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alexdobin / STAR

RNA-seq aligner
MIT License
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STAR indexing stops without error #1525

Open aralap opened 2 years ago

aralap commented 2 years ago

Hi, im trying to generate a genome index with STAR and while the log shows no errors, half of the files are not there. Under the same parameters other genomes run just fine. Any help will be appreciated, thanks.

Copying the log below:

STAR version=2.7.10a
STAR compilation time,server,dir= :/Users/travis/build/alexdobin/travis-tests/STARcompile/source
STAR git: On branch master ; commit 51b64d4fafb7586459b8a61303e40beceeead8c0 ; diff files: 
##### Command Line:
/Users/aaptekmann/Desktop/CDI/Xue/pipe_copy/STAR-2.7.10a/bin/MacOSX_x86_64/STAR --runThreadN 32 --runMode genomeGenerate --genomeDir /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS --genomeFastaFiles /Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.99.gtf --sjdbOverhang 149
##### Initial USER parameters from Command Line:
###### All USER parameters from Command Line:
runThreadN                    32     ~RE-DEFINED
runMode                       genomeGenerate        ~RE-DEFINED
genomeDir                     /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS     ~RE-DEFINED
genomeFastaFiles              /Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa        ~RE-DEFINED
sjdbGTFfile                   /Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.99.gtf     ~RE-DEFINED
sjdbOverhang                  149     ~RE-DEFINED
##### Finished reading parameters from all sources

##### Final user re-defined parameters-----------------:
runMode                           genomeGenerate   
runThreadN                        32
genomeDir                         /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS
genomeFastaFiles                  /Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa   
sjdbGTFfile                       /Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.99.gtf
sjdbOverhang                      149

-------------------------------
##### Final effective command line:
/Users/aaptekmann/Desktop/CDI/Xue/pipe_copy/STAR-2.7.10a/bin/MacOSX_x86_64/STAR   --runMode genomeGenerate      --runThreadN 32   --genomeDir /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS   --genomeFastaFiles /Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa      --sjdbGTFfile /Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.99.gtf   --sjdbOverhang 149
----------------------------------------

Number of fastq files for each mate = 1
ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters:  3000 0.99 10
Finished loading and checking parameters
--genomeDir directory exists and will be overwritten: /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS/
Apr 13 16:37:27 ... starting to generate Genome files
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 0  "1" chrStart: 0
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 1  "10" chrStart: 249036800
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 2  "11" chrStart: 382992384
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 3  "12" chrStart: 518258688
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 4  "13" chrStart: 651689984
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 5  "14" chrStart: 766246912
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 6  "15" chrStart: 873463808
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 7  "16" chrStart: 975699968
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 8  "17" chrStart: 1066139648
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 9  "18" chrStart: 1149501440
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 10  "19" chrStart: 1229979648
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 11  "2" chrStart: 1288699904
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 12  "20" chrStart: 1530920960
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 13  "21" chrStart: 1595408384
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 14  "22" chrStart: 1642332160
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 15  "3" chrStart: 1693188096
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 16  "4" chrStart: 1891631104
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 17  "5" chrStart: 2081947648
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 18  "6" chrStart: 2263613440
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 19  "7" chrStart: 2434531328
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 20  "8" chrStart: 2593914880
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 21  "9" chrStart: 2739142656
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 22  "MT" chrStart: 2877554688
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 23  "X" chrStart: 2877816832
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 24  "Y" chrStart: 3034054656
