STAR version=2.7.8a
STAR compilation time,server,dir=Sat Feb 20 13:34:37 EST 2021 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
##### Command Line:
/usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.6DJG8gVLqU/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand "gunzip -c"
##### Initial USER parameters from Command Line:
###### All USER parameters from Command Line:
runThreadN 8 ~RE-DEFINED
genomeDir /tmp/nxf.6DJG8gVLqU/ctat_genome_lib_build_dir/ref_genome.fa.star.idx ~RE-DEFINED
outSAMtype BAM SortedByCoordinate ~RE-DEFINED
twopassMode None ~RE-DEFINED
alignSJDBoverhangMin 10 ~RE-DEFINED
genomeSuffixLengthMax 10000 ~RE-DEFINED
limitBAMsortRAM 47271261705 ~RE-DEFINED
alignInsertionFlush Right ~RE-DEFINED
alignMatesGapMax 100000 ~RE-DEFINED
alignIntronMax 100000 ~RE-DEFINED
outSAMattributes All ~RE-DEFINED
readFilesIn /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_2.fastp.fastq.gz ~RE-DEFINED
genomeFastaFiles /tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa ~RE-DEFINED
outSAMfilter KeepAllAddedReferences ~RE-DEFINED
sjdbGTFfile /tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.gtf ~RE-DEFINED
alignSJstitchMismatchNmax 5 -1 5 5 ~RE-DEFINED
scoreGapNoncan -6 ~RE-DEFINED
readFilesCommand "gunzip -c" ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runThreadN 8
genomeDir /tmp/nxf.6DJG8gVLqU/ctat_genome_lib_build_dir/ref_genome.fa.star.idx
genomeFastaFiles /tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa
genomeSuffixLengthMax 10000
readFilesIn /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_2.fastp.fastq.gz
readFilesCommand "gunzip -c"
limitBAMsortRAM 47271261705
outSAMtype BAM SortedByCoordinate
outSAMattributes All
outSAMfilter KeepAllAddedReferences
scoreGapNoncan -6
alignIntronMax 100000
alignMatesGapMax 100000
alignSJDBoverhangMin 10
alignSJstitchMismatchNmax 5 -1 5 5
alignInsertionFlush Right
sjdbGTFfile /tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.gtf
twopassMode None
-------------------------------
##### Final effective command line:
/usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.6DJG8gVLqU/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --genomeFastaFiles /tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa --genomeSuffixLengthMax 10000 --readFilesIn /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_2.fastp.fastq.gz --readFilesCommand "gunzip -c" --limitBAMsortRAM 47271261705 --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMfilter KeepAllAddedReferences --scoreGapNoncan -6 --alignIntronMax 100000 --alignMatesGapMax 100000 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5 --alignInsertionFlush Right --sjdbGTFfile /tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.gtf --twopassMode None
----------------------------------------
Number of fastq files for each mate = 1
Input read files for mate 1 :
-rw-r--r--. 1 1000 root 13085992641 Jun 8 10:20 /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_1.fastp.fastq.gz
readsCommandsFile:
exec > "./_STARtmp/tmp.fifo.read1"
echo FILE 0
gunzip -c "/tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_1.fastp.fastq.gz"
Input read files for mate 2 :
-rw-r--r--. 1 1000 root 13143546011 Jun 8 10:20 /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_2.fastp.fastq.gz
readsCommandsFile:
exec > "./_STARtmp/tmp.fifo.read2"
echo FILE 0
gunzip -c "/tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_2.fastp.fastq.gz"
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 10:21:04 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
/tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa : chr # 194 "MAPKAPK5--ACAD10" chrStart: 3108831232
/tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa : chr # 195 "PCDHA3--PCDHAC2" chrStart: 3108896768
/tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa : chr # 196 "PCDHA3--PCDHAC1" chrStart: 3108962304
/tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa : chr # 197 "PCDHA3--PCDHA13" chrStart: 3109027840
/tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa : chr # 198 "STX16--NPEPL1" chrStart: 3109093376
/tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa : chr # 199 "TLK2--AC240565.1" chrStart: 3109158912
/tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa : chr # 200 "TLK2P1--AC110079.1" chrStart: 3109224448
/tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.fa : chr # 201 "TVP23C--CDRT4" chrStart: 3109289984
Chromosome sequence lengths:
chr1 248956422
chr2 242193529
chr3 198295559
chr4 190214555
chr5 181538259
chr6 170805979
chr7 159345973
chr8 145138636
chr9 138394717
chr10 133797422
chr11 135086622
chr12 133275309
chr13 114364328
chr14 107043718
chr15 101991189
chr16 90338345
chr17 83257441
chr18 80373285
chr19 58617616
chr20 64444167
chr21 46709983
chr22 50818468
chrX 156040895
chrY 57227415
chrM 16569
GL000008.2 209709
GL000009.2 201709
GL000194.1 191469
GL000195.1 182896
GL000205.2 185591
GL000208.1 92689
GL000213.1 164239
GL000214.1 137718
GL000216.2 176608
GL000218.1 161147
GL000219.1 179198
GL000220.1 161802
GL000221.1 155397
GL000224.1 179693
GL000225.1 211173
GL000226.1 15008
KI270302.1 2274
KI270303.1 1942
KI270304.1 2165
KI270305.1 1472
KI270310.1 1201
KI270311.1 12399
KI270312.1 998
KI270315.1 2276
KI270316.1 1444
KI270317.1 37690
KI270320.1 4416
KI270322.1 21476
KI270329.1 1040
KI270330.1 1652
KI270333.1 2699
KI270334.1 1368
KI270335.1 1048
KI270336.1 1026
KI270337.1 1121
KI270338.1 1428
KI270340.1 1428
KI270362.1 3530
KI270363.1 1803
KI270364.1 2855
KI270366.1 8320
KI270371.1 2805
KI270372.1 1650
KI270373.1 1451
KI270374.1 2656
KI270375.1 2378
KI270376.1 1136
KI270378.1 1048
KI270379.1 1045
KI270381.1 1930
KI270382.1 4215
KI270383.1 1750
KI270384.1 1658
KI270385.1 990
KI270386.1 1788
KI270387.1 1537
KI270388.1 1216
KI270389.1 1298
KI270390.1 2387
KI270391.1 1484
KI270392.1 971
KI270393.1 1308
KI270394.1 970
KI270395.1 1143
KI270396.1 1880
KI270411.1 2646
KI270412.1 1179
KI270414.1 2489
KI270417.1 2043
KI270418.1 2145
KI270419.1 1029
KI270420.1 2321
KI270422.1 1445
KI270423.1 981
KI270424.1 2140
KI270425.1 1884
KI270429.1 1361
KI270435.1 92983
KI270438.1 112505
KI270442.1 392061
KI270448.1 7992
KI270465.1 1774
KI270466.1 1233
KI270467.1 3920
KI270468.1 4055
KI270507.1 5353
KI270508.1 1951
KI270509.1 2318
KI270510.1 2415
KI270511.1 8127
KI270512.1 22689
KI270515.1 6361
KI270516.1 1300
KI270517.1 3253
KI270518.1 2186
KI270519.1 138126
KI270521.1 7642
KI270522.1 5674
KI270528.1 2983
KI270529.1 1899
KI270530.1 2168
KI270538.1 91309
KI270539.1 993
KI270544.1 1202
KI270548.1 1599
KI270579.1 31033
KI270580.1 1553
KI270581.1 7046
KI270582.1 6504
KI270583.1 1400
KI270584.1 4513
KI270587.1 2969
KI270588.1 6158
KI270589.1 44474
KI270590.1 4685
KI270591.1 5796
KI270593.1 3041
KI270706.1 175055
KI270707.1 32032
KI270708.1 127682
KI270709.1 66860
KI270710.1 40176
KI270711.1 42210
KI270712.1 176043
KI270713.1 40745
KI270714.1 41717
KI270715.1 161471
KI270716.1 153799
KI270717.1 40062
KI270718.1 38054
KI270719.1 176845
KI270720.1 39050
KI270721.1 100316
KI270722.1 194050
KI270723.1 38115
KI270724.1 39555
KI270725.1 172810
KI270726.1 43739
KI270727.1 448248
KI270728.1 1872759
KI270729.1 280839
KI270730.1 112551
KI270731.1 150754
KI270732.1 41543
KI270733.1 179772
KI270734.1 165050
KI270735.1 42811
