Starting /dee2/code/volunteer_pipeline.sh SRR5030840
    current disk space = 160661356544
    free memory = 56731552 
SRR5030840 SRAfilesize
d622aa3a1b8fbd41aa360a87b8fe1381  SRR5030840.sra
SRR5030840.sra file validated
SRR5030840 is single end
SRR5030840 is conventional basespace
SRR5030840 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030840_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	52
>>END_MODULE
>>Per base sequence quality	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.3915	33.0	31.0	34.0	31.0	34.0
2	32.74125	34.0	31.0	34.0	31.0	34.0
3	32.802	34.0	31.0	34.0	31.0	34.0
4	36.27925	37.0	37.0	37.0	35.0	37.0
5	36.25275	37.0	37.0	37.0	35.0	37.0
6	36.00275	37.0	35.0	37.0	35.0	37.0
7	36.16275	37.0	35.0	37.0	35.0	37.0
8	36.17425	37.0	36.0	37.0	35.0	37.0
9	37.964	39.0	38.0	39.0	35.0	39.0
10	37.97675	39.0	38.0	39.0	35.0	39.0
11	37.8635	39.0	38.0	39.0	35.0	39.0
12	37.97225	39.0	38.0	39.0	35.0	39.0
13	37.82975	39.0	38.0	39.0	35.0	39.0
14	39.1575	41.0	39.0	41.0	35.0	41.0
15	39.175	40.0	38.0	41.0	36.0	41.0
16	39.203	40.0	39.0	41.0	36.0	41.0
17	39.3255	41.0	39.0	41.0	36.0	41.0
18	39.23225	41.0	39.0	41.0	36.0	41.0
19	39.03625	40.0	38.0	41.0	36.0	41.0
20	39.17575	40.0	39.0	41.0	36.0	41.0
21	39.24825	41.0	39.0	41.0	36.0	41.0
22	39.2115	41.0	39.0	41.0	36.0	41.0
23	39.155	40.0	39.0	41.0	36.0	41.0
24	38.503	40.0	38.0	41.0	34.0	41.0
25	38.7325	40.0	38.0	41.0	34.0	41.0
26	38.769	40.0	38.0	41.0	34.0	41.0
27	38.70725	40.0	38.0	41.0	34.0	41.0
28	38.695	40.0	38.0	41.0	34.0	41.0
29	38.3145	40.0	38.0	41.0	33.0	41.0
30	38.12575	40.0	38.0	41.0	33.0	41.0
31	38.5785	40.0	38.0	41.0	34.0	41.0
32	38.87125	40.0	38.0	41.0	35.0	41.0
33	37.21725	40.0	37.0	41.0	30.0	41.0
34	36.5865	40.0	37.0	41.0	30.0	41.0
35	32.544	38.0	31.0	40.0	12.0	41.0
36	29.65125	37.0	21.0	40.0	8.0	41.0
37	29.61625	36.0	23.0	39.0	6.0	40.0
38	32.13875	37.0	30.0	40.0	9.0	41.0
39	31.52575	37.0	30.0	40.0	6.0	41.0
40	32.334	37.0	31.0	40.0	2.0	41.0
41	30.06525	36.0	26.0	40.0	2.0	41.0
42	31.65075	37.0	30.0	40.0	2.0	41.0
43	30.15925	36.0	26.0	40.0	2.0	41.0
44	30.955	37.0	30.0	40.0	2.0	41.0
45	28.74225	36.0	24.0	40.0	2.0	41.0
46	26.7645	34.0	9.0	39.0	2.0	40.0
47	26.77225	34.0	9.0	39.0	2.0	41.0
48	27.3055	35.0	2.0	39.0	2.0	41.0
49	25.54725	34.0	2.0	39.0	2.0	41.0
50	22.55575	30.0	2.0	37.0	2.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
10	1.0
11	0.0
12	1.0
13	0.0
14	0.0
15	1.0
16	3.0
17	4.0
18	1.0
19	6.0
20	5.0
21	20.0
22	16.0
23	29.0
24	42.0
25	56.0
26	104.0
27	171.0
28	65.0
29	111.0
30	146.0
31	176.0
32	171.0
33	181.0
34	228.0
35	257.0
36	351.0
37	442.0
38	658.0
39	754.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.892839258888333	25.237856785177765	45.443164747120676	17.426139208813222
2	24.95	26.875	19.900000000000002	28.275
3	22.25	21.875	22.95	32.925
4	30.8	27.150000000000002	16.225	25.825
5	21.725	39.85	25.974999999999998	12.45
6	34.1	17.025000000000002	32.9	15.975
7	19.15	18.825	26.5	35.525
8	26.5	28.275	17.7	27.525
9	18.8	35.075	28.349999999999998	17.775
10	23.375	23.474999999999998	27.525	25.624999999999996
11	33.525	12.825000000000001	16.2	37.45
12	17.625	21.6	28.050000000000004	32.725
13	30.675	19.075	31.75	18.5
14	31.05	28.425	22.375	18.15
15	31.55	24.15	27.950000000000003	16.35
16	20.325	20.05	21.45	38.175
17	22.275	23.125	38.75	15.85
18	23.825	19.125	27.800000000000004	29.25
19	32.925	14.000000000000002	34.300000000000004	18.775
