STAR version=2.7.10a
STAR compilation time,server,dir=2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
STAR git: On branch master ; commit ae26add7ea1724f3281ec8abedb71bcff6a4ae73 ; diff files: CHANGES.md README.md RELEASEnotes.md doc/STARmanual.pdf extras/doc-latex/STARmanual.tex extras/doc-latex/convertParDefToLatexTable.awk extras/doc-latex/parametersDefault.tex extras/docker/Dockerfile source/VERSION
##### Command Line:
STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz input2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:659_bGW-T1-TRNA-1_B23WHTKLT4_1 SM:659_bGW-T1-TRNA-1_B23WHTKLT4_1 --twopassMode None --chimSegmentMin 12 --chimJunctionOverhangMin 5 --chimMultimapNmax 50 --chimScoreJunctionNonGTAG -4 --chimScoreSeparation 1 --alignIntronMax 140000 --outReadsUnmapped None --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMunmapped Within --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLmin 30 --alignSplicedMateMapLminOverLmate 0.5 --quantMode GeneCounts --runRNGseed 1 --chimOutType Junctions WithinBAM --limitBAMsortRAM 38654705664
##### Initial USER parameters from Command Line:
outFileNamePrefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1.
###### All USER parameters from Command Line:
genomeDir ref_genome.fa.star.idx ~RE-DEFINED
readFilesIn input1/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz input2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz ~RE-DEFINED
runThreadN 24 ~RE-DEFINED
outFileNamePrefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1. ~RE-DEFINED
sjdbGTFfile ref_annot.gtf ~RE-DEFINED
outSAMattrRGline ID:659_bGW-T1-TRNA-1_B23WHTKLT4_1 SM:659_bGW-T1-TRNA-1_B23WHTKLT4_1 ~RE-DEFINED
twopassMode None ~RE-DEFINED
chimSegmentMin 12 ~RE-DEFINED
chimJunctionOverhangMin 5 ~RE-DEFINED
chimMultimapNmax 50 ~RE-DEFINED
chimScoreJunctionNonGTAG -4 ~RE-DEFINED
chimScoreSeparation 1 ~RE-DEFINED
alignIntronMax 140000 ~RE-DEFINED
outReadsUnmapped None ~RE-DEFINED
readFilesCommand zcat ~RE-DEFINED
outSAMtype BAM SortedByCoordinate ~RE-DEFINED
outSAMstrandField intronMotif ~RE-DEFINED
outSAMunmapped Within ~RE-DEFINED
chimOutJunctionFormat 1 ~RE-DEFINED
alignSJDBoverhangMin 10 ~RE-DEFINED
alignMatesGapMax 100000 ~RE-DEFINED
alignSJstitchMismatchNmax 5 -1 5 5 ~RE-DEFINED
chimMultimapScoreRange 3 ~RE-DEFINED
chimNonchimScoreDropMin 10 ~RE-DEFINED
peOverlapNbasesMin 12 ~RE-DEFINED
peOverlapMMp 0.1 ~RE-DEFINED
alignInsertionFlush Right ~RE-DEFINED
alignSplicedMateMapLmin 30 ~RE-DEFINED
alignSplicedMateMapLminOverLmate0.5 ~RE-DEFINED
quantMode GeneCounts ~RE-DEFINED
runRNGseed 1 ~RE-DEFINED
chimOutType Junctions WithinBAM ~RE-DEFINED
limitBAMsortRAM 38654705664 ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runThreadN 24
runRNGseed 1
genomeDir ref_genome.fa.star.idx
readFilesIn input1/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz input2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz
readFilesCommand zcat
limitBAMsortRAM 38654705664
outFileNamePrefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1.
