STAR version=STAR_2.4.2a
STAR compilation time,server,dir=Fri Jun 19 17:13:08 EDT 2015 modena.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/Releases/STAR_2.4.2a/source
##### DEFAULT parameters:
versionSTAR                       20201
versionGenome                     20101   20200   
parametersFiles                   -   
sysShell                          -
runMode                           alignReads
runThreadN                        1
runDirPerm                        User_RWX
genomeDir                         ./GenomeDir/
genomeLoad                        NoSharedMemory
genomeFastaFiles                  -   
genomeSAindexNbases               14
genomeChrBinNbits                 18
genomeSAsparseD                   1
readFilesIn                       Read1   Read2   
readFilesCommand                  -   
readMatesLengthsIn                NotEqual
readMapNumber                     18446744073709551615
inputBAMfile                      -
bamRemoveDuplicatesType           -
bamRemoveDuplicatesMate2basesN    0
limitGenomeGenerateRAM            31000000000
limitIObufferSize                 150000000
limitOutSAMoneReadBytes           100000
limitOutSJcollapsed               1000000
limitOutSJoneRead                 1000
limitBAMsortRAM                   0
limitSjdbInsertNsj                1000000
outTmpDir                         -
outReadsUnmapped                  None
outQSconversionAdd                0
outSAMtype                        SAM   
outSAMmode                        Full
outSAMstrandField                 None
outSAMattributes                  Standard   
outSAMunmapped                    None
outSAMorder                       Paired
outSAMprimaryFlag                 OneBestScore
outSAMreadID                      Standard
outSAMmapqUnique                  255
outSAMflagOR                      0
outSAMflagAND                     65535
outSAMattrRGline                  -   
outSAMheaderHD                    -   
outSAMheaderPG                    -   
outSAMheaderCommentFile           -
outBAMcompression                 1
outBAMsortingThreadN              0
outSJfilterReads                  All
outSJfilterCountUniqueMin         3   1   1   1   
outSJfilterCountTotalMin          3   1   1   1   
outSJfilterOverhangMin            30   12   12   12   
outSJfilterDistToOtherSJmin       10   0   5   10   
outSJfilterIntronMaxVsReadN       50000   100000   200000   
outWigType                        None   
outWigStrand                      Stranded   
outWigReferencesPrefix            -
outWigNorm                        RPM   
outFilterType                     Normal
outFilterMultimapNmax             10
outFilterMultimapScoreRange       1
outFilterScoreMin                 0
outFilterScoreMinOverLread        0.66
outFilterMatchNmin                0
outFilterMatchNminOverLread       0.66
outFilterMismatchNmax             10
outFilterMismatchNoverLmax        0.3
outFilterMismatchNoverReadLmax    1
outFilterIntronMotifs             None
clip5pNbases                      0   
clip3pNbases                      0   
clip3pAfterAdapterNbases          0   
clip3pAdapterSeq                  -   
clip3pAdapterMMp                  0.1   
winBinNbits                       16
winAnchorDistNbins                9
winFlankNbins                     4
winAnchorMultimapNmax             50
scoreGap                          0
scoreGapNoncan                    -8
scoreGapGCAG                      -4
scoreGapATAC                      -8
scoreStitchSJshift                1
scoreGenomicLengthLog2scale       -0.25
scoreDelBase                      -2
scoreDelOpen                      -2
scoreInsOpen                      -2
scoreInsBase                      -2
seedSearchLmax                    0
seedSearchStartLmax               50
seedSearchStartLmaxOverLread      1
seedPerReadNmax                   1000
seedPerWindowNmax                 50
seedNoneLociPerWindow             10
seedMultimapNmax                  10000
alignIntronMin                    21
alignIntronMax                    0
alignMatesGapMax                  0
alignTranscriptsPerReadNmax       10000
alignSJoverhangMin                5