20	37.85	16.775000000000002	30.125	15.25
21	24.25	20.075000000000003	28.975	26.700000000000003
22	28.849999999999998	14.249999999999998	43.175000000000004	13.725000000000001
23	27.6	14.174999999999999	41.05	17.175
24	51.175000000000004	13.700000000000001	24.575	10.549999999999999
25	47.425	24.525	15.174999999999999	12.875
26	27.525	42.85	14.774999999999999	14.85
27	17.375	43.05	23.525	16.05
28	14.924999999999999	23.799999999999997	44.55	16.725
29	13.900000000000002	14.399999999999999	52.15	19.55
30	11.675	8.450000000000001	36.15	43.725
31	15.0	7.825	43.7	33.475
32	29.849999999999998	6.925000000000001	22.725	40.5
33	50.525	10.925	15.25	23.3
34	57.775	7.225	16.875	18.125
35	55.900000000000006	8.475000000000001	20.95	14.674999999999999
36	61.775000000000006	9.65	15.125	13.450000000000001
37	37.1	13.0	21.325	28.575
38	26.525	14.924999999999999	14.45	44.1
39	19.675	25.05	12.575	42.699999999999996
40	18.325	45.175	13.65	22.85
41	28.95	40.45	11.875	18.725
42	47.55	27.675	13.700000000000001	11.075
43	44.2	33.15	11.125	11.525
44	30.599999999999998	45.925	9.475	14.000000000000002
45	21.575	42.375	11.774999999999999	24.275
46	16.925	26.950000000000003	26.224999999999998	29.9
47	11.899999999999999	17.575	32.125	38.4
48	13.825000000000001	13.25	21.349999999999998	51.575
49	15.299999999999999	25.7	15.049999999999999	43.95
50	30.575000000000003	25.75	11.875	31.8
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.5
8	1.0
9	0.5
10	0.0
11	1.0
12	2.0
13	1.5
14	1.0
15	0.5
16	0.0
17	0.5
18	1.0
19	1.0
20	1.0
21	0.5
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	1.5
28	2.0
29	1.5
30	1.0
31	5.0
32	9.0
33	19.0
34	29.0
35	43.0
36	57.0
37	69.0
38	81.0
39	73.5
40	66.0
41	63.0
42	60.0
43	88.0
44	116.0
45	163.0
46	210.0
47	254.5
48	299.0
49	363.0
50	427.0
51	601.5
52	776.0
53	645.0
54	514.0
55	467.5
56	421.0
57	377.0
58	333.0
59	246.0
60	159.0
61	119.5
62	80.0
63	135.0
64	190.0
65	110.5
66	31.0
67	23.5
68	16.0
69	19.0
70	22.0
71	46.5
72	71.0
73	39.5
74	8.0
75	5.5
76	3.0
77	3.0
78	3.0
79	5.0
80	7.0
81	4.0
82	1.0
83	0.5
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.15
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	51.025
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.35276825085742	41.0
2	8.182263596276334	8.35
3	3.3806957373836357	5.175
4	1.8618324350808426	3.8
5	1.6168544830965212	4.125
6	0.7839294463498285	2.4
7	0.4899559039686428	1.7500000000000002
8	0.39196472317491426	1.6
9	0.19598236158745713	0.8999999999999999
>10	2.596766291033807	23.525
>50	0.09799118079372857	4.8
>100	0.04899559039686428	2.5749999999999997
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	103	2.5749999999999997	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	95	2.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	28	0.7000000000000001	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	26	0.65	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	24	0.6	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	24	0.6	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	19	0.475	RNA PCR Primer, Index 1 (100% over 33bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	19	0.475	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	17	0.42500000000000004	RNA PCR Primer, Index 7 (97% over 35bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	16	0.4	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	16	