gz EE_EE5Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:EE_EE5ActSM:EE_EE5ActPL:Illumina 2> bwa.EE_EE5Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > EE_EE5Ac.2.2-RAW.bam 2>samtools.sort.bam.EE_EE5Ac.2.2.log

Fri Dec 22 03:46:52 PM CET 2023  run samtools index EE_EE5Ac
FILE=FI_FI10Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:46:54 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI10Ac.R1.fq.gz FI_FI10Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI10ActSM:FI_FI10ActPL:Illumina 2> bwa.FI_FI10Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI10Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI10Ac.2.2.log

Fri Dec 22 03:48:13 PM CET 2023  run samtools index FI_FI10Ac
FILE=FI_FI11Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:48:16 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI11Ac.R1.fq.gz FI_FI11Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI11ActSM:FI_FI11ActPL:Illumina 2> bwa.FI_FI11Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI11Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI11Ac.2.2.log

Fri Dec 22 03:48:49 PM CET 2023  run samtools index FI_FI11Ac
FILE=FI_FI12Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:48:51 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI12Ac.R1.fq.gz FI_FI12Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI12ActSM:FI_FI12ActPL:Illumina 2> bwa.FI_FI12Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI12Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI12Ac.2.2.log

Fri Dec 22 03:49:40 PM CET 2023  run samtools index FI_FI12Ac
FILE=FI_FI13Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:49:41 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI13Ac.R1.fq.gz FI_FI13Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI13ActSM:FI_FI13ActPL:Illumina 2> bwa.FI_FI13Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI13Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI13Ac.2.2.log

Fri Dec 22 03:50:30 PM CET 2023  run samtools index FI_FI13Ac
FILE=FI_FI14Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:50:32 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI14Ac.R1.fq.gz FI_FI14Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI14ActSM:FI_FI14ActPL:Illumina 2> bwa.FI_FI14Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI14Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI14Ac.2.2.log

Fri Dec 22 03:51:21 PM CET 2023  run samtools index FI_FI14Ac
FILE=FI_FI15Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:51:22 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI15Ac.R1.fq.gz FI_FI15Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI15ActSM:FI_FI15ActPL:Illumina 2> bwa.FI_FI15Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI15Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI15Ac.2.2.log

Fri Dec 22 03:52:17 PM CET 2023  run samtools index FI_FI15Ac
FILE=FI_FI16Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:52:19 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI16Ac.R1.fq.gz FI_FI16Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI16ActSM:FI_FI16ActPL:Illumina 2> bwa.FI_FI16Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI16Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI16Ac.2.2.log

Fri Dec 22 03:52:52 PM CET 2023  run samtools index FI_FI16Ac
FILE=FI_FI17Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:52:54 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI17Ac.R1.fq.gz FI_FI17Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI17ActSM:FI_FI17ActPL:Illumina 2> bwa.FI_FI17Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI17Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI17Ac.2.2.log

Fri Dec 22 03:53:26 PM CET 2023  run samtools index FI_FI17Ac
FILE=FI_FI19Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:53:27 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI19Ac.R1.fq.gz FI_FI19Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI19ActSM:FI_FI19ActPL:Illumina 2> bwa.FI_FI19Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI19Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI19Ac.2.2.log

Fri Dec 22 03:54:18 PM CET 2023  run samtools index FI_FI19Ac
FILE=FI_FI1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:54:19 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI1Ac.R1.fq.gz FI_FI1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI1ActSM:FI_FI1ActPL:Illumina 2> bwa.FI_FI1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI1Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI1Ac.2.2.log

Fri Dec 22 03:56:01 PM CET 2023  run samtools index FI_FI1Ac
FILE=FI_FI20Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:56:04 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI20Ac.R1.fq.gz FI_FI20Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI20ActSM:FI_FI20ActPL:Illumina 2> bwa.FI_FI20Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI20Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI20Ac.2.2.log

Fri Dec 22 03:57:05 PM CET 2023  run samtools index FI_FI20Ac
FILE=FI_FI21Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:57:08 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI21Ac.R1.fq.gz FI_FI21Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI21ActSM:FI_FI21ActPL:Illumina 2> bwa.FI_FI21Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI21Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI21Ac.2.2.log