alignSJDBoverhangMin              3
alignSplicedMateMapLmin           0
alignSplicedMateMapLminOverLmate    0.66
alignWindowsPerReadNmax           10000
alignTranscriptsPerWindowNmax     100
alignEndsType                     Local
alignSoftClipAtReferenceEnds      Yes
chimSegmentMin                    0
chimScoreMin                      0
chimScoreDropMax                  20
chimScoreSeparation               10
chimScoreJunctionNonGTAG          -1
chimJunctionOverhangMin           20
chimOutType                       SeparateSAMold
sjdbFileChrStartEnd               -   
sjdbGTFfile                       -
sjdbGTFchrPrefix                  -
sjdbGTFfeatureExon                exon
sjdbGTFtagExonParentTranscript    transcript_id
sjdbGTFtagExonParentGene          gene_id
sjdbOverhang                      100
sjdbScore                         2
sjdbInsertSave                    Basic
quantMode                         -   
quantTranscriptomeBAMcompression    1
quantTranscriptomeBan             IndelSoftclipSingleend
twopass1readsN                    18446744073709551615
twopassMode                       None
##### Command Line:
STAR --genomeLoad NoSharedMemory --genomeSAsparseD 2 --outSAMstrandField intronMotif --genomeDir pathto/STARgenome --sjdbGTFfile pathto/STARgenome/gencode.v23.annotation.gtf --runThreadN 2 --quantMode GeneCounts --readFilesIn pathto/sample_R1.fastq.gz pathto/sample_R2.fastq.gz --readFilesCommand zcat --outFileNamePrefix sample --outSAMtype BAM Unsorted --outStd BAM_Unsorted
##### Initial USER parameters from Command Line:
outFileNamePrefix                 sample
outStd                            BAM_Unsorted
###### All USER parameters from Command Line:
genomeLoad                    NoSharedMemory     ~RE-DEFINED
genomeSAsparseD               2     ~RE-DEFINED
outSAMstrandField             intronMotif     ~RE-DEFINED
genomeDir                     /pathto/STARgenome     ~RE-DEFINED
sjdbGTFfile                   /pathto/STARgenome/gencode.v23.annotation.gtf     ~RE-DEFINED
runThreadN                    2     ~RE-DEFINED
quantMode                     GeneCounts        ~RE-DEFINED
readFilesIn                   /pathto/sample_R1.fastq.gz   pathto/sample_R2.fastq.gz        ~RE-DEFINED
readFilesCommand              zcat        ~RE-DEFINED
outFileNamePrefix             sample     ~RE-DEFINED
outSAMtype                    BAM   Unsorted        ~RE-DEFINED
outStd                        BAM_Unsorted     ~RE-DEFINED
##### Finished reading parameters from all sources

##### Final user re-defined parameters-----------------:
runThreadN                        2
genomeDir                         pathto/STARgenome
genomeLoad                        NoSharedMemory
genomeSAsparseD                   2
readFilesIn                       pathto/sample_R1.fastq.gz   pathto/sample_R2.fastq.gz   
readFilesCommand                  zcat   
outFileNamePrefix                 sample
outStd                            BAM_Unsorted
outSAMtype                        BAM   Unsorted   
outSAMstrandField                 intronMotif
sjdbGTFfile                       pathto/STARgenome/gencode.v23.annotation.gtf
quantMode                         GeneCounts   

-------------------------------
##### Final effective command line:
STAR   --runThreadN 2   --genomeDir pathto/STARgenome   --genomeLoad NoSharedMemory   --genomeSAsparseD 2   --readFilesIn pathto/sample_R1.fastq.gz   pathto/sample_R2.fastq.gz      --readFilesCommand zcat      --outFileNamePrefix sample   --outStd BAM_Unsorted   --outSAMtype BAM   Unsorted      --outSAMstrandField intronMotif   --sjdbGTFfile pathto/STARgenome/gencode.v23.annotation.gtf   --quantMode GeneCounts   

##### Final parameters after user input--------------------------------:
versionSTAR                       20201
versionGenome                     20101   20200   
parametersFiles                   -   
sysShell                          -
runMode                           alignReads
runThreadN                        2
runDirPerm                        User_RWX
genomeDir                         pathto/STARgenome
genomeLoad                        NoSharedMemory