KI270736.1 181920
KI270737.1 103838
KI270738.1 99375
KI270739.1 73985
KI270740.1 37240
KI270741.1 157432
KI270742.1 186739
KI270743.1 210658
KI270744.1 168472
KI270745.1 41891
KI270746.1 66486
KI270747.1 198735
KI270748.1 93321
KI270749.1 158759
KI270750.1 148850
KI270751.1 150742
KI270752.1 27745
KI270753.1 62944
KI270754.1 40191
KI270755.1 36723
KI270756.1 79590
KI270757.1 71251
MAPKAPK5--ACAD10 59156
PCDHA3--PCDHAC2 20336
PCDHA3--PCDHAC1 19610
PCDHA3--PCDHA13 18035
STX16--NPEPL1 33741
TLK2--AC240565.1 49301
TLK2P1--AC110079.1 20707
TVP23C--CDRT4 26887
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 10:21:24 2026
Jun 08 10:21:24 ..... inserting extra sequences into genome indexes
Jun 08 10:22:15 Finished SA search, number of new SA indices = 477606
Jun 08 10:22:15 Finished qsort
Jun 08 10:22:15 Finished sorting SA indices
Jun 08 10:22:48 Finished inserting SA indices
Jun 08 10:22:48 ... generating Suffix Array index
Jun 08 10:26:42 ... completed Suffix Array index
Jun 08 10:26:42 Finished SAi
Processing splice junctions database sjdbN=386086, pGe.sjdbOverhang=150
To accommodate alignIntronMax=100000 redefined winBinNbits=16
To accommodate alignIntronMax=100000 and alignMatesGapMax=100000, redefined winFlankNbins=2 and winAnchorDistNbins=4
Jun 08 10:26:42 Loaded database junctions from the generated genome /tmp/nxf.6DJG8gVLqU/ctat_genome_lib_build_dir/ref_genome.fa.star.idx//sjdbList.out.tab: 386086 total junctions
Jun 08 10:26:42 ..... processing annotations GTF
Processing pGe.sjdbGTFfile=/tmp/nxf.6DJG8gVLqU/fi_workdir/tih_rna_sample_00660_B23MVV7LT4_1.gtf, found:
111 transcripts
731 exons (non-collapsed)
195 collapsed junctions
Total junctions: 386281
Jun 08 10:26:42 ..... finished GTF processing
Jun 08 10:26:42 Finished preparing junctions
Jun 08 10:26:42 ..... inserting junctions into the genome indices
Jun 08 10:26:44 Finished SA search: number of new junctions=195, old junctions=386086
Jun 08 10:26:44 Finished sorting SA indicesL nInd=117000
Genome size with junctions=3225626101 3109355520 116270581
GstrandBit1=32 GstrandBit=32
Jun 08 10:27:39 Finished inserting junction indices
Jun 08 10:27:43 Finished SAi
Jun 08 10:27:43 ..... finished inserting junctions into genome
Created thread # 1
Created thread # 2
Created thread # 3
Created thread # 4
Created thread # 5
Created thread # 6
Created thread # 7
Starting to map file # 0
mate 1: /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_1.fastp.fastq.gz
mate 2: /tmp/nxf.6DJG8gVLqU/tih_rna_sample_00660_B23MVV7LT4_1_2.fastp.fastq.gz
Thread #0 end of input stream, nextChar=-1
BAM sorting: 31958 mapped reads
BAM sorting bins genomic start loci:
1 194 3195
2 194 6283
3 194 8247
4 194 12923
5 194 16476
6 194 34136
7 194 41207
8 194 47317
9 194 48612
10 194 50838
11 194 55530
12 194 57417
13 195 3714
14 196 1424
15 196 11511
16 197 2396
17 197 11042
18 198 1740
19 198 1849
20 198 4248
21 198 4700
22 198 5849
23 198 7630
24 198 8772
25 198 18419
26 198 18508
27 198 19292
28 198 19985
29 198 21667
30 198 24985
31 198 27068
32 198 28131
33 198 28778
34 199 9327
35 199 13480
36 199 14648
37 199 17052
38 199 19947
39 199 29019
40 199 41301
41 200 1616
42 201 1071
43 201 3444
44 201 5640
45 201 7869
46 201 7973
47 201 10422
48 201 15077
Completed: thread #0
Completed: thread #2
Completed: thread #1
Joined thread # 1
Joined thread # 2
Completed: thread #6
Completed: thread #5
Completed: thread #4
Completed: thread #3
Joined thread # 3
Joined thread # 4
Joined thread # 5
Joined thread # 6
Completed: thread #7
Joined thread # 7
Jun 08 11:46:55 ..... started sorting BAM
Max memory needed for sorting = 2149734
ALL DONE!