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 25  "KI270728.1" chrStart: 3091464192
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 26  "KI270727.1" chrStart: 3093561344
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 27  "KI270442.1" chrStart: 3094085632
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 28  "KI270729.1" chrStart: 3094609920
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 29  "GL000225.1" chrStart: 3095134208
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 30  "KI270743.1" chrStart: 3095396352
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 31  "GL000008.2" chrStart: 3095658496
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 32  "GL000009.2" chrStart: 3095920640
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 33  "KI270747.1" chrStart: 3096182784
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 34  "KI270722.1" chrStart: 3096444928
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 35  "GL000194.1" chrStart: 3096707072
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 36  "KI270742.1" chrStart: 3096969216
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 37  "GL000205.2" chrStart: 3097231360
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 38  "GL000195.1" chrStart: 3097493504
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 39  "KI270736.1" chrStart: 3097755648
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 40  "KI270733.1" chrStart: 3098017792
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 41  "GL000224.1" chrStart: 3098279936
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 42  "GL000219.1" chrStart: 3098542080
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 43  "KI270719.1" chrStart: 3098804224
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 44  "GL000216.2" chrStart: 3099066368
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 45  "KI270712.1" chrStart: 3099328512
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 46  "KI270706.1" chrStart: 3099590656
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 47  "KI270725.1" chrStart: 3099852800
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 48  "KI270744.1" chrStart: 3100114944
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 49  "KI270734.1" chrStart: 3100377088
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 50  "GL000213.1" chrStart: 3100639232
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 51  "GL000220.1" chrStart: 3100901376
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 52  "KI270715.1" chrStart: 3101163520
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 53  "GL000218.1" chrStart: 3101425664
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 54  "KI270749.1" chrStart: 3101687808
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 55  "KI270741.1" chrStart: 3101949952
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 56  "GL000221.1" chrStart: 3102212096
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 57  "KI270716.1" chrStart: 3102474240
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 58  "KI270731.1" chrStart: 3102736384
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 59  "KI270751.1" chrStart: 3102998528
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 60  "KI270750.1" chrStart: 3103260672
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 61  "KI270519.1" chrStart: 3103522816
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 62  "GL000214.1" chrStart: 3103784960
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 63  "KI270708.1" chrStart: 3104047104
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 64  "KI270730.1" chrStart: 3104309248
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 65  "KI270438.1" chrStart: 3104571392
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 66  "KI270737.1" chrStart: 3104833536
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 67  "KI270721.1" chrStart: 3105095680
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 68  "KI270738.1" chrStart: 3105357824
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 69  "KI270748.1" chrStart: 3105619968
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 70  "KI270435.1" chrStart: 3105882112
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 71  "GL000208.1" chrStart: 3106144256
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 72  "KI270538.1" chrStart: 3106406400
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 73  "KI270756.1" chrStart: 3106668544
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 74  "KI270739.1" chrStart: 3106930688
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 75  "KI270757.1" chrStart: 3107192832
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 76  "KI270709.1" chrStart: 3107454976
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 77  "KI270746.1" chrStart: 3107717120
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 78  "KI270753.1" chrStart: 3107979264
