Starting /dee2/code/volunteer_pipeline.sh SRR5030849
    current disk space = 160665190400
    free memory = 73948016 
SRR5030849 SRAfilesize
3b4637f3d1cd1480be50731c97a63b71  SRR5030849.sra
SRR5030849.sra file validated
SRR5030849 is single end
SRR5030849 is conventional basespace
SRR5030849 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030849_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	32.3395	33.0	31.0	34.0	31.0	34.0
2	32.72875	34.0	31.0	34.0	31.0	34.0
3	32.743	34.0	31.0	34.0	31.0	34.0
4	36.22375	37.0	37.0	37.0	35.0	37.0
5	36.252	37.0	37.0	37.0	35.0	37.0
6	36.018	37.0	35.0	37.0	35.0	37.0
7	36.10675	37.0	35.0	37.0	35.0	37.0
8	36.19875	37.0	36.0	37.0	35.0	37.0
9	37.927	39.0	38.0	39.0	35.0	39.0
10	37.8635	39.0	38.0	39.0	35.0	39.0
11	37.837	39.0	38.0	39.0	35.0	39.0
12	37.88925	39.0	38.0	39.0	35.0	39.0
13	37.84125	39.0	38.0	39.0	35.0	39.0
14	39.3045	41.0	39.0	41.0	36.0	41.0
15	39.22825	41.0	39.0	41.0	36.0	41.0
16	39.1635	40.0	39.0	41.0	36.0	41.0
17	39.28975	41.0	39.0	41.0	36.0	41.0
18	39.25425	41.0	39.0	41.0	36.0	41.0
19	39.0205	40.0	39.0	41.0	36.0	41.0
20	39.09825	40.0	39.0	41.0	36.0	41.0
21	39.18125	41.0	39.0	41.0	36.0	41.0
22	39.27	41.0	39.0	41.0	36.0	41.0
23	39.236	41.0	39.0	41.0	36.0	41.0
24	38.481	40.0	38.0	41.0	34.0	41.0
25	38.7205	40.0	38.0	41.0	34.0	41.0
26	38.56525	40.0	38.0	41.0	34.0	41.0
27	38.56275	40.0	38.0	41.0	34.0	41.0
28	38.65725	40.0	38.0	41.0	34.0	41.0
29	38.64375	40.0	38.0	41.0	34.0	41.0
30	38.52725	40.0	38.0	41.0	34.0	41.0
31	38.8335	40.0	38.0	41.0	35.0	41.0
32	39.0905	41.0	39.0	41.0	35.0	41.0
33	37.5765	40.0	38.0	41.0	32.0	41.0
34	36.6365	40.0	37.0	41.0	28.0	41.0
35	32.39275	38.0	30.0	40.0	9.0	41.0
36	29.058	37.0	16.0	40.0	8.0	41.0
37	29.211	35.0	22.0	39.0	6.0	41.0
38	31.92075	37.0	30.0	39.0	9.0	41.0
39	31.205	37.0	29.0	40.0	6.0	41.0
40	32.312	37.0	31.0	40.0	2.0	41.0
41	29.9955	36.0	26.0	40.0	2.0	41.0
42	31.68775	37.0	30.0	40.0	2.0	41.0
43	29.9875	36.0	26.0	40.0	2.0	41.0
44	30.99675	37.0	30.0	40.0	2.0	41.0
45	28.67775	36.0	23.0	40.0	2.0	41.0
46	26.54475	34.0	8.0	39.0	2.0	41.0
47	26.60425	34.0	8.0	39.0	2.0	41.0
48	27.32175	35.0	2.0	39.0	2.0	41.0
49	25.34975	34.0	2.0	39.0	2.0	41.0
50	22.3325	29.0	2.0	38.0	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
7	1.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	2.0
15	0.0
16	1.0
17	1.0
18	3.0
19	8.0
20	10.0
21	12.0
22	19.0
23	36.0
24	40.0
25	64.0
26	97.0
27	162.0
28	63.0
29	104.0
30	177.0
31	173.0
32	186.0
33	180.0
34	226.0
35	292.0
36	351.0
37	378.0
38	595.0
39	819.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.350877192982457	26.591478696741856	47.54385964912281	15.513784461152882
2	24.875	28.275	18.725	28.125
3	23.575	21.8	22.650000000000002	31.974999999999998
4	30.625000000000004	28.299999999999997	15.475	25.6
5	21.8	40.325	25.95	11.924999999999999
6	32.65	18.725	35.05	13.575000000000001
7	17.875	19.400000000000002	25.474999999999998	37.25
8	26.325	30.825000000000003	14.299999999999999	28.549999999999997
9	18.725	35.775	29.925	15.575
10	22.900000000000002	22.375	28.375	26.35
11	32.525	12.950000000000001	17.424999999999997	37.1
12	16.675	21.15	28.675	33.5
13	30.275000000000002	18.85	31.5	19.375
14	31.974999999999998	29.425	22.25	16.35
15	32.375	24.3	27.675	15.65
16	19.175	19.275000000000002	23.1	38.45
17	23.200000000000003	23.849999999999998	37.925	15.024999999999999
18	24.85	18.575	29.75	26.825
19	33.15	14.899999999999999	33.5	18.45
20	40.475	16.025	28.625	14.875
21	23.724999999999998	22.400000000000002	28.299999999999997	25.575
22	29.375	12.075	46.725	11.825
23	27.175	13.05	43.4	16.375
24	51.824999999999996	14.399999999999999	24.349999999999998	9.425
25	48.525	24.425	16.025	11.025
26	27.224999999999998	45.550000000000004	15.174999999999999	12.049999999999999
27	16.925	44.824999999999996	23.825	14.424999999999999
28	12.4	23.799999999999997	47.75	16.05
29	10.5	15.075	54.275	20.150000000000002
30	10.549999999999999	7.375	36.8	45.275
31	14.575	6.5	46.625	32.300000000000004
32	30.475	5.65	20.225	43.65
33	53.300000000000004	8.825	14.325	23.549999999999997
34	59.925	7.875	14.95	17.25
35	58.650000000000006	7.475	21.5	12.375
36	63.3	7.85	15.35	13.5
37	40.0	11.075	20.0	28.925
38	23.65	15.325	13.4	47.625
39	18.45	27.150000000000002	11.600000000000001	42.8
40	17.299999999999997	48.15	10.85	23.7
41	30.099999999999998	42.0	10.6	17.299999999999997
42	50.025	28.4	11.85	9.725
43	44.025	35.4	9.475	11.1
44	29.325000000000003	48.625	8.55	13.5
45	20.025000000000002	43.1	11.75	25.124999999999996
46	13.325000000000001	26.974999999999998	26.650000000000002	33.050000000000004
47	9.475	17.1	32.625	40.8
48	11.175	12.975	19.825	56.025000000000006
49	14.674999999999999	26.474999999999998	14.575	44.275
50	31.474999999999998	24.775	10.100000000000001	33.650000000000006
>>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	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.5
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	1.5
24	3.0
25	1.5
26	0.0
27	1.0
28	2.0
29	1.5
30	1.0
31	5.0
32	9.0
33	13.0
34	17.0
35	26.5
36	36.0
37	57.0
38	78.0
39	62.5
40	47.0
41	56.0
42	65.0
43	95.5
44	126.0
45	173.0
46	220.0
47	276.0
48	332.0
49	419.5
50	507.0
51	685.0
52	863.0
53	686.0
54	509.0
55	448.5
56	388.0
57	340.0
58	292.0
59	225.0
60	158.0
61	121.5
62	85.0
63	99.0