genomeFastaFiles                  -   
genomeSAindexNbases               14
genomeChrBinNbits                 18
genomeSAsparseD                   2
readFilesIn                       pathto/sample_R1.fastq.gz   pathto/sample_R2.fastq.gz   
readFilesCommand                  zcat   
readMatesLengthsIn                NotEqual
readMapNumber                     18446744073709551615
inputBAMfile                      -
bamRemoveDuplicatesType           -
bamRemoveDuplicatesMate2basesN    0
limitGenomeGenerateRAM            31000000000
limitIObufferSize                 150000000
limitOutSAMoneReadBytes           100000
limitOutSJcollapsed               1000000
limitOutSJoneRead                 1000
limitBAMsortRAM                   0
limitSjdbInsertNsj                1000000
outFileNamePrefix                 sample
outTmpDir                         -
outStd                            BAM_Unsorted
outReadsUnmapped                  None
outQSconversionAdd                0
outSAMtype                        BAM   Unsorted   
outSAMmode                        Full
outSAMstrandField                 intronMotif
outSAMattributes                  Standard   
outSAMunmapped                    None
outSAMorder                       Paired
outSAMprimaryFlag                 OneBestScore
outSAMreadID                      Standard
outSAMmapqUnique                  255
outSAMflagOR                      0
outSAMflagAND                     65535
outSAMattrRGline                  -   
outSAMheaderHD                    -   
outSAMheaderPG                    -   
outSAMheaderCommentFile           -
outBAMcompression                 1
outBAMsortingThreadN              0
outSJfilterReads                  All
outSJfilterCountUniqueMin         3   1   1   1   
outSJfilterCountTotalMin          3   1   1   1   
outSJfilterOverhangMin            30   12   12   12   
outSJfilterDistToOtherSJmin       10   0   5   10   
outSJfilterIntronMaxVsReadN       50000   100000   200000   
outWigType                        None   
outWigStrand                      Stranded   
outWigReferencesPrefix            -
outWigNorm                        RPM   
outFilterType                     Normal
outFilterMultimapNmax             10
outFilterMultimapScoreRange       1
outFilterScoreMin                 0
outFilterScoreMinOverLread        0.66
outFilterMatchNmin                0
outFilterMatchNminOverLread       0.66
outFilterMismatchNmax             10
outFilterMismatchNoverLmax        0.3
outFilterMismatchNoverReadLmax    1
outFilterIntronMotifs             None
clip5pNbases                      0   
clip3pNbases                      0   
clip3pAfterAdapterNbases          0   
clip3pAdapterSeq                  -   
clip3pAdapterMMp                  0.1   
winBinNbits                       16
winAnchorDistNbins                9
winFlankNbins                     4
winAnchorMultimapNmax             50
scoreGap                          0
scoreGapNoncan                    -8
scoreGapGCAG                      -4
scoreGapATAC                      -8
scoreStitchSJshift                1
scoreGenomicLengthLog2scale       -0.25
scoreDelBase                      -2
scoreDelOpen                      -2
scoreInsOpen                      -2
scoreInsBase                      -2
seedSearchLmax                    0
seedSearchStartLmax               50
seedSearchStartLmaxOverLread      1
seedPerReadNmax                   1000
seedPerWindowNmax                 50
seedNoneLociPerWindow             10
seedMultimapNmax                  10000
alignIntronMin                    21
alignIntronMax                    0
alignMatesGapMax                  0
alignTranscriptsPerReadNmax       10000
alignSJoverhangMin                5
alignSJDBoverhangMin              3
alignSplicedMateMapLmin           0
alignSplicedMateMapLminOverLmate    0.66
alignWindowsPerReadNmax           10000
alignTranscriptsPerWindowNmax     100
alignEndsType                     Local
alignSoftClipAtReferenceEnds      Yes
chimSegmentMin                    0
chimScoreMin                      0
chimScoreDropMax                  20
chimScoreSeparation               10