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 79  "KI270589.1" chrStart: 3108241408
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 80  "KI270726.1" chrStart: 3108503552
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 81  "KI270735.1" chrStart: 3108765696
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 82  "KI270711.1" chrStart: 3109027840
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 83  "KI270745.1" chrStart: 3109289984
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 84  "KI270714.1" chrStart: 3109552128
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 85  "KI270732.1" chrStart: 3109814272
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 86  "KI270713.1" chrStart: 3110076416
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 87  "KI270754.1" chrStart: 3110338560
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 88  "KI270710.1" chrStart: 3110600704
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 89  "KI270717.1" chrStart: 3110862848
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 90  "KI270724.1" chrStart: 3111124992
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 91  "KI270720.1" chrStart: 3111387136
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 92  "KI270723.1" chrStart: 3111649280
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 93  "KI270718.1" chrStart: 3111911424
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 94  "KI270317.1" chrStart: 3112173568
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 95  "KI270740.1" chrStart: 3112435712
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 96  "KI270755.1" chrStart: 3112697856
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 97  "KI270707.1" chrStart: 3112960000
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 98  "KI270579.1" chrStart: 3113222144
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 99  "KI270752.1" chrStart: 3113484288
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 100  "KI270512.1" chrStart: 3113746432
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 101  "KI270322.1" chrStart: 3114008576
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 102  "GL000226.1" chrStart: 3114270720
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 103  "KI270311.1" chrStart: 3114532864
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 104  "KI270366.1" chrStart: 3114795008
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 105  "KI270511.1" chrStart: 3115057152
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 106  "KI270448.1" chrStart: 3115319296
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 107  "KI270521.1" chrStart: 3115581440
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 108  "KI270581.1" chrStart: 3115843584
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 109  "KI270582.1" chrStart: 3116105728
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 110  "KI270515.1" chrStart: 3116367872
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 111  "KI270588.1" chrStart: 3116630016
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 112  "KI270591.1" chrStart: 3116892160
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 113  "KI270522.1" chrStart: 3117154304
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 114  "KI270507.1" chrStart: 3117416448
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 115  "KI270590.1" chrStart: 3117678592
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 116  "KI270584.1" chrStart: 3117940736
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 117  "KI270320.1" chrStart: 3118202880
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 118  "KI270382.1" chrStart: 3118465024
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 119  "KI270468.1" chrStart: 3118727168
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 120  "KI270467.1" chrStart: 3118989312
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 121  "KI270362.1" chrStart: 3119251456
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 122  "KI270517.1" chrStart: 3119513600
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 123  "KI270593.1" chrStart: 3119775744
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 124  "KI270528.1" chrStart: 3120037888
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 125  "KI270587.1" chrStart: 3120300032
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 126  "KI270364.1" chrStart: 3120562176
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 127  "KI270371.1" chrStart: 3120824320
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 128  "KI270333.1" chrStart: 3121086464
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 129  "KI270374.1" chrStart: 3121348608
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 130  "KI270411.1" chrStart: 3121610752
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 131  "KI270414.1" chrStart: 3121872896
