STAR version=2.7.11b
STAR compilation time,server,dir=2024-11-25T09:14:51+0000 :/opt/conda/conda-bld/star_1732525954305/work/source
##### Command Line:
/home/keita/miniconda3/bin/STAR-avx2 --runThreadN 1 --genomeDir 001_data/001_reference/STAR_index_chr8_MYC_masked --readFilesIn 006_fastq/pg_005_07_tiny1.cb.umi.qc.woAdapter.trimPolyA.fastq --outFileNamePrefix 006_fastq/pg_006_01_tiny1.star_
##### Initial USER parameters from Command Line:
outFileNamePrefix                 006_fastq/pg_006_01_tiny1.star_
###### All USER parameters from Command Line:
runThreadN                    1     ~RE-DEFINED
genomeDir                     001_data/001_reference/STAR_index_chr8_MYC_masked     ~RE-DEFINED
readFilesIn                   006_fastq/pg_005_07_tiny1.cb.umi.qc.woAdapter.trimPolyA.fastq        ~RE-DEFINED
outFileNamePrefix             006_fastq/pg_006_01_tiny1.star_     ~RE-DEFINED
##### Finished reading parameters from all sources

##### Final user re-defined parameters-----------------:
runThreadN                        1
genomeDir                         001_data/001_reference/STAR_index_chr8_MYC_masked
readFilesIn                       006_fastq/pg_005_07_tiny1.cb.umi.qc.woAdapter.trimPolyA.fastq   
outFileNamePrefix                 006_fastq/pg_006_01_tiny1.star_

-------------------------------
##### Final effective command line:
/home/keita/miniconda3/bin/STAR-avx2   --runThreadN 1   --genomeDir 001_data/001_reference/STAR_index_chr8_MYC_masked   --readFilesIn 006_fastq/pg_005_07_tiny1.cb.umi.qc.woAdapter.trimPolyA.fastq      --outFileNamePrefix 006_fastq/pg_006_01_tiny1.star_
----------------------------------------

Number of fastq files for each mate = 1
ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters:  3000 0.99 10
Finished loading and checking parameters
Reading genome generation parameters:
### /home/keita/miniconda3/bin/STAR-avx2   --runMode genomeGenerate      --runThreadN 4   --genomeDir 001_data/001_reference/STAR_index_chr8_MYC_masked   --genomeFastaFiles 001_data/001_reference/chr8_MYC_masked.fa      --genomeSAindexNbases 10   --sjdbGTFfile 001_data/001_reference/myc.gtf   --sjdbOverhang 100
### GstrandBit=32
versionGenome                 2.7.4a     ~RE-DEFINED
genomeType                    Full     ~RE-DEFINED
genomeFastaFiles              001_data/001_reference/chr8_MYC_masked.fa        ~RE-DEFINED
genomeSAindexNbases           10     ~RE-DEFINED
genomeChrBinNbits             18     ~RE-DEFINED
genomeSAsparseD               1     ~RE-DEFINED
genomeTransformType           None     ~RE-DEFINED
genomeTransformVCF            -     ~RE-DEFINED
sjdbOverhang                  100     ~RE-DEFINED
sjdbFileChrStartEnd           -        ~RE-DEFINED
sjdbGTFfile                   001_data/001_reference/myc.gtf     ~RE-DEFINED
sjdbGTFchrPrefix              -     ~RE-DEFINED
sjdbGTFfeatureExon            exon     ~RE-DEFINED
sjdbGTFtagExonParentTranscripttranscript_id     ~RE-DEFINED
sjdbGTFtagExonParentGene      gene_id     ~RE-DEFINED
sjdbInsertSave                Basic     ~RE-DEFINED
genomeFileSizes               145230188   81819        ~RE-DEFINED
Genome version is compatible with current STAR
Number of real (reference) chromosomes= 1
1	8	145138636	0
--sjdbOverhang = 100 taken from the generated genome
Started loading the genome: Tue Dec  2 14:21:11 2025

Genome: size given as a parameter = 145230188
SA: size given as a parameter = 81819
SAindex: size given as a parameter = 1
Read from SAindex: pGe.gSAindexNbases=10  nSAi=1398100
nGenome=145230188;  nSAbyte=81819
GstrandBit=32   SA number of indices=19834
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 145230188 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 145230188 bytes
SA file size: 81819 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 81819 bytes
Loading SAindex ... done: 6116787 bytes
Finished loading the genome: Tue Dec  2 14:21:12 2025

Processing splice junctions database sjdbN=12,   pGe.sjdbOverhang=100 
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Thread #0 end of input stream, nextChar=-1
Completed: thread #0
Dec 02 14:21:12 ..... finished mapping
RAM after mapping:
VmPeak:	  308324 kB; VmSize:	  308324 kB; VmHWM:	  253732 kB; VmRSS:	  253732 kB; 
RAM after freeing genome index memory:
VmPeak:	  308324 kB; VmSize:	  160520 kB; VmHWM:	  253732 kB; VmRSS:	  105996 kB; 
ALL DONE!