0.4	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGC	13	0.325	RNA PCR Primer, Index 23 (100% over 50bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTC	13	0.325	RNA PCR Primer, Index 23 (100% over 44bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	13	0.325	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	13	0.325	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	13	0.325	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	13	0.325	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	12	0.3	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	12	0.3	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	12	0.3	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	12	0.3	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	11	0.27499999999999997	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	10	0.25	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	10	0.25	RNA PCR Primer, Index 1 (96% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	10	0.25	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	9	0.22499999999999998	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	8	0.2	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	7	0.17500000000000002	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	6	0.15	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (96% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
CTGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTC	6	0.15	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAATTCCA	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	5	0.125	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACGA	5	0.125	RNA PCR Primer, Index 9 (97% over 35bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCA	5	0.125	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCAG	5	0.125	RNA PCR Primer, Index 1 (96% over 26bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	5	0.125	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	5	0.125	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	5	0.125	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	5	0.125	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	5	0.125	No Hit
CTTAATGATGATTGTCTGTTTGATTGCTTGATGCAATGTGAAAACCACAT	5	0.125	No Hit
AATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATG	5	0.125	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.35	0.0	0.0	0.0
2	0.0	0.4	0.0	0.0	0.0
3	0.0	0.425	0.0	0.0	0.0
4	0.0	0.425	0.0	0.0	0.0
5	0.0	0.5	0.0	0.0	0.0
6	0.0	0.6	0.0	0.0	0.0
7	0.0	0.925	0.0	0.0	0.0
8	0.0	1.075	0.0	0.0	0.0
9	0.0	1.125	0.0	0.0	0.0
10	0.0	1.15	0.0	0.0	0.0
11	0.0	1.225	0.0	0.0	0.0
12	0.0	1.45	0.0	0.0	0.0
13	0.0	1.725	0.0	0.0	0.0
14	0.0	1.975	0.0	0.0	0.0
15	0.0	2.3	0.0	0.0	0.0
16	0.0	3.2	0.0	0.0	0.0
17	0.0	3.525	0.0	0.0	0.0
18	0.0	4.425	0.0	0.0	0.0
19	0.0	4.85	0.0	0.0	0.0
20	0.0	5.575	0.0	0.0	0.0
21	0.0	9.65	0.0	0.0	0.0
22	0.0	20.475	0.0	0.0	0.0
23	0.0	45.175	0.0	0.0	0.0
24	0.0	56.65	0.0	0.0	0.0
25	0.0	61.975	0.0	0.0	0.0
26	0.0	63.85	0.0	0.0	0.0
27	0.0	64.575	0.0	0.0	0.0
28	0.0	65.25	0.0	0.0	0.0
29	0.0	65.425	0.0	0.0	0.0
30	0.0	65.875	0.0	0.0	0.0
31	0.0	66.425	0.0	0.0	0.0
32	0.0	67.65	0.0	0.0	0.0
33	0.0	68.575	0.0	0.0	0.0
34	0.0	72.325	0.0	0.0	0.0
35	0.0	73.25	0.0	0.0	0.0
36	0.0	73.75	0.0	0.0	0.0
37	0.0	74.575	0.0	0.0	0.0
38	0.0	74.975	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGTTGTG	20	6.952051E-4	44.000004	7