Fri Dec 22 03:57:48 PM CET 2023  run samtools index FI_FI21Ac
FILE=FI_FI22Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:57:50 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI22Ac.R1.fq.gz FI_FI22Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI22ActSM:FI_FI22ActPL:Illumina 2> bwa.FI_FI22Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI22Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI22Ac.2.2.log

Fri Dec 22 03:59:14 PM CET 2023  run samtools index FI_FI22Ac
FILE=FI_FI23Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 03:59:17 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI23Ac.R1.fq.gz FI_FI23Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI23ActSM:FI_FI23ActPL:Illumina 2> bwa.FI_FI23Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI23Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI23Ac.2.2.log

Fri Dec 22 04:00:02 PM CET 2023  run samtools index FI_FI23Ac
FILE=FI_FI24Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:00:04 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI24Ac.R1.fq.gz FI_FI24Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI24ActSM:FI_FI24ActPL:Illumina 2> bwa.FI_FI24Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI24Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI24Ac.2.2.log

Fri Dec 22 04:00:36 PM CET 2023  run samtools index FI_FI24Ac
FILE=FI_FI25Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:00:38 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI25Ac.R1.fq.gz FI_FI25Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI25ActSM:FI_FI25ActPL:Illumina 2> bwa.FI_FI25Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI25Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI25Ac.2.2.log

Fri Dec 22 04:01:29 PM CET 2023  run samtools index FI_FI25Ac
FILE=FI_FI26Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:01:30 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI26Ac.R1.fq.gz FI_FI26Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI26ActSM:FI_FI26ActPL:Illumina 2> bwa.FI_FI26Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI26Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI26Ac.2.2.log

Fri Dec 22 04:02:11 PM CET 2023  run samtools index FI_FI26Ac
FILE=FI_FI27Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:02:12 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI27Ac.R1.fq.gz FI_FI27Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI27ActSM:FI_FI27ActPL:Illumina 2> bwa.FI_FI27Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI27Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI27Ac.2.2.log

Fri Dec 22 04:03:04 PM CET 2023  run samtools index FI_FI27Ac
FILE=FI_FI2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:03:06 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI2Ac.R1.fq.gz FI_FI2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI2ActSM:FI_FI2ActPL:Illumina 2> bwa.FI_FI2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI2Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI2Ac.2.2.log

Fri Dec 22 04:05:32 PM CET 2023  run samtools index FI_FI2Ac
FILE=FI_FI3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:05:36 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI3Ac.R1.fq.gz FI_FI3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI3ActSM:FI_FI3ActPL:Illumina 2> bwa.FI_FI3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI3Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI3Ac.2.2.log

Fri Dec 22 04:07:15 PM CET 2023  run samtools index FI_FI3Ac
FILE=FI_FI4Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:07:18 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI4Ac.R1.fq.gz FI_FI4Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI4ActSM:FI_FI4ActPL:Illumina 2> bwa.FI_FI4Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI4Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI4Ac.2.2.log

Fri Dec 22 04:08:27 PM CET 2023  run samtools index FI_FI4Ac
FILE=FI_FI5Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:08:29 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI5Ac.R1.fq.gz FI_FI5Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI5ActSM:FI_FI5ActPL:Illumina 2> bwa.FI_FI5Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI5Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI5Ac.2.2.log

Fri Dec 22 04:09:28 PM CET 2023  run samtools index FI_FI5Ac
FILE=FI_FI6Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:09:30 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI6Ac.R1.fq.gz FI_FI6Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI6ActSM:FI_FI6ActPL:Illumina 2> bwa.FI_FI6Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI6Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI6Ac.2.2.log

Fri Dec 22 04:10:11 PM CET 2023  run samtools index FI_FI6Ac
FILE=FI_FI7Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:10:12 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI7Ac.R1.fq.gz FI_FI7Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI7ActSM:FI_FI7ActPL:Illumina 2> bwa.FI_FI7Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI7Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI7Ac.2.2.log

Fri Dec 22 04:10:50 PM CET 2023  run samtools index FI_FI7Ac
FILE=FI_FI8Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:10:52 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI8Ac.R1.fq.gz FI_FI8Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI8ActSM:FI_FI8ActPL:Illumina 2> bwa.FI_FI8Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI8Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI8Ac.2.2.log