outReadsUnmapped None
outSAMtype BAM SortedByCoordinate
outSAMstrandField intronMotif
outSAMunmapped Within
outSAMattrRGline ID:659_bGW-T1-TRNA-1_B23WHTKLT4_1 SM:659_bGW-T1-TRNA-1_B23WHTKLT4_1
alignIntronMax 140000
alignMatesGapMax 100000
alignSJDBoverhangMin 10
alignSJstitchMismatchNmax 5 -1 5 5
alignSplicedMateMapLmin 30
alignSplicedMateMapLminOverLmate 0.5
alignInsertionFlush Right
peOverlapNbasesMin 12
peOverlapMMp 0.1
chimSegmentMin 12
chimScoreSeparation 1
chimScoreJunctionNonGTAG -4
chimJunctionOverhangMin 5
chimOutType Junctions WithinBAM
chimMultimapNmax 50
chimMultimapScoreRange 3
chimNonchimScoreDropMin 10
chimOutJunctionFormat 1
sjdbGTFfile ref_annot.gtf
quantMode GeneCounts
twopassMode None
-------------------------------
##### Final effective command line:
STAR --runThreadN 24 --runRNGseed 1 --genomeDir ref_genome.fa.star.idx --readFilesIn input1/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz input2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --readFilesCommand zcat --limitBAMsortRAM 38654705664 --outFileNamePrefix 659_bGW-T1-TRNA-1_B23WHTKLT4_1. --outReadsUnmapped None --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMattrRGline ID:659_bGW-T1-TRNA-1_B23WHTKLT4_1 SM:659_bGW-T1-TRNA-1_B23WHTKLT4_1 --alignIntronMax 140000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSplicedMateMapLmin 30 --alignSplicedMateMapLminOverLmate 0.5 --alignInsertionFlush Right --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimSegmentMin 12 --chimScoreSeparation 1 --chimScoreJunctionNonGTAG -4 --chimJunctionOverhangMin 5 --chimOutType Junctions WithinBAM --chimMultimapNmax 50 --chimMultimapScoreRange 3 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --sjdbGTFfile ref_annot.gtf --quantMode GeneCounts --twopassMode None
----------------------------------------
Number of fastq files for each mate = 1
Input read files for mate 1 :
-rw-r--r-- 1 1000 root 16424567950 Jun 8 07:39 input1/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz
readsCommandsFile:
exec > "659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp/tmp.fifo.read1"
echo FILE 0
zcat "input1/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz"
Input read files for mate 2 :
-rw-r--r-- 1 1000 root 16625747795 Jun 8 07:39 input2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz
readsCommandsFile:
exec > "659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp/tmp.fifo.read2"
echo FILE 0
zcat "input2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute
WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute
ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10
Finished loading and checking parameters
Reading genome generation parameters:
### STAR --runMode genomeGenerate --runThreadN 4 --genomeDir /seq/RNASEQ/__ctat_genome_lib_building/Mar2021/GRCh38_gencode_v37_CTAT_lib_Mar012021/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --genomeFastaFiles /seq/RNASEQ/__ctat_genome_lib_building/Mar2021/GRCh38_gencode_v37_CTAT_lib_Mar012021/GRCh38.primary_assembly.genome.fa.pseudo_masked.fa --genomeChrBinNbits 16 --limitGenomeGenerateRAM 40419136213 --sjdbGTFfile /seq/RNASEQ/__ctat_genome_lib_building/Mar2021/GRCh38_gencode_v37_CTAT_lib_Mar012021/gencode.v37.annotation.gtf.revised.custom.gtf --sjdbOverhang 150
### GstrandBit=32
versionGenome 2.7.4a ~RE-DEFINED
genomeType Full ~RE-DEFINED
genomeFastaFiles /seq/RNASEQ/__ctat_genome_lib_building/Mar2021/GRCh38_gencode_v37_CTAT_lib_Mar012021/GRCh38.primary_assembly.genome.fa.pseudo_masked.fa ~RE-DEFINED
genomeSAindexNbases 14 ~RE-DEFINED
genomeChrBinNbits 16 ~RE-DEFINED
genomeSAsparseD 1 ~RE-DEFINED
genomeTransformType None ~RE-DEFINED
genomeTransformVCF - ~RE-DEFINED
sjdbOverhang 150 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
sjdbGTFfile /seq/RNASEQ/__ctat_genome_lib_building/Mar2021/GRCh38_gencode_v37_CTAT_lib_Mar012021/gencode.v37.annotation.gtf.revised.custom.gtf ~RE-DEFINED
sjdbGTFchrPrefix - ~RE-DEFINED
sjdbGTFfeatureExon exon ~RE-DEFINED
sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED
sjdbGTFtagExonParentGene gene_id ~RE-DEFINED
sjdbInsertSave Basic ~RE-DEFINED
genomeFileSizes 3225043118 25262353185 ~RE-DEFINED
Genome version is compatible with current STAR
Number of real (reference) chromosomes= 194
1 chr1 248956422 0
2 chr2 242193529 248971264
3 chr3 198295559 491192320
4 chr4 190214555 689504256
5 chr5 181538259 879755264
6 chr6 170805979 1061355520
7 chr7 159345973 1232207872
8 chr8 145138636 1391591424
9 chr9 138394717 1536753664
10 chr10 133797422 1675165696
11 chr11 135086622 1808990208
12 chr12 133275309 1944125440
13 chr13 114364328 2077425664
14 chr14 107043718 2191851520
15 chr15 101991189 2298937344
16 chr16 90338345 2400976896
17 chr17 83257441 2491351040
18 chr18 80373285 2574647296
19 chr19 58617616 2655059968
20 chr20 64444167 2713714688
21 chr21 46709983 2778202112
22 chr22 50818468 2824929280
23 chrX 156040895 2875785216
24 chrY 57227415 3031826432
25 chrM 16569 3089104896
26 GL000008.2 209709 3089170432
27 GL000009.2 201709 3089432576
28 GL000194.1 191469 3089694720
29 GL000195.1 182896 3089891328
30 GL000205.2 185591 3090087936
31 GL000208.1 92689 3090284544
32 GL000213.1 164239 3090415616
33 GL000214.1 137718 3090612224
34 GL000216.2 176608 3090808832
35 GL000218.1 161147 3091005440
36 GL000219.1 179198 3091202048
37 GL000220.1 161802 3091398656
38 GL000221.1 155397 3091595264
39 GL000224.1 179693 3091791872
40 GL000225.1 211173 3091988480
41 GL000226.1 15008 3092250624
42 KI270302.1 2274 3092316160
43 KI270303.1 1942 3092381696
44 KI270304.1 2165 3092447232
45 KI270305.1 1472 3092512768
46 KI270310.1 1201 3092578304
47 KI270311.1 12399 3092643840
48 KI270312.1 998 3092709376
49 KI270315.1 2276 3092774912
50 KI270316.1 1444 3092840448
51 KI270317.1 37690 3092905984
52 KI270320.1 4416 3092971520
53 KI270322.1 21476 3093037056
54 KI270329.1 1040 3093102592
55 KI270330.1 1652 3093168128
56 KI270333.1 2699 3093233664
57 KI270334.1 1368 3093299200
58 KI270335.1 1048 3093364736
59 KI270336.1 1026 3093430272
60 KI270337.1 1121 3093495808
61 KI270338.1 1428 3093561344
62 KI270340.1 1428 3093626880
63 KI270362.1 3530 3093692416
64 KI270363.1 1803 3093757952
65 KI270364.1 2855 3093823488
66 KI270366.1 8320 3093889024
67 KI270371.1 2805 3093954560
68 KI270372.1 1650 3094020096
69 KI270373.1 1451 3094085632
70 KI270374.1 2656 3094151168
71 KI270375.1 2378 3094216704
72 KI270376.1 1136 3094282240
73 KI270378.1 1048 3094347776
74 KI270379.1 1045 3094413312
75 KI270381.1 1930 3094478848
76 KI270382.1 4215 3094544384
77 KI270383.1 1750 3094609920
78 KI270384.1 1658 3094675456
79 KI270385.1 990 3094740992
80 KI270386.1 1788 3094806528
81 KI270387.1 1537 3094872064
82 KI270388.1 1216 3094937600
83 KI270389.1 1298 3095003136
84 KI270390.1 2387 3095068672
85 KI270391.1 1484 3095134208
86 KI270392.1 971 3095199744
87 KI270393.1 1308 3095265280
88 KI270394.1 970 3095330816
89 KI270395.1 1143 3095396352
90 KI270396.1 1880 3095461888
91 KI270411.1 2646 3095527424
92 KI270412.1 1179 3095592960
93 KI270414.1 2489 3095658496
94 KI270417.1 2043 3095724032
95 KI270418.1 2145 3095789568
96 KI270419.1 1029 3095855104
97 KI270420.1 2321 3095920640
98 KI270422.1 1445 3095986176
99 KI270423.1 981 3096051712
100 KI270424.1 2140 3096117248
101 KI270425.1 1884 3096182784
102 KI270429.1 1361 3096248320
103 KI270435.1 92983 3096313856
104 KI270438.1 112505 3096444928
105 KI270442.1 392061 3096576000
106 KI270448.1 7992 3096969216
107 KI270465.1 1774 3097034752
108 KI270466.1 1233 3097100288
109 KI270467.1 3920 3097165824
110 KI270468.1 4055 3097231360
111 KI270507.1 5353 3097296896
112 KI270508.1 1951 3097362432
113 KI270509.1 2318 3097427968
114 KI270510.1 2415 3097493504
115 KI270511.1 8127 3097559040
116 KI270512.1 22689 3097624576
117 KI270515.1 6361 3097690112
118 KI270516.1 1300 3097755648
119 KI270517.1 3253 3097821184
120 KI270518.1 2186 3097886720
121 KI270519.1 138126 3097952256
122 KI270521.1 7642 3098148864
123 KI270522.1 5674 3098214400
124 KI270528.1 2983 3098279936
125 KI270529.1 1899 3098345472
126 KI270530.1 2168 3098411008