CGCGACC	20	6.952051E-4	44.000004	1
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
TGTGAAT	20	6.952051E-4	44.000004	10
GTGTTGT	20	6.952051E-4	44.000004	6
AACCGGT	20	6.952051E-4	44.000004	9
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
GCGACCT	20	6.952051E-4	44.000004	2
GCGACCC	20	6.952051E-4	44.000004	22
GCTGGTG	20	6.952051E-4	44.000004	2
GGTCTCT	20	6.952051E-4	44.000004	13
GGCGACC	20	6.952051E-4	44.000004	21
ACCCGCT	20	6.952051E-4	44.000004	25
CATTCAA	20	6.952051E-4	44.000004	3
ACATCCT	20	6.952051E-4	44.000004	6
CCCGCTG	20	6.952051E-4	44.000004	26
CGTGGCG	20	6.952051E-4	44.000004	18
CTGGTGT	20	6.952051E-4	44.000004	3
>>END_MODULE
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218028 spots for SRR5030840.sra
Written 218028 spots for SRR5030840.sra
Read 218032 spots for SRR5030840.sra
Written 218032 spots for SRR5030840.sra
SRR ids: ['SRR5030840.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_c0ms2_jh
SRR5030840.sra spots: 2616340
blocks: [[1, 218028], [218029, 436056], [436057, 654084], [654085, 872112], [872113, 1090140], [1090141, 1308168], [1308169, 1526196], [1526197, 1744224], [1744225, 1962252], [1962253, 2180280], [2180281, 2398308], [2398309, 2616340]]
SRR5030840 file size 452392
SRR5030840 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030840 SRR5030840_1.fastq
Input file:	SRR5030840_1.fastq
trimmed:	SRR5030840-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 06:24:46 2020 >> started

Wed Mar  4 06:24:48 2020 >> done (2.003s)
2616340 reads processed; of these:
    153 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
2616182 (99.99%) reads available; of these:
 299111 (11.43%) trimmed reads available after processing
2317071 (88.57%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     42	  0.00%
 19	     30	  0.00%
 20	    101	  0.00%
 21	    122	  0.00%
 22	    234	  0.01%
 23	    281	  0.01%
 24	    324	  0.01%
 25	    447	  0.02%
 26	    364	  0.01%
 27	    465	  0.02%
 28	    622	  0.02%
 29	    750	  0.03%
 30	    701	  0.03%
 31	   1063	  0.04%
 32	   2701	  0.10%
 33	   9248	  0.35%
 34	  22393	  0.86%
 35	   5369	  0.21%
 36	   5649	  0.22%
 37	   3115	  0.12%
 38	   6393	  0.24%
 39	   5848	  0.22%
 40	  10760	  0.41%
 41	   6343	  0.24%
 42	  14428	  0.55%
 43	   6956	  0.27%
 44	  29928	  1.14%
 45	  19248	  0.74%
 46	  18324	  0.70%
 47	  18439	  0.70%
 48	  53816	  2.06%
 49	  54607	  2.09%
 50	2317071	 88.57%
2616182 reads passed initial QC


criterion=sequence-density
sequence-density=75.26
sequence-density-rank=1
fanout-score=21.12
fanout-score-rank=3
prefix-density=78.14
prefix-fanout=20.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC


criterion=fanout-score
sequence-density=1.56
sequence-density-rank=5
fanout-score=462.07
fanout-score-rank=1
prefix-density=77.31
prefix-fanout=9.3
sequence=GGAATTCTCGGTGCCAAGGA
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC -o SRR5030840 -
Input file:	STDIN
trimmed:	SRR5030840-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 06:25:03 2020 >> started

Wed Mar  4 06:25:08 2020 >> done (4.549s)
2547335 reads processed; of these:
 109365 ( 4.29%) short reads filtered out after trimming by size control
   9371 ( 0.37%) empty reads filtered out after trimming by size control
2428599 (95.34%) reads available; of these:
2036269 (83.85%) trimmed reads available after processing