Fri Dec 22 04:11:37 PM CET 2023  run samtools index FI_FI8Ac
FILE=FI_FI9Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:11:39 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta FI_FI9Ac.R1.fq.gz FI_FI9Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:FI_FI9ActSM:FI_FI9ActPL:Illumina 2> bwa.FI_FI9Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > FI_FI9Ac.2.2-RAW.bam 2>samtools.sort.bam.FI_FI9Ac.2.2.log

Fri Dec 22 04:11:51 PM CET 2023  run samtools index FI_FI9Ac
FILE=GR_GR1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:11:51 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta GR_GR1Ac.R1.fq.gz GR_GR1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:GR_GR1ActSM:GR_GR1ActPL:Illumina 2> bwa.GR_GR1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > GR_GR1Ac.2.2-RAW.bam 2>samtools.sort.bam.GR_GR1Ac.2.2.log

Fri Dec 22 04:12:49 PM CET 2023  run samtools index GR_GR1Ac
FILE=HR_HR12Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:12:51 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta HR_HR12Ac.R1.fq.gz HR_HR12Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:HR_HR12ActSM:HR_HR12ActPL:Illumina 2> bwa.HR_HR12Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > HR_HR12Ac.2.2-RAW.bam 2>samtools.sort.bam.HR_HR12Ac.2.2.log

Fri Dec 22 04:13:49 PM CET 2023  run samtools index HR_HR12Ac
FILE=HR_HR1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:13:51 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta HR_HR1Ac.R1.fq.gz HR_HR1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:HR_HR1ActSM:HR_HR1ActPL:Illumina 2> bwa.HR_HR1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > HR_HR1Ac.2.2-RAW.bam 2>samtools.sort.bam.HR_HR1Ac.2.2.log

Fri Dec 22 04:13:55 PM CET 2023  run samtools index HR_HR1Ac
FILE=HR_HR4Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:13:55 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta HR_HR4Ac.R1.fq.gz HR_HR4Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:HR_HR4ActSM:HR_HR4ActPL:Illumina 2> bwa.HR_HR4Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > HR_HR4Ac.2.2-RAW.bam 2>samtools.sort.bam.HR_HR4Ac.2.2.log

Fri Dec 22 04:14:28 PM CET 2023  run samtools index HR_HR4Ac
FILE=HR_HR5Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:14:30 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta HR_HR5Ac.R1.fq.gz HR_HR5Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:HR_HR5ActSM:HR_HR5ActPL:Illumina 2> bwa.HR_HR5Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > HR_HR5Ac.2.2-RAW.bam 2>samtools.sort.bam.HR_HR5Ac.2.2.log

Fri Dec 22 04:15:10 PM CET 2023  run samtools index HR_HR5Ac
FILE=HR_HR6Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:15:11 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta HR_HR6Ac.R1.fq.gz HR_HR6Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:HR_HR6ActSM:HR_HR6ActPL:Illumina 2> bwa.HR_HR6Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > HR_HR6Ac.2.2-RAW.bam 2>samtools.sort.bam.HR_HR6Ac.2.2.log

Fri Dec 22 04:16:05 PM CET 2023  run samtools index HR_HR6Ac
FILE=HR_HR7Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:16:07 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta HR_HR7Ac.R1.fq.gz HR_HR7Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:HR_HR7ActSM:HR_HR7ActPL:Illumina 2> bwa.HR_HR7Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > HR_HR7Ac.2.2-RAW.bam 2>samtools.sort.bam.HR_HR7Ac.2.2.log

Fri Dec 22 04:16:57 PM CET 2023  run samtools index HR_HR7Ac
FILE=HR_HR9Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:16:59 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta HR_HR9Ac.R1.fq.gz HR_HR9Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:HR_HR9ActSM:HR_HR9ActPL:Illumina 2> bwa.HR_HR9Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > HR_HR9Ac.2.2-RAW.bam 2>samtools.sort.bam.HR_HR9Ac.2.2.log

Fri Dec 22 04:17:51 PM CET 2023  run samtools index HR_HR9Ac
FILE=LT_LT1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:17:52 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta LT_LT1Ac.R1.fq.gz LT_LT1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:LT_LT1ActSM:LT_LT1ActPL:Illumina 2> bwa.LT_LT1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > LT_LT1Ac.2.2-RAW.bam 2>samtools.sort.bam.LT_LT1Ac.2.2.log