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 132  "KI270510.1" chrStart: 3122135040
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 133  "KI270390.1" chrStart: 3122397184
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 134  "KI270375.1" chrStart: 3122659328
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 135  "KI270420.1" chrStart: 3122921472
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 136  "KI270509.1" chrStart: 3123183616
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 137  "KI270315.1" chrStart: 3123445760
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 138  "KI270302.1" chrStart: 3123707904
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 139  "KI270518.1" chrStart: 3123970048
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 140  "KI270530.1" chrStart: 3124232192
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 141  "KI270304.1" chrStart: 3124494336
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 142  "KI270418.1" chrStart: 3124756480
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 143  "KI270424.1" chrStart: 3125018624
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 144  "KI270417.1" chrStart: 3125280768
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 145  "KI270508.1" chrStart: 3125542912
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 146  "KI270303.1" chrStart: 3125805056
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 147  "KI270381.1" chrStart: 3126067200
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 148  "KI270529.1" chrStart: 3126329344
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 149  "KI270425.1" chrStart: 3126591488
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 150  "KI270396.1" chrStart: 3126853632
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 151  "KI270363.1" chrStart: 3127115776
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 152  "KI270386.1" chrStart: 3127377920
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 153  "KI270465.1" chrStart: 3127640064
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 154  "KI270383.1" chrStart: 3127902208
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 155  "KI270384.1" chrStart: 3128164352
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 156  "KI270330.1" chrStart: 3128426496
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 157  "KI270372.1" chrStart: 3128688640
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 158  "KI270548.1" chrStart: 3128950784
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 159  "KI270580.1" chrStart: 3129212928
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 160  "KI270387.1" chrStart: 3129475072
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 161  "KI270391.1" chrStart: 3129737216
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 162  "KI270305.1" chrStart: 3129999360
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 163  "KI270373.1" chrStart: 3130261504
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 164  "KI270422.1" chrStart: 3130523648
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 165  "KI270316.1" chrStart: 3130785792
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 166  "KI270340.1" chrStart: 3131047936
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 167  "KI270338.1" chrStart: 3131310080
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 168  "KI270583.1" chrStart: 3131572224
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 169  "KI270334.1" chrStart: 3131834368
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 170  "KI270429.1" chrStart: 3132096512
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 171  "KI270393.1" chrStart: 3132358656
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 172  "KI270516.1" chrStart: 3132620800
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 173  "KI270389.1" chrStart: 3132882944
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 174  "KI270466.1" chrStart: 3133145088
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 175  "KI270388.1" chrStart: 3133407232
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 176  "KI270544.1" chrStart: 3133669376
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 177  "KI270310.1" chrStart: 3133931520
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 178  "KI270412.1" chrStart: 3134193664
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 179  "KI270395.1" chrStart: 3134455808
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 180  "KI270376.1" chrStart: 3134717952
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 181  "KI270337.1" chrStart: 3134980096
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 182  "KI270335.1" chrStart: 3135242240
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 183  "KI270378.1" chrStart: 3135504384
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 184  "KI270379.1" chrStart: 3135766528