 392330 (16.15%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13847	  0.57%
 19	  22649	  0.93%
 20	 105577	  4.35%
 21	 263996	 10.87%
 22	 637092	 26.23%
 23	 323762	 13.33%
 24	 153682	  6.33%
 25	  37564	  1.55%
 26	  19773	  0.81%
 27	  15704	  0.65%
 28	  16152	  0.67%
 29	  14216	  0.59%
 30	  20258	  0.83%
 31	  29489	  1.21%
 32	  23242	  0.96%
 33	  94632	  3.90%
 34	  23477	  0.97%
 35	  16880	  0.70%
 36	  23336	  0.96%
 37	  11655	  0.48%
 38	  13966	  0.58%
 39	  13913	  0.57%
 40	  21096	  0.87%
 41	  26199	  1.08%
 42	  34659	  1.43%
 43	  22743	  0.94%
 44	  20442	  0.84%
 45	  25421	  1.05%
 46	  20726	  0.85%
 47	  17233	  0.71%
 48	   5596	  0.23%
 49	  10167	  0.42%
 50	 329455	 13.57%


criterion=sequence-density
sequence-density=6.69
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=40
fanout-score=294.99
fanout-score-rank=1
prefix-density=2.22
prefix-fanout=1.7
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:25:32
                             Started mapping on |	Mar 04 06:25:32
                                    Finished on |	Mar 04 06:25:56
       Mapping speed, Million of reads per hour |	374.62

                          Number of input reads |	2497446
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1291932
                        Uniquely mapped reads % |	51.73%
                          Average mapped length |	28.01
                       Number of splices: Total |	1340
            Number of splices: Annotated (sjdb) |	177
                       Number of splices: GT/AG |	1227
                       Number of splices: GC/AG |	19
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	94
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.06
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	771267
             % of reads mapped to multiple loci |	30.88%
        Number of reads mapped to too many loci |	56830
             % of reads mapped to too many loci |	2.28%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	14.61%
                     % of reads unmapped: other |	0.50%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	434247	434247	434247
N_multimapping	771267	771267	771267
N_noFeature	72792	89057	957014
N_ambiguous	693039	403009	15024
UnstrandedReadsAssigned:526101 PositiveStrandReadsAssigned:799866 NegativeStrandReadsAssigned:319894
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030840 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[index] k-mer length: 19
[index] number of targets: 109,282
[index] number of k-mers: 92,755,666
[index] number of equivalence classes: 769,752
[quant] running in single-end mode
[quant] will process file 1: SRR5030840-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,497,446 reads, 569,935 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,083 rounds

 109283 SRR5030840.ke.tsv
  52636 SRR5030840.se.tsv
 161919 total
==> SRR5030840.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSMUST00000177564.1	16	4.59059	0	0
ENSMUST00000196221.1	9	3.70903	0	0
ENSMUST00000179664.1	11	4.02702	0	0
ENSMUST00000178537.1	12	4.16231	0	0
ENSMUST00000178862.1	14	4.39563	0	0
ENSMUST00000179520.1	11	4.02702	0	0
ENSMUST00000179883.1	16	4.59059	0	0
ENSMUST00000195858.1	10	3.87667	0	0
ENSMUST00000179932.1	12	4.16231	0	0

==> SRR5030840.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030840 completed mapping pipeline successfully