Fri Dec 22 04:19:11 PM CET 2023  run samtools index LT_LT1Ac
FILE=LT_LT2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:19:13 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta LT_LT2Ac.R1.fq.gz LT_LT2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:LT_LT2ActSM:LT_LT2ActPL:Illumina 2> bwa.LT_LT2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > LT_LT2Ac.2.2-RAW.bam 2>samtools.sort.bam.LT_LT2Ac.2.2.log

Fri Dec 22 04:21:42 PM CET 2023  run samtools index LT_LT2Ac
FILE=LT_LT3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:21:46 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta LT_LT3Ac.R1.fq.gz LT_LT3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:LT_LT3ActSM:LT_LT3ActPL:Illumina 2> bwa.LT_LT3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > LT_LT3Ac.2.2-RAW.bam 2>samtools.sort.bam.LT_LT3Ac.2.2.log

Fri Dec 22 04:23:09 PM CET 2023  run samtools index LT_LT3Ac
FILE=LT_LT4Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:23:12 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta LT_LT4Ac.R1.fq.gz LT_LT4Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:LT_LT4ActSM:LT_LT4ActPL:Illumina 2> bwa.LT_LT4Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > LT_LT4Ac.2.2-RAW.bam 2>samtools.sort.bam.LT_LT4Ac.2.2.log

Fri Dec 22 04:24:46 PM CET 2023  run samtools index LT_LT4Ac
FILE=LT_LT5Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:24:48 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta LT_LT5Ac.R1.fq.gz LT_LT5Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:LT_LT5ActSM:LT_LT5ActPL:Illumina 2> bwa.LT_LT5Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > LT_LT5Ac.2.2-RAW.bam 2>samtools.sort.bam.LT_LT5Ac.2.2.log

Fri Dec 22 04:26:32 PM CET 2023  run samtools index LT_LT5Ac
FILE=LT_LT6Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:26:35 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta LT_LT6Ac.R1.fq.gz LT_LT6Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:LT_LT6ActSM:LT_LT6ActPL:Illumina 2> bwa.LT_LT6Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > LT_LT6Ac.2.2-RAW.bam 2>samtools.sort.bam.LT_LT6Ac.2.2.log

Fri Dec 22 04:27:37 PM CET 2023  run samtools index LT_LT6Ac
FILE=NO_NO10Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:27:39 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO10Ac.R1.fq.gz NO_NO10Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO10ActSM:NO_NO10ActPL:Illumina 2> bwa.NO_NO10Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO10Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO10Ac.2.2.log

Fri Dec 22 04:28:54 PM CET 2023  run samtools index NO_NO10Ac
FILE=NO_NO11Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:28:56 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO11Ac.R1.fq.gz NO_NO11Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO11ActSM:NO_NO11ActPL:Illumina 2> bwa.NO_NO11Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO11Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO11Ac.2.2.log

Fri Dec 22 04:29:53 PM CET 2023  run samtools index NO_NO11Ac
FILE=NO_NO12Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:29:55 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO12Ac.R1.fq.gz NO_NO12Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO12ActSM:NO_NO12ActPL:Illumina 2> bwa.NO_NO12Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO12Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO12Ac.2.2.log

Fri Dec 22 04:31:05 PM CET 2023  run samtools index NO_NO12Ac
FILE=NO_NO13Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:31:08 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO13Ac.R1.fq.gz NO_NO13Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO13ActSM:NO_NO13ActPL:Illumina 2> bwa.NO_NO13Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO13Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO13Ac.2.2.log

Fri Dec 22 04:32:03 PM CET 2023  run samtools index NO_NO13Ac
FILE=NO_NO14Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:32:05 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO14Ac.R1.fq.gz NO_NO14Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO14ActSM:NO_NO14ActPL:Illumina 2> bwa.NO_NO14Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO14Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO14Ac.2.2.log

Fri Dec 22 04:32:57 PM CET 2023  run samtools index NO_NO14Ac
FILE=NO_NO15Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:32:59 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO15Ac.R1.fq.gz NO_NO15Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO15ActSM:NO_NO15ActPL:Illumina 2> bwa.NO_NO15Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO15Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO15Ac.2.2.log