chimScoreJunctionNonGTAG          -1
chimJunctionOverhangMin           20
chimOutType                       SeparateSAMold
sjdbFileChrStartEnd               -   
sjdbGTFfile                       pathto/STARgenome/gencode.v23.annotation.gtf
sjdbGTFchrPrefix                  -
sjdbGTFfeatureExon                exon
sjdbGTFtagExonParentTranscript    transcript_id
sjdbGTFtagExonParentGene          gene_id
sjdbOverhang                      100
sjdbScore                         2
sjdbInsertSave                    Basic
quantMode                         GeneCounts   
quantTranscriptomeBAMcompression    1
quantTranscriptomeBan             IndelSoftclipSingleend
twopass1readsN                    18446744073709551615
twopassMode                       None
----------------------------------------


   Input read files for mate 1, from input string pathto/sample_R1.fastq.gz
-rw-r--r-- 1 rvann 1660827268 Nov  2 00:59 pathto/sample_R1.fastq.gz

   readsCommandsFile:
exec > “sample_STARtmp/tmp.fifo.read1"
echo FILE 0
zcat      “pathto/sample_R1.fastq.gz"


   Input read files for mate 2, from input string pathto/sample_R2.fastq.gz
-rw-r--r-- 1 rvann 1771074804 Nov  2 00:59 pathto/sample_R2.fastq.gz

   readsCommandsFile:
exec > “sample_STARtmp/tmp.fifo.read2"
echo FILE 0
zcat      “pathto/sample_R2.fastq.gz"

WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute
Finished loading and checking parameters
Reading genome generation parameters:
versionGenome                 20201        ~RE-DEFINED
genomeFastaFiles              pathto/STARgenome/GRCh38.p3.genome.fa        ~RE-DEFINED
genomeSAindexNbases           14     ~RE-DEFINED
genomeChrBinNbits             18     ~RE-DEFINED
genomeSAsparseD               2     ~RE-DEFINED
sjdbOverhang                  100     ~RE-DEFINED
sjdbFileChrStartEnd           -        ~RE-DEFINED
sjdbGTFfile                   pathto/STARgenome/gencode.v23.annotation.gtf     ~RE-DEFINED
sjdbGTFchrPrefix              -     ~RE-DEFINED
sjdbGTFfeatureExon            exon     ~RE-DEFINED
sjdbGTFtagExonParentTranscripttranscript_id     ~RE-DEFINED
sjdbGTFtagExonParentGene      gene_id     ~RE-DEFINED
sjdbInsertSave                Basic     ~RE-DEFINED
Genome version is compatible with current STAR version
--sjdbOverhang = 100 taken from the generated genome
Started loading the genome: Sat Nov 28 17:47:51 2015

checking Genome sizefile size: 3366881431 bytes; state: good=1 eof=0 fail=0 bad=0
checking SA sizefile size: 13194954242 bytes; state: good=1 eof=0 fail=0 bad=0
checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0
Read from SAindex: genomeSAindexNbases=14  nSAi=357913940
nGenome=3366881431;  nSAbyte=13194954242
GstrandBit=32   SA number of indices=3198776785
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 3366881431 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3366881431 bytes
SA file size: 13194954242 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 13194954242 bytes
Loading SAindex ... done: 1565873619 bytes
Finished loading the genome: Sat Nov 28 17:49:17 2015

Number of real (reference) chromosmes= 493
1	chr1	248956422	0
2	chr2	242193529	249036800
3	chr3	198295559	491257856
4	chr4	190214555	689700864
5	chr5	181538259	880017408
6	chr6	170805979	1061683200
7	chr7	159345973	1232601088
8	chr8	145138636	1391984640
9	chr9	138394717	1537212416
10	chr10	133797422	1675624448
11	chr11	135086622	1809580032
12	chr12	133275309	1944846336
13	chr13	114364328	2078277632
14	chr14	107043718	2192834560
15	chr15	101991189	2300051456
16	chr16	90338345	2402287616
17	chr17	83257441	2492727296
18	chr18	80373285	2576089088
19	chr19	58617616	2656567296
20	chr20	64444167	2715287552
21	chr21	46709983	2779774976
22	chr22	50818468	2826698752
23	chrX	156040895	2877554688
24	chrY	57227415	3033792512
25	chrM	16569	3091202048
26	GL000008.2	209709	3091464192
27	GL000009.2	201709	3091726336
28	GL000194.1	191469	3091988480
29	GL000195.1	182896	3092250624
30	GL000205.2	185591	3092512768
31	GL000208.1	92689	3092774912
32	GL000213.1	164239	3093037056
33	GL000214.1	137718	3093299200
34	GL000216.2	176608	3093561344
35	GL000218.1	161147	3093823488
36	GL000219.1	179198	3094085632