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 185  "KI270329.1" chrStart: 3136028672
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 186  "KI270419.1" chrStart: 3136290816
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 187  "KI270336.1" chrStart: 3136552960
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 188  "KI270312.1" chrStart: 3136815104
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 189  "KI270539.1" chrStart: 3137077248
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 190  "KI270385.1" chrStart: 3137339392
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 191  "KI270423.1" chrStart: 3137601536
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 192  "KI270392.1" chrStart: 3137863680
/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 193  "KI270394.1" chrStart: 3138125824
Chromosome sequence lengths: 
1   248956422
10  133797422
11  135086622
12  133275309
13  114364328
14  107043718
15  101991189
16  90338345
17  83257441
18  80373285
19  58617616
2   242193529
20  64444167
21  46709983
22  50818468
3   198295559
4   190214555
5   181538259
6   170805979
7   159345973
8   145138636
9   138394717
MT  16569
X   156040895
Y   57227415
KI270728.1  1872759
KI270727.1  448248
KI270442.1  392061
KI270729.1  280839
GL000225.1  211173
KI270743.1  210658
GL000008.2  209709
GL000009.2  201709
KI270747.1  198735
KI270722.1  194050
GL000194.1  191469
KI270742.1  186739
GL000205.2  185591
GL000195.1  182896
KI270736.1  181920
KI270733.1  179772
GL000224.1  179693
GL000219.1  179198
KI270719.1  176845
GL000216.2  176608
KI270712.1  176043
KI270706.1  175055
KI270725.1  172810
KI270744.1  168472
KI270734.1  165050
GL000213.1  164239
GL000220.1  161802
KI270715.1  161471
GL000218.1  161147
KI270749.1  158759
KI270741.1  157432
GL000221.1  155397
KI270716.1  153799
KI270731.1  150754
KI270751.1  150742
KI270750.1  148850
KI270519.1  138126
GL000214.1  137718
KI270708.1  127682
KI270730.1  112551
KI270438.1  112505
KI270737.1  103838
KI270721.1  100316
KI270738.1  99375
KI270748.1  93321
KI270435.1  92983
GL000208.1  92689
KI270538.1  91309
KI270756.1  79590
KI270739.1  73985
KI270757.1  71251
KI270709.1  66860
KI270746.1  66486
KI270753.1  62944
KI270589.1  44474
KI270726.1  43739
KI270735.1  42811
KI270711.1  42210
KI270745.1  41891
KI270714.1  41717
KI270732.1  41543
KI270713.1  40745
KI270754.1  40191
KI270710.1  40176
KI270717.1  40062
KI270724.1  39555
KI270720.1  39050
KI270723.1  38115
KI270718.1  38054
KI270317.1  37690
KI270740.1  37240
KI270755.1  36723
KI270707.1  32032
KI270579.1  31033
KI270752.1  27745
KI270512.1  22689
KI270322.1  21476
GL000226.1  15008
KI270311.1  12399
KI270366.1  8320
KI270511.1  8127
KI270448.1  7992
KI270521.1  7642
KI270581.1  7046
KI270582.1  6504
KI270515.1  6361
KI270588.1  6158
KI270591.1  5796
KI270522.1  5674
KI270507.1  5353
KI270590.1  4685
KI270584.1  4513
KI270320.1  4416
KI270382.1  4215
KI270468.1  4055
KI270467.1  3920
KI270362.1  3530
KI270517.1  3253
KI270593.1  3041
KI270528.1  2983
KI270587.1  2969
KI270364.1  2855
KI270371.1  2805
KI270333.1  2699
KI270374.1  2656
KI270411.1  2646
KI270414.1  2489
KI270510.1  2415
KI270390.1  2387
KI270375.1  2378
KI270420.1  2321
KI270509.1  2318
KI270315.1  2276
KI270302.1  2274
KI270518.1  2186
KI270530.1  2168
KI270304.1  2165
KI270418.1  2145
KI270424.1  2140
KI270417.1  2043
KI270508.1  1951
KI270303.1  1942
KI270381.1  1930
KI270529.1  1899
KI270425.1  1884
KI270396.1  1880
KI270363.1  1803
KI270386.1  1788
KI270465.1  1774
KI270383.1  1750
KI270384.1  1658
KI270330.1  1652
KI270372.1  1650
KI270548.1  1599
KI270580.1  1553
KI270387.1  1537
KI270391.1  1484
KI270305.1  1472
KI270373.1  1451
KI270422.1  1445
KI270316.1  1444
KI270340.1  1428
KI270338.1  1428
KI270583.1  1400
KI270334.1  1368
KI270429.1  1361
KI270393.1  1308
KI270516.1  1300
KI270389.1  1298
KI270466.1  1233
KI270388.1  1216
KI270544.1  1202
KI270310.1  1201
KI270412.1  1179
KI270395.1  1143
KI270376.1  1136
KI270337.1  1121
KI270335.1  1048
KI270378.1  1048
KI270379.1  1045
KI270329.1  1040
KI270419.1  1029
KI270336.1  1026
KI270312.1  998
KI270539.1  993
KI270385.1  990
KI270423.1  981
KI270392.1  971
KI270394.1  970
Genome sequence total length = 3099750718
Genome size with padding = 3138387968
Apr 13 16:38:12 ..... processing annotations GTF
Processing pGe.sjdbGTFfile=/Users/aaptekmann/Desktop/CDI/Reference_Genomes/Sapiens/Homo_sapiens.GRCh38.99.gtf, found:
        227818 transcripts
        1376499 exons (non-collapsed)
        383262 collapsed junctions
Total junctions: 383262
Apr 13 16:38:28 ..... finished GTF processing

Estimated genome size with padding and SJs: total=genome+SJ=3437387968 = 3138387968 + 299000000
GstrandBit=32
Number of SA indices: 5891698134
Apr 13 16:38:38 ... starting to sort Suffix Array. This may take a long time...
Number of chunks: 132;   chunks size limit: 463560440 bytes
Apr 13 16:38:50 ... sorting Suffix Array chunks and saving them to disk...