Fri Dec 22 04:34:10 PM CET 2023  run samtools index NO_NO15Ac
FILE=NO_NO16Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:34:12 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO16Ac.R1.fq.gz NO_NO16Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO16ActSM:NO_NO16ActPL:Illumina 2> bwa.NO_NO16Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO16Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO16Ac.2.2.log

Fri Dec 22 04:36:21 PM CET 2023  run samtools index NO_NO16Ac
FILE=NO_NO17Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:36:24 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO17Ac.R1.fq.gz NO_NO17Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO17ActSM:NO_NO17ActPL:Illumina 2> bwa.NO_NO17Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO17Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO17Ac.2.2.log

Fri Dec 22 04:38:22 PM CET 2023  run samtools index NO_NO17Ac
FILE=NO_NO18Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:38:26 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO18Ac.R1.fq.gz NO_NO18Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO18ActSM:NO_NO18ActPL:Illumina 2> bwa.NO_NO18Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO18Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO18Ac.2.2.log

Fri Dec 22 04:40:05 PM CET 2023  run samtools index NO_NO18Ac
FILE=NO_NO19Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:40:07 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO19Ac.R1.fq.gz NO_NO19Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO19ActSM:NO_NO19ActPL:Illumina 2> bwa.NO_NO19Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO19Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO19Ac.2.2.log

Fri Dec 22 04:41:53 PM CET 2023  run samtools index NO_NO19Ac
FILE=NO_NO1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:41:56 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO1Ac.R1.fq.gz NO_NO1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO1ActSM:NO_NO1ActPL:Illumina 2> bwa.NO_NO1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO1Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO1Ac.2.2.log

Fri Dec 22 04:43:04 PM CET 2023  run samtools index NO_NO1Ac
FILE=NO_NO20Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:43:06 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO20Ac.R1.fq.gz NO_NO20Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO20ActSM:NO_NO20ActPL:Illumina 2> bwa.NO_NO20Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO20Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO20Ac.2.2.log

Fri Dec 22 04:44:51 PM CET 2023  run samtools index NO_NO20Ac
FILE=NO_NO21Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:44:54 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO21Ac.R1.fq.gz NO_NO21Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO21ActSM:NO_NO21ActPL:Illumina 2> bwa.NO_NO21Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO21Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO21Ac.2.2.log

Fri Dec 22 04:46:21 PM CET 2023  run samtools index NO_NO21Ac
FILE=NO_NO22Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:46:24 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO22Ac.R1.fq.gz NO_NO22Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO22ActSM:NO_NO22ActPL:Illumina 2> bwa.NO_NO22Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO22Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO22Ac.2.2.log

Fri Dec 22 04:47:33 PM CET 2023  run samtools index NO_NO22Ac
FILE=NO_NO23Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:47:35 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO23Ac.R1.fq.gz NO_NO23Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO23ActSM:NO_NO23ActPL:Illumina 2> bwa.NO_NO23Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO23Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO23Ac.2.2.log

Fri Dec 22 04:49:04 PM CET 2023  run samtools index NO_NO23Ac
FILE=NO_NO24Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:49:07 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO24Ac.R1.fq.gz NO_NO24Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO24ActSM:NO_NO24ActPL:Illumina 2> bwa.NO_NO24Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO24Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO24Ac.2.2.log

Fri Dec 22 04:50:28 PM CET 2023  run samtools index NO_NO24Ac
FILE=NO_NO25Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:50:31 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO25Ac.R1.fq.gz NO_NO25Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO25ActSM:NO_NO25ActPL:Illumina 2> bwa.NO_NO25Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO25Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO25Ac.2.2.log

Fri Dec 22 04:52:16 PM CET 2023  run samtools index NO_NO25Ac
FILE=NO_NO27Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:52:19 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO27Ac.R1.fq.gz NO_NO27Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO27ActSM:NO_NO27ActPL:Illumina 2> bwa.NO_NO27Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO27Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO27Ac.2.2.log

Fri Dec 22 04:53:44 PM CET 2023  run samtools index NO_NO27Ac
FILE=NO_NO28Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:53:47 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO28Ac.R1.fq.gz NO_NO28Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO28ActSM:NO_NO28ActPL:Illumina 2> bwa.NO_NO28Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO28Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO28Ac.2.2.log