37	GL000220.1	161802	3094347776
38	GL000221.1	155397	3094609920
39	GL000224.1	179693	3094872064
40	GL000225.1	211173	3095134208
41	GL000226.1	15008	3095396352
42	KN538364.1	415308	3095658496
43	KQ031383.1	467143	3096182784
44	KN538369.1	541038	3096707072
45	JH159136.1	200998	3097493504
46	JH159137.1	191409	3097755648
47	KQ031387.1	320750	3098017792
48	KN538360.1	460100	3098542080
49	KN196484.1	370917	3099066368
50	KN196476.1	305979	3099590656
51	KN196479.1	330164	3100114944
52	KN196473.1	166200	3100639232
53	KN196487.1	101150	3100901376
54	KN196475.1	451168	3101163520
55	KN538361.1	305542	3101687808
56	KN196474.1	122022	3102212096
57	KN196478.1	268330	3102474240
58	KN196480.1	277797	3102998528
59	KN196483.1	35455	3103522816
60	KN196481.1	108875	3103784960
61	KN538363.1	365499	3104047104
62	KN538362.1	208149	3104571392
63	KQ031385.1	373699	3104833536
64	KQ031386.1	165718	3105357824
65	KQ031388.1	179932	3105619968
66	KN538365.1	14347	3105882112
67	KN538366.1	85284	3106144256
68	KN538367.1	420164	3106406400
69	KN538370.1	86533	3106930688
70	KN538373.1	148762	3107192832
71	KN538371.1	206320	3107454976
72	KQ031384.1	481245	3107717120
73	KN538372.1	356766	3108241408
74	KN196482.1	211377	3108765696
75	KN196472.1	186494	3109027840
76	GL383545.1	179254	3109289984
77	GL383546.1	309802	3109552128
78	KI270824.1	181496	3110076416
79	KI270825.1	188315	3110338560
80	GL383547.1	154407	3110600704
81	KN538368.1	203552	3110862848
82	KI270826.1	186169	3111124992
83	KI270827.1	67707	3111387136
84	KI270829.1	204059	3111649280
85	KI270830.1	177092	3111911424
86	KI270831.1	296895	3112173568
87	KI270832.1	210133	3112697856
88	KI270902.1	106711	3112960000
89	KI270903.1	214625	3113222144
90	KI270927.1	218612	3113484288
91	GL877875.1	167313	3113746432
92	GL383549.1	120804	3114008576
93	GL383550.2	169178	3114270720
94	GL877876.1	408271	3114532864
95	GL383552.1	138655	3115057152
96	KI270904.1	572349	3115319296
97	GL383553.2	152874	3116105728
98	KI270835.1	238139	3116367872
99	GL383551.1	184319	3116630016
100	KI270837.1	40090	3116892160
101	KI270833.1	76061	3117154304
102	KI270834.1	119498	3117416448
103	KI270836.1	56134	3117678592
104	KI270838.1	306913	3117940736
105	KI270839.1	180306	3118465024
106	KI270840.1	191684	3118727168
107	KI270841.1	169134	3118989312
108	KI270842.1	37287	3119251456
109	KI270843.1	103832	3119513600
110	KI270844.1	322166	3119775744
111	KI270845.1	180703	3120300032
112	KI270846.1	1351393	3120562176
113	KI270847.1	1511111	3122135040
114	KI270852.1	478999	3123707904
115	KI270848.1	327382	3124232192
116	GL383554.1	296527	3124756480
117	KI270906.1	196384	3125280768
118	GL383555.2	388773	3125542912
119	KI270851.1	263054	3126067200
120	KI270849.1	244917	3126591488
121	KI270905.1	5161414	3126853632
122	KI270850.1	430880	3132096512
123	KQ031389.1	2365364	3132620800
124	KI270853.1	2659700	3135242240
125	GL383556.1	192462	3138125824
126	GL383557.1	89672	3138387968
127	KI270855.1	232857	3138650112
128	KQ031390.1	169136	3138912256
129	KI270856.1	63982	3139174400
130	KI270854.1	134193	3139436544
131	KI270909.1	325800	3139698688
132	GL383563.3	375691	3140222976
133	KI270861.1	196688	3140747264
134	GL383564.2	133151	3141009408
135	GL000258.2	1821992	3141271552
136	KI270860.1	178921	3143106560
137	KI270907.1	137721	3143368704
138	KI270862.1	391357	3143630848
139	GL383565.1	223995	3144155136
140	KI270908.1	1423190	3144417280
141	KI270910.1	157099	3145990144
142	GL383566.1	90219	3146252288
143	JH159146.1	278131	3146514432
144	JH159147.1	70345	3147038720
145	JH159148.1	88070	3147300864
146	KI270857.1	2877074	3147563008
147	KI270858.1	235827	3150446592
148	KI270859.1	108763	3150708736
149	GL383567.1	289831	3150970880
150	GL383568.1	104552	3151495168
151	GL383569.1	167950	3151757312
152	GL383570.1	164789	3152019456
153	GL383571.1	198278	3152281600
154	GL383572.1	159547	3152543744
155	KI270863.1	167999	3152805888
156	KI270864.1	111737	3153068032
157	KI270912.1	174061	3153330176
158	KI270911.1	157710	3153592320
159	KI270917.1	190932	3153854464
160	KI270918.1	123111	3154116608
161	KI270919.1	170701	3154378752
162	KI270920.1	198005	3154640896
163	KI270921.1	282224	3154903040
164	KI270922.1	187935	3155427328