Writing 311514168 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_28 ; empty space on disk = 14339845128192 bytes ... done
Writing 193960968 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_10 ; empty space on disk = 14259551469568 bytes ... done
Writing 260350264 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_23 ; empty space on disk = 14204664807424 bytes ... done
Writing 349223624 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_12 ; empty space on disk = 14137956499456 bytes ... done
Writing 279164656 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_11 ; empty space on disk = 14048550715392 bytes ... done
Writing 232985656 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_8 ; empty space on disk = 13977073483776 bytes ... done
Writing 348732728 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_9 ; empty space on disk = 13917401120768 bytes ... done
Writing 326959608 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_29 ; empty space on disk = 13828116971520 bytes ... done
Writing 385188576 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_24 ; empty space on disk = 13744408100864 bytes ... done
Writing 361339568 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_25 ; empty space on disk = 13645793722368 bytes ... done
Writing 320306280 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_6 ; empty space on disk = 13553256890368 bytes ... done
Writing 249543648 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_14 ; empty space on disk = 13471255101440 bytes ... done
Writing 426361960 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_22 ; empty space on disk = 13407369560064 bytes ... done
Writing 449655288 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_15 ; empty space on disk = 13298171904000 bytes ... done
Writing 359679512 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_26 ; empty space on disk = 13181018701824 bytes ... done
Writing 225322440 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_27 ; empty space on disk = 13088923320320 bytes ... done
Writing 473007664 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_3 ; empty space on disk = 13031236960256 bytes ... done
Writing 439070848 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_4 ; empty space on disk = 12910129577984 bytes ... done
Writing 270535776 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_1 ; empty space on disk = 12797706502144 bytes ... done
Writing 328240512 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_30 ; empty space on disk = 12728368365568 bytes ... done
Writing 391472656 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_7 ; empty space on disk = 12644336533504 bytes ... done
Writing 346685312 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_2 ; empty space on disk = 12544104202240 bytes ... done
Writing 429897560 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_16 ; empty space on disk = 12455349583872 bytes ... done
Writing 398565768 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_31 ; empty space on disk = 12345292095488 bytes ... done
Writing 439896160 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_18 ; empty space on disk = 12243258310656 bytes ... done
Writing 357285120 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_17 ; empty space on disk = 12130350792704 bytes ... done
Writing 256750224 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_5 ; empty space on disk = 12038876168192 bytes ... done
Writing 461573144 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_21 ; empty space on disk = 11973147230208 bytes ... done
Writing 374644360 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_19 ; empty space on disk = 11854969569280 bytes ... done
Writing 453326792 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_13 ; empty space on disk = 11759059468288 bytes ... done
Writing 444091872 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_20 ; empty space on disk = 11642987347968 bytes ... done
Writing 725537968 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_0 ; empty space on disk = 11529226289152 bytes ... done
Writing 274629512 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_35 ; empty space on disk = 11059364626432 bytes ... done
Writing 257262440 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_45 ; empty space on disk = 10988873056256 bytes ... done
Writing 197785264 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_40 ; empty space on disk = 10923001511936 bytes ... done
Writing 257262440 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_54 ; empty space on disk = 10872059592704 bytes ... done
Writing 257001680 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_50 ; empty space on disk = 10806168125440 bytes ... done
Writing 217070184 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_44 ; empty space on disk = 10740326989824 bytes ... done
Writing 257001680 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_62 ; empty space on disk = 10684739878912 bytes ... done
Writing 266836664 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_59 ; empty space on disk = 10618850508800 bytes ... done
Writing 232422760 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_32 ; empty space on disk = 10550003105792 bytes ... done
Writing 279165992 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_48 ; empty space on disk = 10490454474752 bytes ... done
Writing 391875176 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_47 ; empty space on disk = 10418601852928 bytes ... done
Writing 448447960 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_51 ; empty space on disk = 10318276198400 bytes ... done
Writing 264479600 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_42 ; empty space on disk = 10203462369280 bytes ... done
Writing 259809456 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_58 ; empty space on disk = 10135724359680 bytes ... done