Fri Dec 22 04:55:31 PM CET 2023  run samtools index NO_NO28Ac
FILE=NO_NO29Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:55:34 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO29Ac.R1.fq.gz NO_NO29Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO29ActSM:NO_NO29ActPL:Illumina 2> bwa.NO_NO29Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO29Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO29Ac.2.2.log

Fri Dec 22 04:57:20 PM CET 2023  run samtools index NO_NO29Ac
FILE=NO_NO2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:57:23 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO2Ac.R1.fq.gz NO_NO2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO2ActSM:NO_NO2ActPL:Illumina 2> bwa.NO_NO2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO2Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO2Ac.2.2.log

Fri Dec 22 04:58:41 PM CET 2023  run samtools index NO_NO2Ac
FILE=NO_NO30Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 04:58:43 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO30Ac.R1.fq.gz NO_NO30Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO30ActSM:NO_NO30ActPL:Illumina 2> bwa.NO_NO30Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO30Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO30Ac.2.2.log

Fri Dec 22 04:59:59 PM CET 2023  run samtools index NO_NO30Ac
FILE=NO_NO31Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:00:01 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO31Ac.R1.fq.gz NO_NO31Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO31ActSM:NO_NO31ActPL:Illumina 2> bwa.NO_NO31Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO31Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO31Ac.2.2.log

Fri Dec 22 05:01:24 PM CET 2023  run samtools index NO_NO31Ac
FILE=NO_NO32Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:01:26 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO32Ac.R1.fq.gz NO_NO32Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO32ActSM:NO_NO32ActPL:Illumina 2> bwa.NO_NO32Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO32Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO32Ac.2.2.log

Fri Dec 22 05:03:23 PM CET 2023  run samtools index NO_NO32Ac
FILE=NO_NO33Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:03:26 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO33Ac.R1.fq.gz NO_NO33Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO33ActSM:NO_NO33ActPL:Illumina 2> bwa.NO_NO33Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO33Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO33Ac.2.2.log

Fri Dec 22 05:04:45 PM CET 2023  run samtools index NO_NO33Ac
FILE=NO_NO34Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:04:47 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO34Ac.R1.fq.gz NO_NO34Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO34ActSM:NO_NO34ActPL:Illumina 2> bwa.NO_NO34Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO34Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO34Ac.2.2.log

Fri Dec 22 05:07:18 PM CET 2023  run samtools index NO_NO34Ac
FILE=NO_NO35Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:07:22 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO35Ac.R1.fq.gz NO_NO35Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO35ActSM:NO_NO35ActPL:Illumina 2> bwa.NO_NO35Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO35Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO35Ac.2.2.log

Fri Dec 22 05:09:17 PM CET 2023  run samtools index NO_NO35Ac
FILE=NO_NO3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:09:20 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO3Ac.R1.fq.gz NO_NO3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO3ActSM:NO_NO3ActPL:Illumina 2> bwa.NO_NO3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO3Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO3Ac.2.2.log

Fri Dec 22 05:10:10 PM CET 2023  run samtools index NO_NO3Ac
FILE=NO_NO4Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:10:11 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO4Ac.R1.fq.gz NO_NO4Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO4ActSM:NO_NO4ActPL:Illumina 2> bwa.NO_NO4Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO4Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO4Ac.2.2.log

Fri Dec 22 05:10:59 PM CET 2023  run samtools index NO_NO4Ac
FILE=NO_NO5Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:11:01 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO5Ac.R1.fq.gz NO_NO5Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO5ActSM:NO_NO5ActPL:Illumina 2> bwa.NO_NO5Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO5Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO5Ac.2.2.log

Fri Dec 22 05:11:44 PM CET 2023  run samtools index NO_NO5Ac
FILE=NO_NO6Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:11:46 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO6Ac.R1.fq.gz NO_NO6Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO6ActSM:NO_NO6ActPL:Illumina 2> bwa.NO_NO6Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO6Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO6Ac.2.2.log

Fri Dec 22 05:13:23 PM CET 2023  run samtools index NO_NO6Ac
FILE=NO_NO7Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:13:26 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO7Ac.R1.fq.gz NO_NO7Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO7ActSM:NO_NO7ActPL:Illumina 2> bwa.NO_NO7Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO7Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO7Ac.2.2.log