165	KI270923.1	189352	3155689472
166	KI270929.1	186203	3155951616
167	KI270930.1	200773	3156213760
168	KI270931.1	170148	3156475904
169	KI270932.1	215732	3156738048
170	KI270933.1	170537	3157000192
171	KI270882.1	248807	3157262336
172	KI270883.1	170399	3157524480
173	KI270884.1	157053	3157786624
174	KI270885.1	171027	3158048768
175	KI270886.1	204239	3158310912
176	KI270887.1	209512	3158573056
177	KI270888.1	155532	3158835200
178	KI270889.1	170698	3159097344
179	KI270890.1	184499	3159359488
180	GL000209.2	177381	3159621632
181	KI270891.1	170680	3159883776
182	KI270914.1	205194	3160145920
183	KI270915.1	170665	3160408064
184	KI270916.1	184516	3160670208
185	GL949746.1	987716	3160932352
186	GL949747.2	729520	3161980928
187	GL949748.2	1064304	3162767360
188	GL949749.2	1091841	3164078080
189	GL949750.2	1066390	3165388800
190	GL949751.2	1002683	3166699520
191	GL949752.1	987100	3167748096
192	GL949753.2	796479	3168796672
193	GL383573.1	385657	3169845248
194	GL383574.1	155864	3170369536
195	GL383575.2	170222	3170631680
196	KI270866.1	43156	3170893824
197	GL383576.1	188024	3171155968
198	KI270867.1	233762	3171418112
199	KI270865.1	52969	3171680256
200	KI270938.1	1066800	3171942400
201	KI270868.1	61734	3173253120
202	KI270760.1	109528	3173515264
203	KI270762.1	354444	3173777408
204	GL383518.1	182439	3174301696
205	KI270759.1	425601	3174563840
206	KI270766.1	256271	3175088128
207	GL383519.1	110268	3175350272
208	KI270761.1	165834	3175612416
209	GL383520.2	366580	3175874560
210	KI270763.1	911658	3176398848
211	KI270765.1	185285	3177447424
212	KI270764.1	50258	3177709568
213	KI270892.1	162212	3177971712
214	GL383577.2	128386	3178233856
215	KI270869.1	118774	3178496000
216	KI270870.1	183433	3178758144
217	KI270871.1	58661	3179020288
218	GL383578.2	63917	3179282432
219	GL383579.2	201197	3179544576
220	GL383580.2	74653	3179806720
221	GL383581.2	116689	3180068864
222	KI270872.1	82692	3180331008
223	KI270873.1	143900	3180593152
224	KI270874.1	166743	3180855296
225	GL383582.2	162811	3181117440
226	GL383583.2	96924	3181379584
227	KI270875.1	259914	3181641728
228	KI270876.1	263666	3181903872
229	KI270877.1	101331	3182428160
230	KI270878.1	186262	3182690304
231	KI270879.1	304135	3182952448
232	KB663609.1	74013	3183476736
233	KI270928.1	176103	3183738880
234	KN196485.1	156562	3184001024
235	KN196486.1	153027	3184263168
236	KI270769.1	120616	3184525312
237	KI270767.1	161578	3184787456
238	GL383521.1	143390	3185049600
239	KI270772.1	133041	3185311744
240	GL383522.1	123821	3185573888
241	KI270770.1	136240	3185836032
242	KI270893.1	161218	3186098176
243	KI270894.1	214158	3186360320
244	GL582966.2	96131	3186622464
245	KI270773.1	70887	3186884608
246	KI270776.1	174166	3187146752
247	KI270768.1	110099	3187408896
248	KI270774.1	223625	3187671040
249	KI270771.1	110395	3187933184
250	KI270775.1	138019	3188195328
251	JH636055.2	173151	3188457472
252	GL383526.1	180671	3188719616
253	KI270779.1	205312	3188981760
254	KI270777.1	173649	3189243904
255	KI270782.1	162429	3189506048
256	KI270783.1	109187	3189768192
257	KI270778.1	248252	3190030336
258	KI270895.1	162896	3190292480
259	KI270780.1	224108	3190554624
260	KI270924.1	166540	3190816768
261	KI270781.1	113034	3191078912
262	KI270934.1	163458	3191341056
263	KI270935.1	197351	3191603200
264	KI270936.1	164170	3191865344
265	KI270937.1	165607	3192127488
266	KI270784.1	184404	3192389632
267	GL383527.1	164536	3192651776
268	KI270790.1	220246	3192913920
269	GL383528.1	376187	3193176064
270	KI270787.1	111943	3193700352
271	GL000257.2	586476	3193962496
272	KI270785.1	119912	3194748928
273	KI270786.1	244096	3195011072
274	KI270788.1	158965	3195273216
275	KI270789.1	205944	3195535360
276	KI270896.1	378547	3195797504
277	KI270925.1	555799	3196321792
278	GL383532.1	82728	3197108224
279	KI270897.1	1144418	3197370368
280	GL383531.1	173459	3198681088
281	GL949742.1	226852	3198943232
282	GL339449.2	1612928	3199205376
283	KI270795.1	131892	3201040384
284	KI270791.1	195710	3201302528
285	GL383530.1	101241	3201564672
286	KI270898.1	130957	3201826816
287	KI270792.1	179043	3202088960
288	KI270796.1	172708	3202351104
289	KI270793.1	126136	3202613248
290	KI270794.1	164558	3202875392