64	113.0
65	73.5
66	34.0
67	22.5
68	11.0
69	22.5
70	34.0
71	45.0
72	56.0
73	31.5
74	7.0
75	4.5
76	2.0
77	2.0
78	2.0
79	1.5
80	1.0
81	1.0
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	0.25
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	51.075
#Duplication Level	Percentage of deduplicated	Percentage of total
1	79.7846304454234	40.75
2	8.761625061184533	8.95
3	3.3284385707293196	5.1
4	2.0558002936857562	4.2
5	0.881057268722467	2.25
6	0.978952520802741	3.0
7	0.5873715124816447	2.1
8	0.7831620166421929	3.2
9	0.39158100832109644	1.7999999999999998
>10	2.3005384238864415	22.025
>50	0.09789525208027411	3.55
>100	0.048947626040137054	3.075
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	123	3.075	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	84	2.1	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	58	1.4500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	27	0.675	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	26	0.65	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	20	0.5	RNA PCR Primer, Index 5 (100% over 35bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGC	19	0.475	RNA PCR Primer, Index 25 (100% over 50bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	18	0.44999999999999996	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 29bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	17	0.42500000000000004	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	14	0.35000000000000003	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	14	0.35000000000000003	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	13	0.325	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	13	0.325	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTC	13	0.325	RNA PCR Primer, Index 25 (100% over 44bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	13	0.325	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	12	0.3	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	11	0.27499999999999997	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	11	0.27499999999999997	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	8	0.2	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	8	0.2	RNA PCR Primer, Index 1 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	8	0.2	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	7	0.17500000000000002	No Hit
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	7	0.17500000000000002	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGTGCCAAGGAACTCCAG	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	6	0.15	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	5	0.125	No Hit
TGTAAACATCCTCGACTGGAAGCTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	5	0.125	No Hit
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>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	0.525	0.0	0.0	0.0
2	0.0	0.55	0.0	0.0	0.0
3	0.0	0.6	0.0	0.0	0.0
4	0.0	0.625	0.0	0.0	0.0
5	0.0	0.65	0.0	0.0	0.0
6	0.0	0.65	0.0	0.0	0.0
7	0.0	1.025	0.0	0.0	0.0
8	0.0	1.075	0.0	0.0	0.0
9	0.0	1.15	0.0	0.0	0.0
10	0.0	1.225	0.0	0.0	0.0
11	0.0	1.275	0.0	0.0	0.0
12	0.0	1.425	0.0	0.0	0.0
13	0.0	1.775	0.0	0.0	0.0
14	0.0	1.95	0.0	0.0	0.0
15	0.0	2.225	0.0	0.0	0.0
16	0.0	3.075	0.0	0.0	0.0
17	0.0	3.55	0.0	0.0	0.0
18	0.0	4.45	0.0	0.0	0.0
19	0.0	4.775	0.0	0.0	0.0
20	0.0	5.725	0.0	0.0	0.0
21	0.0	10.65	0.0	0.0	0.0
22	0.0	22.4	0.0	0.0	0.0
23	0.0	50.15	0.0	0.0	0.0
24	0.0	61.475	0.0	0.0	0.0
25	0.0	67.875	0.0	0.0	0.0
26	0.0	69.475	0.0	0.0	0.0
27	0.0	70.075	0.0	0.0	0.0
28	0.0	70.5	0.0	0.0	0.0
29	0.0	70.675	0.0	0.0	0.0
30	0.0	71.2	0.0	0.0	0.0
31	0.0	72.025	0.0	0.0	0.0
32	0.0	72.7	0.0	0.0	0.0
33	0.0	73.525	0.0	0.0	0.0
34	0.0	76.325	0.0	0.0	0.0
35	0.0	77.2	0.0	0.0	0.0
36	0.0	77.925	0.0	0.0	0.0
37	0.0	78.6	0.0	0.0	0.0
38	0.0	78.875	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
ATCCAGG	20	6.952051E-4	44.000004	9
TTCAAGT	20	6.952051E-4	44.000004	1
AGGATAG	20	6.952051E-4	44.000004	13
TCGGTGC	20	6.952051E-4	44.000004	31
ATAGGCT	20	6.952051E-4	44.000004	16
TCCAGGA	20	6.952051E-4	44.000004	10
GGATAGG	20	6.952051E-4	44.000004	14
AGTAATC	20	6.952051E-4	44.000004	5
AGGCTTG	20	6.952051E-4	44.000004	18
CGGTGCC	20	6.952051E-4	44.000004	32
TAATCCA	20	6.952051E-4	44.000004	7
CAGGATA	20	6.952051E-4	44.000004	12
GTAATCC	20	6.952051E-4	44.000004	6
GATAGGC	20	6.952051E-4	44.000004	15
CCAGGAT	20	6.952051E-4	44.000004	11
TAGGCTT	20	6.952051E-4	44.000004	17
CTGAGCT	25	3.6958358E-5	44.0	11
ATGATGA	25	3.6958358E-5	44.0	5
>>END_MODULE
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
Read 313675 spots for SRR5030849.sra
Written 313675 spots for SRR5030849.sra
Read 313670 spots for SRR5030849.sra
Written 313670 spots for SRR5030849.sra
SRR ids: ['SRR5030849.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_btid2ous
SRR5030849.sra spots: 3764045
blocks: [[1, 313670], [313671, 627340], [627341, 941010], [941011, 1254680], [1254681, 1568350], [1568351, 1882020], [1882021, 2195690], [2195691, 2509360], [2509361, 2823030], [2823031, 3136700], [3136701, 3450370], [3450371, 3764045]]
SRR5030849 file size 651317
SRR5030849 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030849 SRR5030849_1.fastq
Input file:	SRR5030849_1.fastq
trimmed:	SRR5030849-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 06:27:48 2020 >> started