Writing 430892376 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_52 ; empty space on disk = 10069171240960 bytes ... done
Writing 403965960 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_33 ; empty space on disk = 9958763528192 bytes ... done
Writing 458337808 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_34 ; empty space on disk = 9855326748672 bytes ... done
Writing 423740296 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_53 ; empty space on disk = 9737971171328 bytes ... done
Writing 398173840 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_46 ; empty space on disk = 9629379592192 bytes ... done
Writing 267574824 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_60 ; empty space on disk = 9527419207680 bytes ... done
Writing 473007664 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_37 ; empty space on disk = 9458551881728 bytes ... done
Writing 399935280 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_49 ; empty space on disk = 9337453936640 bytes ... done
Writing 352301192 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_39 ; empty space on disk = 9235043713024 bytes ... done
Writing 421677216 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_63 ; empty space on disk = 9144813748224 bytes ... done
Writing 348436192 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_38 ; empty space on disk = 9036845023232 bytes ... done
Writing 423443000 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_36 ; empty space on disk = 8947635322880 bytes ... done
Writing 425242032 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_57 ; empty space on disk = 8839208370176 bytes ... done
Writing 271756752 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_43 ; empty space on disk = 8729962479616 bytes ... done
Writing 446454000 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_61 ; empty space on disk = 8654403141632 bytes ... done
Writing 446096120 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_41 ; empty space on disk = 8540089483264 bytes ... done
Writing 433766512 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_56 ; empty space on disk = 8425621684224 bytes ... done
Writing 437431312 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_55 ; empty space on disk = 8313982943232 bytes ... done
Writing 274629672 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_94 ; empty space on disk = 8196249878528 bytes ... done
Writing 267302744 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_69 ; empty space on disk = 8125829611520 bytes ... done
Writing 406278656 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_83 ; empty space on disk = 8056560680960 bytes ... done
Writing 390591000 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_84 ; empty space on disk = 7947564351488 bytes ... done
Writing 425945584 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_64 ; empty space on disk = 7846344261632 bytes ... done
Writing 365831024 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_81 ; empty space on disk = 7736684183552 bytes ... done
Writing 346899408 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_75 ; empty space on disk = 7641626574848 bytes ... done
Writing 308516952 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_93 ; empty space on disk = 7551158583296 bytes ... done
Writing 362545216 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_67 ; empty space on disk = 7471615705088 bytes ... done
Writing 391545784 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_82 ; empty space on disk = 7378776883200 bytes ... done
Writing 346693088 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_65 ; empty space on disk = 7278513094656 bytes ... done
Writing 291975240 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_77 ; empty space on disk = 7189679833088 bytes ... done
Writing 398530000 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_85 ; empty space on disk = 7112988033024 bytes ...Writing 384787632 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_80 ; empty space on disk = 7084950159360 bytes ... done
 done
Writing 383205784 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_92 ; empty space on disk = 6911549243392 bytes ... done
Writing 390463192 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_78 ; empty space on disk = 6813231611904 bytes ... done
Writing 296401384 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_87 ; empty space on disk = 6713239404544 bytes ... done
Writing 405140504 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_70 ; empty space on disk = 6637339279360 bytes ... done
Writing 452426896 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_76 ; empty space on disk = 6533573246976 bytes ... done
Writing 339630192 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_74 ; empty space on disk = 6417717133312 bytes ... done
Writing 429418728 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_86 ; empty space on disk = 6330748239872 bytes ... done
Writing 354252424 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_95 ; empty space on disk = 6220791414784 bytes ... done
Writing 329854880 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_88 ; empty space on disk = 6130082250752 bytes ... done
Writing 372961400 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_73 ; empty space on disk = 6045635182592 bytes ... done
Writing 358593720 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_66 ; empty space on disk = 5950131929088 bytes ... done
Writing 345185552 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_79 ; empty space on disk = 5858116239360 bytes ... done
Writing 437027224 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_72 ; empty space on disk = 5769711845376 bytes ... done