291	KN196477.1	139087	3203137536
292	GL383533.1	124736	3203399680
293	KB021644.2	185823	3203661824
294	KI270797.1	197536	3203923968
295	KI270798.1	271782	3204186112
296	KI270799.1	152148	3204710400
297	KI270800.1	175808	3204972544
298	KI270801.1	870480	3205234688
299	KI270802.1	75005	3206283264
300	KI270758.1	76752	3206545408
301	GL000250.2	4672374	3206807552
302	GL000251.2	4795265	3211526144
303	GL000252.2	4604811	3216506880
304	GL000253.2	4677643	3221225472
305	GL000254.2	4827813	3225944064
306	GL000255.2	4606388	3230924800
307	GL000256.2	4929269	3235643392
308	KI270804.1	157952	3240624128
309	KI270806.1	158166	3240886272
310	GL383534.2	119183	3241148416
311	KI270805.1	209988	3241410560
312	KI270899.1	190869	3241672704
313	KI270809.1	209586	3241934848
314	KI270803.1	1111570	3242196992
315	KI270807.1	126434	3243507712
316	KI270808.1	271455	3243769856
317	KI270811.1	292436	3244294144
318	KI270814.1	141812	3244818432
319	KI270810.1	374415	3245080576
320	KI270812.1	282736	3245604864
321	KI270815.1	132244	3246129152
322	KI270813.1	300230	3246391296
323	KI270816.1	305841	3246915584
324	KI270818.1	145606	3247439872
325	KI270817.1	158983	3247702016
326	KI270900.1	318687	3247964160
327	KI270819.1	133535	3248488448
328	KI270901.1	136959	3248750592
329	KI270820.1	36640	3249012736
330	KI270926.1	229282	3249274880
331	KI270821.1	985506	3249537024
332	KI270822.1	624492	3250585600
333	GL383539.1	162988	3251372032
334	GL383540.1	71551	3251634176
335	GL383541.1	171286	3251896320
336	GL383542.1	60032	3252158464
337	KI270823.1	439082	3252420608
338	KI270880.1	284869	3252944896
339	KI270881.1	144206	3253469184
340	KI270913.1	274009	3253731328
341	KI270302.1	2274	3254255616
342	KI270303.1	1942	3254517760
343	KI270304.1	2165	3254779904
344	KI270305.1	1472	3255042048
345	KI270310.1	1201	3255304192
346	KI270311.1	12399	3255566336
347	KI270312.1	998	3255828480
348	KI270315.1	2276	3256090624
349	KI270316.1	1444	3256352768
350	KI270317.1	37690	3256614912
351	KI270320.1	4416	3256877056
352	KI270322.1	21476	3257139200
353	KI270329.1	1040	3257401344
354	KI270330.1	1652	3257663488
355	KI270333.1	2699	3257925632
356	KI270334.1	1368	3258187776
357	KI270335.1	1048	3258449920
358	KI270336.1	1026	3258712064
359	KI270337.1	1121	3258974208
360	KI270338.1	1428	3259236352
361	KI270340.1	1428	3259498496
362	KI270362.1	3530	3259760640
363	KI270363.1	1803	3260022784
364	KI270364.1	2855	3260284928
365	KI270366.1	8320	3260547072
366	KI270371.1	2805	3260809216
367	KI270372.1	1650	3261071360
368	KI270373.1	1451	3261333504
369	KI270374.1	2656	3261595648
370	KI270375.1	2378	3261857792
371	KI270376.1	1136	3262119936
372	KI270378.1	1048	3262382080
373	KI270379.1	1045	3262644224
374	KI270381.1	1930	3262906368
375	KI270382.1	4215	3263168512
376	KI270383.1	1750	3263430656
377	KI270384.1	1658	3263692800
378	KI270385.1	990	3263954944
379	KI270386.1	1788	3264217088
380	KI270387.1	1537	3264479232
381	KI270388.1	1216	3264741376
382	KI270389.1	1298	3265003520
383	KI270390.1	2387	3265265664
384	KI270391.1	1484	3265527808
385	KI270392.1	971	3265789952
386	KI270393.1	1308	3266052096
387	KI270394.1	970	3266314240
388	KI270395.1	1143	3266576384
389	KI270396.1	1880	3266838528
390	KI270411.1	2646	3267100672
391	KI270412.1	1179	3267362816
392	KI270414.1	2489	3267624960
393	KI270417.1	2043	3267887104
394	KI270418.1	2145	3268149248
395	KI270419.1	1029	3268411392
396	KI270420.1	2321	3268673536
397	KI270422.1	1445	3268935680
398	KI270423.1	981	3269197824
399	KI270424.1	2140	3269459968
400	KI270425.1	1884	3269722112
401	KI270429.1	1361	3269984256
402	KI270435.1	92983	3270246400
403	KI270438.1	112505	3270508544
404	KI270442.1	392061	3270770688
405	KI270448.1	7992	3271294976
406	KI270465.1	1774	3271557120
407	KI270466.1	1233	3271819264
408	KI270467.1	3920	3272081408
409	KI270468.1	4055	3272343552
410	KI270507.1	5353	3272605696
411	KI270508.1	1951	3272867840
412	KI270509.1	2318	3273129984
413	KI270510.1	2415	3273392128
414	KI270511.1	8127	3273654272
415	KI270512.1	22689	3273916416
416	KI270515.1	6361	3274178560
417	KI270516.1	1300	3274440704
418	KI270517.1	3253	3274702848
419	KI270518.1	2186	3274964992
420	KI270519.1	138126	3275227136