127 KI270538.1 91309 3098476544
128 KI270539.1 993 3098607616
129 KI270544.1 1202 3098673152
130 KI270548.1 1599 3098738688
131 KI270579.1 31033 3098804224
132 KI270580.1 1553 3098869760
133 KI270581.1 7046 3098935296
134 KI270582.1 6504 3099000832
135 KI270583.1 1400 3099066368
136 KI270584.1 4513 3099131904
137 KI270587.1 2969 3099197440
138 KI270588.1 6158 3099262976
139 KI270589.1 44474 3099328512
140 KI270590.1 4685 3099394048
141 KI270591.1 5796 3099459584
142 KI270593.1 3041 3099525120
143 KI270706.1 175055 3099590656
144 KI270707.1 32032 3099787264
145 KI270708.1 127682 3099852800
146 KI270709.1 66860 3099983872
147 KI270710.1 40176 3100114944
148 KI270711.1 42210 3100180480
149 KI270712.1 176043 3100246016
150 KI270713.1 40745 3100442624
151 KI270714.1 41717 3100508160
152 KI270715.1 161471 3100573696
153 KI270716.1 153799 3100770304
154 KI270717.1 40062 3100966912
155 KI270718.1 38054 3101032448
156 KI270719.1 176845 3101097984
157 KI270720.1 39050 3101294592
158 KI270721.1 100316 3101360128
159 KI270722.1 194050 3101491200
160 KI270723.1 38115 3101687808
161 KI270724.1 39555 3101753344
162 KI270725.1 172810 3101818880
163 KI270726.1 43739 3102015488
164 KI270727.1 448248 3102081024
165 KI270728.1 1872759 3102539776
166 KI270729.1 280839 3104440320
167 KI270730.1 112551 3104768000
168 KI270731.1 150754 3104899072
169 KI270732.1 41543 3105095680
170 KI270733.1 179772 3105161216
171 KI270734.1 165050 3105357824
172 KI270735.1 42811 3105554432
173 KI270736.1 181920 3105619968
174 KI270737.1 103838 3105816576
175 KI270738.1 99375 3105947648
176 KI270739.1 73985 3106078720
177 KI270740.1 37240 3106209792
178 KI270741.1 157432 3106275328
179 KI270742.1 186739 3106471936
180 KI270743.1 210658 3106668544
181 KI270744.1 168472 3106930688
182 KI270745.1 41891 3107127296
183 KI270746.1 66486 3107192832
184 KI270747.1 198735 3107323904
185 KI270748.1 93321 3107586048
186 KI270749.1 158759 3107717120
187 KI270750.1 148850 3107913728
188 KI270751.1 150742 3108110336
189 KI270752.1 27745 3108306944
190 KI270753.1 62944 3108372480
191 KI270754.1 40191 3108438016
192 KI270755.1 36723 3108503552
193 KI270756.1 79590 3108569088
194 KI270757.1 71251 3108700160
--sjdbOverhang = 150 taken from the generated genome
Started loading the genome: Mon Jun 8 07:39:23 2026
Genome: size given as a parameter = 3225043118
SA: size given as a parameter = 25262353185
SAindex: size given as a parameter = 1
Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940
nGenome=3225043118; nSAbyte=25262353185
GstrandBit=32 SA number of indices=6124206832
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 3225043118 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3225043118 bytes
SA file size: 25262353185 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 25262353185 bytes
Loading SAindex ... done: 1565873619 bytes
Finished loading the genome: Mon Jun 8 07:39:51 2026
Processing splice junctions database sjdbN=386086, pGe.sjdbOverhang=150
To accommodate alignIntronMax=140000 redefined winBinNbits=16
To accommodate alignIntronMax=140000 and alignMatesGapMax=100000, redefined winFlankNbins=3 and winAnchorDistNbins=6
Jun 08 07:39:51 Loaded database junctions from the generated genome ref_genome.fa.star.idx//sjdbList.out.tab: 386086 total junctions
Jun 08 07:39:51 ..... processing annotations GTF
Processing pGe.sjdbGTFfile=ref_annot.gtf, found:
232170 transcripts
1442754 exons (non-collapsed)
386143 collapsed junctions
Total junctions: 772229
Jun 08 07:40:02 ..... finished GTF processing
Jun 08 07:40:03 Finished preparing junctions
Jun 08 07:40:03 ..... inserting junctions into the genome indices
Jun 08 07:40:06 Finished SA search: number of new junctions=0, old junctions=386086
Jun 08 07:40:06 Finished sorting SA indicesL nInd=0
Genome size with junctions=3225043118 3108831232 116211886
GstrandBit1=32 GstrandBit=32
Jun 08 07:41:40 Finished inserting junction indices
Jun 08 07:41:44 Finished SAi
Jun 08 07:41:45 ..... finished inserting junctions into genome