Fri Dec 22 05:14:10 PM CET 2023  run samtools index NO_NO7Ac
FILE=NO_NO8Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:14:12 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO8Ac.R1.fq.gz NO_NO8Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO8ActSM:NO_NO8ActPL:Illumina 2> bwa.NO_NO8Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO8Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO8Ac.2.2.log

Fri Dec 22 05:15:16 PM CET 2023  run samtools index NO_NO8Ac
FILE=NO_NO9Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:15:18 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta NO_NO9Ac.R1.fq.gz NO_NO9Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:NO_NO9ActSM:NO_NO9ActPL:Illumina 2> bwa.NO_NO9Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > NO_NO9Ac.2.2-RAW.bam 2>samtools.sort.bam.NO_NO9Ac.2.2.log

Fri Dec 22 05:16:41 PM CET 2023  run samtools index NO_NO9Ac
FILE=PL_PL1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:16:43 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta PL_PL1Ac.R1.fq.gz PL_PL1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:PL_PL1ActSM:PL_PL1ActPL:Illumina 2> bwa.PL_PL1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > PL_PL1Ac.2.2-RAW.bam 2>samtools.sort.bam.PL_PL1Ac.2.2.log

Fri Dec 22 05:18:56 PM CET 2023  run samtools index PL_PL1Ac
FILE=PL_PL2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:19:00 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta PL_PL2Ac.R1.fq.gz PL_PL2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:PL_PL2ActSM:PL_PL2ActPL:Illumina 2> bwa.PL_PL2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > PL_PL2Ac.2.2-RAW.bam 2>samtools.sort.bam.PL_PL2Ac.2.2.log

Fri Dec 22 05:19:52 PM CET 2023  run samtools index PL_PL2Ac
FILE=PL_PL3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:19:54 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta PL_PL3Ac.R1.fq.gz PL_PL3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:PL_PL3ActSM:PL_PL3ActPL:Illumina 2> bwa.PL_PL3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > PL_PL3Ac.2.2-RAW.bam 2>samtools.sort.bam.PL_PL3Ac.2.2.log

Fri Dec 22 05:20:50 PM CET 2023  run samtools index PL_PL3Ac
FILE=RU_RU1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:20:52 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta RU_RU1Ac.R1.fq.gz RU_RU1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:RU_RU1ActSM:RU_RU1ActPL:Illumina 2> bwa.RU_RU1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > RU_RU1Ac.2.2-RAW.bam 2>samtools.sort.bam.RU_RU1Ac.2.2.log

Fri Dec 22 05:22:10 PM CET 2023  run samtools index RU_RU1Ac
FILE=RU_RU2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:22:12 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta RU_RU2Ac.R1.fq.gz RU_RU2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:RU_RU2ActSM:RU_RU2ActPL:Illumina 2> bwa.RU_RU2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > RU_RU2Ac.2.2-RAW.bam 2>samtools.sort.bam.RU_RU2Ac.2.2.log

Fri Dec 22 05:23:41 PM CET 2023  run samtools index RU_RU2Ac
FILE=RU_RU3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:23:44 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta RU_RU3Ac.R1.fq.gz RU_RU3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:RU_RU3ActSM:RU_RU3ActPL:Illumina 2> bwa.RU_RU3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > RU_RU3Ac.2.2-RAW.bam 2>samtools.sort.bam.RU_RU3Ac.2.2.log

Fri Dec 22 05:23:51 PM CET 2023  run samtools index RU_RU3Ac
FILE=RU_RU4Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:23:52 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta RU_RU4Ac.R1.fq.gz RU_RU4Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:RU_RU4ActSM:RU_RU4ActPL:Illumina 2> bwa.RU_RU4Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > RU_RU4Ac.2.2-RAW.bam 2>samtools.sort.bam.RU_RU4Ac.2.2.log

Fri Dec 22 05:24:16 PM CET 2023  run samtools index RU_RU4Ac
FILE=RU_RU5Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:24:17 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta RU_RU5Ac.R1.fq.gz RU_RU5Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:RU_RU5ActSM:RU_RU5ActPL:Illumina 2> bwa.RU_RU5Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > RU_RU5Ac.2.2-RAW.bam 2>samtools.sort.bam.RU_RU5Ac.2.2.log