Writing 389080440 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_71 ; empty space on disk = 5657798377472 bytes ... done
Writing 270540176 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_91 ; empty space on disk = 5558503473152 bytes ... done
Writing 380720840 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_89 ; empty space on disk = 5489217765376 bytes ... done
Writing 401092024 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_68 ; empty space on disk = 5391709634560 bytes ... done
Writing 425284392 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_90 ; empty space on disk = 5288854814720 bytes ... done
Writing 191263704 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_99 ; empty space on disk = 5172648476672 bytes ... done
Writing 410363920 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_97 ; empty space on disk = 5123536322560 bytes ... done
Writing 372419584 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_96 ; empty space on disk = 5018416578560 bytes ... done
Writing 308166112 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_118 ; empty space on disk = 4922080755712 bytes ... done
Writing 311514392 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_120 ; empty space on disk = 4843135565824 bytes ... done
Writing 209469016 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_125 ; empty space on disk = 4762798915584 bytes ... done
Writing 243676312 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_103 ; empty space on disk = 4708328538112 bytes ... done
Writing 237802800 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_102 ; empty space on disk = 4646896664576 bytes ... done
Writing 439765448 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_114 ; empty space on disk = 4584219082752 bytes ... done
Writing 346671904 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_119 ; empty space on disk = 4472010964992 bytes ... done
Writing 263072896 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_126 ; empty space on disk = 4382808604672 bytes ... done
Writing 383205784 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_127 ; empty space on disk = 4315391459328 bytes ... done
Writing 259809456 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_110 ; empty space on disk = 4217204899840 bytes ... done
Writing 426717616 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_98 ; empty space on disk = 4150629761024 bytes ... done
Writing 287930184 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_117 ; empty space on disk = 4041308372992 bytes ... done
Writing 348733736 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_100 ; empty space on disk = 3967275761664 bytes ... done
Writing 7616 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_131 ; empty space on disk = 3877926600704 bytes ... done
Writing 320310296 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_108 ; empty space on disk = 3877822791680 bytes ... done
Writing 268644208 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_116 ; empty space on disk = 3795759136768 bytes ... done
Writing 441044184 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_112 ; empty space on disk = 3726906490880 bytes ... done
Writing 423822696 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_113 ; empty space on disk = 3613876289536 bytes ... done
Writing 397984088 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_115 ; empty space on disk = 3505133715456 bytes ... done
Writing 269471120 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_122 ; empty space on disk = 3403114610688 bytes ... done
Writing 394552536 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_105 ; empty space on disk = 3334104678400 bytes ... done
Writing 302679784 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_121 ; empty space on disk = 3232988397568 bytes ... done
Writing 456380760 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_111 ; empty space on disk = 3155102269440 bytes ... done
Writing 271756752 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_107 ; empty space on disk = 3038146199552 bytes ... done
Writing 374646376 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_123 ; empty space on disk = 6384563257344 bytes ... done
Writing 459095704 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_106 ; empty space on disk = 6288481189888 bytes ... done
Writing 441699152 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_104 ; empty space on disk = 6170951548928 bytes ... done
Writing 425973832 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_124 ; empty space on disk = 6057786081280 bytes ... done
Writing 449014824 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_109 ; empty space on disk = 5948481470464 bytes ... done
Writing 348429288 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_129 ; empty space on disk = 5832913715200 bytes ... done
Writing 445851688 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_101 ; empty space on disk = 5743713452032 bytes ... done
Writing 358593720 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_128 ; empty space on disk = 5629540302848 bytes ... done
Writing 725537968 bytes into /Users/aaptekmann/Desktop/CDI/Reference_Genomes/HS//SA_130 ; empty space on disk = 5537483718656 bytes ... done
Apr 13 17:27:49 ... loading chunks from disk, packing SA...
Apr 13 17:29:12 ... finished generating suffix array
Apr 13 17:29:12 ... generating Suffix Array index
Apr 13 17:35:24 ... completed Suffix Array index
WARNING: long repeat for junction # 126354 : 15 88855522 88855578; left shift = 14; right shift = 255
Apr 13 17:35:25   Finished preparing junctions
Apr 13 17:35:25 ..... inserting junctions into the genome indices
alexdobin commented 2 years ago

Hi Ariel,

sorry for the delayed reply. It seems the job did not complete and got stuck at the splice junction processing step. How much RAM do you have?

aralap commented 2 years ago

32 G