Wed Mar  4 06:27:50 2020 >> done (2.129s)
3764045 reads processed; of these:
    216 ( 0.01%) short reads filtered out after trimming by size control
     11 ( 0.00%) empty reads filtered out after trimming by size control
3763818 (99.99%) reads available; of these:
 446153 (11.85%) trimmed reads available after processing
3317665 (88.15%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     58	  0.00%
 19	     90	  0.00%
 20	    149	  0.00%
 21	    202	  0.01%
 22	    344	  0.01%
 23	    435	  0.01%
 24	    469	  0.01%
 25	    653	  0.02%
 26	    527	  0.01%
 27	    701	  0.02%
 28	    879	  0.02%
 29	   1393	  0.04%
 30	   1023	  0.03%
 31	   1425	  0.04%
 32	   3766	  0.10%
 33	  14352	  0.38%
 34	  33706	  0.90%
 35	   8378	  0.22%
 36	   8996	  0.24%
 37	   4462	  0.12%
 38	   9275	  0.25%
 39	   8093	  0.22%
 40	  15564	  0.41%
 41	   8616	  0.23%
 42	  20778	  0.55%
 43	   9561	  0.25%
 44	  41856	  1.11%
 45	  26673	  0.71%
 46	  24371	  0.65%
 47	  26392	  0.70%
 48	  86257	  2.29%
 49	  86709	  2.30%
 50	3317665	 88.15%
3763818 reads passed initial QC