Fri Dec 22 05:25:18 PM CET 2023  run samtools index RU_RU5Ac
FILE=RU_RU6Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:25:20 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta RU_RU6Ac.R1.fq.gz RU_RU6Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:RU_RU6ActSM:RU_RU6ActPL:Illumina 2> bwa.RU_RU6Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > RU_RU6Ac.2.2-RAW.bam 2>samtools.sort.bam.RU_RU6Ac.2.2.log

Fri Dec 22 05:26:05 PM CET 2023  run samtools index RU_RU6Ac
FILE=SK_SK1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:26:07 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta SK_SK1Ac.R1.fq.gz SK_SK1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:SK_SK1ActSM:SK_SK1ActPL:Illumina 2> bwa.SK_SK1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > SK_SK1Ac.2.2-RAW.bam 2>samtools.sort.bam.SK_SK1Ac.2.2.log

Fri Dec 22 05:28:44 PM CET 2023  run samtools index SK_SK1Ac
FILE=SK_SK2Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:28:49 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta SK_SK2Ac.R1.fq.gz SK_SK2Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:SK_SK2ActSM:SK_SK2ActPL:Illumina 2> bwa.SK_SK2Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > SK_SK2Ac.2.2-RAW.bam 2>samtools.sort.bam.SK_SK2Ac.2.2.log

Fri Dec 22 05:31:04 PM CET 2023  run samtools index SK_SK2Ac
FILE=SK_SK3Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:31:07 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta SK_SK3Ac.R1.fq.gz SK_SK3Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:SK_SK3ActSM:SK_SK3ActPL:Illumina 2> bwa.SK_SK3Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > SK_SK3Ac.2.2-RAW.bam 2>samtools.sort.bam.SK_SK3Ac.2.2.log

Fri Dec 22 05:32:50 PM CET 2023  run samtools index SK_SK3Ac
FILE=SK_SK4Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:32:52 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta SK_SK4Ac.R1.fq.gz SK_SK4Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:SK_SK4ActSM:SK_SK4ActPL:Illumina 2> bwa.SK_SK4Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > SK_SK4Ac.2.2-RAW.bam 2>samtools.sort.bam.SK_SK4Ac.2.2.log

Fri Dec 22 05:34:53 PM CET 2023  run samtools index SK_SK4Ac
FILE=SK_SK5Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:34:56 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta SK_SK5Ac.R1.fq.gz SK_SK5Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:SK_SK5ActSM:SK_SK5ActPL:Illumina 2> bwa.SK_SK5Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > SK_SK5Ac.2.2-RAW.bam 2>samtools.sort.bam.SK_SK5Ac.2.2.log

Fri Dec 22 05:36:39 PM CET 2023  run samtools index SK_SK5Ac
FILE=US_US1Ac
CUTOFFS=2.2
MAPPING_CLIPPING_PENALTY=30,5
MAPPING_MIN_ALIGNMENT_SCORE=50
optA=1
optB=6
optO=10
freeMEM=41279092
memSortPerPARALLEL=41279080
threadsPerPARALLEL=40
threadsSortPerPARALLEL=40
memSortPerThreadPerPARALLEL=1031977
ATYPE=PE
INSERT_MEAN=
INSERT_SD=
INSERT_MAX=
INSERT_MIN=

Fri Dec 22 05:36:42 PM CET 2023  Running bwa-meme_mode1 (RAM: 38G, Free Memory: 41279092)
      bwa-meme_mode1 mem -7 reference.2.2.fasta US_US1Ac.R1.fq.gz US_US1Ac.R2.fq.gz -L 30,5 -t  -a -M -T 50 -A 1 -B 6 -O 10 -R @RGtID:US_US1ActSM:US_US1ActPL:Illumina 2> bwa.US_US1Ac.2.2.log | mbuffer -m 41279080 | samtools sort -m  --output-fmt bam,level=1 -@ 40 > US_US1Ac.2.2-RAW.bam 2>samtools.sort.bam.US_US1Ac.2.2.log

Fri Dec 22 05:37:13 PM CET 2023  run samtools index US_US1Ac

Fri Dec 22 05:37:14 PM CET 2023 mkBAM completed!

Compress large filesFri Dec 22 05:37:16 PM CET 2023