WARNING --chimOutType=WithinBAM, therefore STAR will output NM attribute
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread0 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread1 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread2 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread3 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread4 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread5 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread6 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread7 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread8 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread9 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread10 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread11 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread12 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread13 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread14 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread15 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread16 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread17 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread18 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread19 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread20 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread21 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread22 ... ok
Opening the file: 659_bGW-T1-TRNA-1_B23WHTKLT4_1._STARtmp//Chimeric.out.junction.thread23 ... ok
Created thread # 1
Starting to map file # 0
mate 1: input1/659_bGW-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz
mate 2: input2/659_bGW-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz
Created thread # 2
Created thread # 3
Created thread # 4
Created thread # 5
Created thread # 6
Created thread # 7
Created thread # 8
Created thread # 9
Created thread # 10
Created thread # 11
Created thread # 12
Created thread # 13
Created thread # 14
Created thread # 15
Created thread # 16
Created thread # 17
Created thread # 18
Created thread # 19
Created thread # 20
Created thread # 21
Created thread # 22
Created thread # 23
BAM sorting: 144141 mapped reads
BAM sorting bins genomic start loci:
1 0 26761010
2 0 109625752
3 0 156137130
4 0 225567295
5 1 43224326
6 1 144398631
7 1 197495311
8 1 219418476
9 2 47825095
10 2 129265745
11 3 8607822
12 4 1076170
13 4 142594580
14 5 28251821
15 5 41598853
16 5 167951239
17 6 73477139
18 6 100998379
19 6 150861058
20 7 117807221
21 7 143868870
22 8 104792855
23 8 137605721
24 9 80163578
25 10 1926699
26 10 62532507
27 10 75569043
28 11 10715755
29 11 57154554
30 11 130874632
31 13 23034723
32 13 102030269
33 14 48432940
34 14 101065803
35 15 18380351
36 15 57788525
37 16 5002461
38 16 42855443
39 16 50190915
40 16 51169962
41 17 49488524
42 18 12720883
43 18 39424382
44 18 48966326
45 19 35174932
46 20 8397782
47 21 37492535
48 22 71101347
Thread #16 end of input stream, nextChar=-1
Completed: thread #15
Completed: thread #20
Completed: thread #3
Completed: thread #22
Completed: thread #12
Completed: thread #6
Completed: thread #2
Completed: thread #18
Completed: thread #4
Completed: thread #10
Completed: thread #19
Completed: thread #7
Completed: thread #8
Completed: thread #9
Completed: thread #17
Completed: thread #1
Completed: thread #13
Completed: thread #14
Completed: thread #0
Joined thread # 1
Joined thread # 2
Joined thread # 3
Joined thread # 4
Completed: thread #5
Joined thread # 5
Joined thread # 6
Joined thread # 7
Joined thread # 8
Joined thread # 9
Joined thread # 10
Completed: thread #21
Completed: thread #11
Joined thread # 11
Joined thread # 12
Joined thread # 13
Joined thread # 14
Joined thread # 15
Completed: thread #16
Joined thread # 16
Joined thread # 17
Joined thread # 18
Joined thread # 19
Joined thread # 20
Joined thread # 21
Joined thread # 22
Completed: thread #23
Joined thread # 23
Jun 08 08:32:36 ..... started sorting BAM
Max memory needed for sorting = 5092324347
ALL DONE!