criterion=sequence-density
sequence-density=77.52
sequence-density-rank=1
fanout-score=21.17
fanout-score-rank=2
prefix-density=80.01
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCC


criterion=fanout-score
sequence-density=4.14
sequence-density-rank=2
fanout-score=56.01
fanout-score-rank=1
prefix-density=80.04
prefix-fanout=2.9
sequence=GAATTCTCGGGGGCCAAGGAACT
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCC -o SRR5030849 -
Input file:	STDIN
trimmed:	SRR5030849-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCC
-- 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 06:28:05 2020 >> started

Wed Mar  4 06:28:10 2020 >> done (4.737s)
3667310 reads processed; of these:
 146601 ( 4.00%) short reads filtered out after trimming by size control
  19653 ( 0.54%) empty reads filtered out after trimming by size control
3501056 (95.47%) reads available; of these:
2984209 (85.24%) trimmed reads available after processing
 516847 (14.76%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18997	  0.54%
 19	  34035	  0.97%
 20	 179827	  5.14%
 21	 416017	 11.88%
 22	 986567	 28.18%
 23	 471652	 13.47%
 24	 224633	  6.42%
 25	  54357	  1.55%
 26	  27106	  0.77%
 27	  20986	  0.60%
 28	  21638	  0.62%
 29	  18243	  0.52%
 30	  26440	  0.76%
 31	  33865	  0.97%
 32	  33682	  0.96%
 33	  90758	  2.59%
 34	  36100	  1.03%
 35	  27141	  0.78%
 36	  39259	  1.12%
 37	  14935	  0.43%
 38	  19465	  0.56%
 39	  17816	  0.51%
 40	  26927	  0.77%
 41	  33373	  0.95%
 42	  42823	  1.22%
 43	  27955	  0.80%
 44	  25631	  0.73%
 45	  33448	  0.96%
 46	  26473	  0.76%
 47	  19665	  0.56%
 48	   7469	  0.21%
 49	  13362	  0.38%
 50	 430411	 12.29%


criterion=sequence-density
sequence-density=6.73
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=42
fanout-score=376.05
fanout-score-rank=1
prefix-density=2.47
prefix-fanout=1.7
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:28:31
                             Started mapping on |	Mar 04 06:28:31
                                    Finished on |	Mar 04 06:28:56
       Mapping speed, Million of reads per hour |	518.05

                          Number of input reads |	3597564
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1909055
                        Uniquely mapped reads % |	53.07%
                          Average mapped length |	27.25
                       Number of splices: Total |	2079
            Number of splices: Annotated (sjdb) |	312
                       Number of splices: GT/AG |	1943
                       Number of splices: GC/AG |	24
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	111
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.41
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.09
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1161166
             % of reads mapped to multiple loci |	32.28%
        Number of reads mapped to too many loci |	66012
             % of reads mapped to too many loci |	1.83%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.38%
                     % of reads unmapped: other |	0.44%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	527343	527343	527343
N_multimapping	1161166	1161166	1161166
N_noFeature	85653	105487	1390348
N_ambiguous	1040219	585803	19043
UnstrandedReadsAssigned:783183 PositiveStrandReadsAssigned:1217765 NegativeStrandReadsAssigned:499664
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030849 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: SRR5030849-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,597,564 reads, 860,736 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,141 rounds

 109283 SRR5030849.ke.tsv
  52636 SRR5030849.se.tsv
 161919 total
==> SRR5030849.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

==> SRR5030849.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030849 completed mapping pipeline successfully