421	KI270521.1	7642	3275489280
422	KI270522.1	5674	3275751424
423	KI270528.1	2983	3276013568
424	KI270529.1	1899	3276275712
425	KI270530.1	2168	3276537856
426	KI270538.1	91309	3276800000
427	KI270539.1	993	3277062144
428	KI270544.1	1202	3277324288
429	KI270548.1	1599	3277586432
430	KI270579.1	31033	3277848576
431	KI270580.1	1553	3278110720
432	KI270581.1	7046	3278372864
433	KI270582.1	6504	3278635008
434	KI270583.1	1400	3278897152
435	KI270584.1	4513	3279159296
436	KI270587.1	2969	3279421440
437	KI270588.1	6158	3279683584
438	KI270589.1	44474	3279945728
439	KI270590.1	4685	3280207872
440	KI270591.1	5796	3280470016
441	KI270593.1	3041	3280732160
442	KI270706.1	175055	3280994304
443	KI270707.1	32032	3281256448
444	KI270708.1	127682	3281518592
445	KI270709.1	66860	3281780736
446	KI270710.1	40176	3282042880
447	KI270711.1	42210	3282305024
448	KI270712.1	176043	3282567168
449	KI270713.1	40745	3282829312
450	KI270714.1	41717	3283091456
451	KI270715.1	161471	3283353600
452	KI270716.1	153799	3283615744
453	KI270717.1	40062	3283877888
454	KI270718.1	38054	3284140032
455	KI270719.1	176845	3284402176
456	KI270720.1	39050	3284664320
457	KI270721.1	100316	3284926464
458	KI270722.1	194050	3285188608
459	KI270723.1	38115	3285450752
460	KI270724.1	39555	3285712896
461	KI270725.1	172810	3285975040
462	KI270726.1	43739	3286237184
463	KI270727.1	448248	3286499328
464	KI270728.1	1872759	3287023616
465	KI270729.1	280839	3289120768
466	KI270730.1	112551	3289645056
467	KI270731.1	150754	3289907200
468	KI270732.1	41543	3290169344
469	KI270733.1	179772	3290431488
470	KI270734.1	165050	3290693632
471	KI270735.1	42811	3290955776
472	KI270736.1	181920	3291217920
473	KI270737.1	103838	3291480064
474	KI270738.1	99375	3291742208
475	KI270739.1	73985	3292004352
476	KI270740.1	37240	3292266496
477	KI270741.1	157432	3292528640
478	KI270742.1	186739	3292790784
479	KI270743.1	210658	3293052928
480	KI270744.1	168472	3293315072
481	KI270745.1	41891	3293577216
482	KI270746.1	66486	3293839360
483	KI270747.1	198735	3294101504
484	KI270748.1	93321	3294363648
485	KI270749.1	158759	3294625792
486	KI270750.1	148850	3294887936
487	KI270751.1	150742	3295150080
488	KI270752.1	27745	3295412224
489	KI270753.1	62944	3295674368
490	KI270754.1	40191	3295936512
491	KI270755.1	36723	3296198656
492	KI270756.1	79590	3296460800
493	KI270757.1	71251	3296722944
Processing splice junctions database sjdbN=347743,   sjdbOverhang=100 
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Nov 28 17:49:18   Loaded database junctions from the generated genome pathto/STARgenome/sjdbList.out.tab: 347743 total junctions

Nov 28 17:49:18 ..... Processing annotations GTF
Processing sjdbGTFfile=/pathto/STARgenome/gencode.v23.annotation.gtf, found:
		198619 transcripts
		1173255 exons (non-collapsed)
		347819 collapsed junctions
Nov 28 17:49:45 ..... Finished GTF processing
Nov 28 17:49:45   Loaded database junctions from the GTF file: /pathto/STARgenome/gencode.v23.annotation.gtf: 695562 total junctions

WARNING: long repeat for junction # 250533 : chr15 88855522 88855578; left shift = 14; right shift = 255
WARNING: long repeat for junction # 292795 : chr18 46969610 47029116; left shift = 183; right shift = 255
WARNING: long repeat for junction # 598332 : chr15 88855522 88855578; left shift = 14; right shift = 255
WARNING: long repeat for junction # 640603 : chr18 46969610 47029116; left shift = 183; right shift = 255
Nov 28 17:49:53   Finished preparing junctions
Nov 28 17:49:53 ..... Inserting junctions into the genome indices
Nov 28 17:52:01   Finished SA search: number of new junctions=0, old junctions=347743
Nov 28 17:52:02   Finished sorting SA indicesL nInd=0
Nov 28 17:54:14   Finished inserting junction indices
Nov 28 17:54:19   Finished SAi
Nov 28 17:54:19 ..... Finished inserting junctions into genome
Created thread # 1
Starting to map file # 0
mate 1:   pathto/sample_R1.fastq.gz
mate 2:   pathto/sample_R2.fastq.gz

EXITING because of FATAL ERROR in reads input: short read sequence line: 1
Read Name=@K00152:8:H3MF5BBXX:4:1101:30404:1773
Read Sequence====
DEF_readNameLengthMax=50000
DEF_readSeqLengthMax=500

Nov 28 17:54:22 ...... FATAL ERROR, exiting
