Starting /dee2/code/volunteer_pipeline.sh SRR5030898
    current disk space = 160664272896
    free memory = 73950248 
SRR5030898 SRAfilesize
954dda6ac89446bec8e928ea867e4e7d  SRR5030898.sra
SRR5030898.sra file validated
SRR5030898 is single end
SRR5030898 is conventional basespace
SRR5030898 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030898_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	32.2855	33.0	31.0	34.0	31.0	34.0
2	32.7065	34.0	31.0	34.0	31.0	34.0
3	32.706	34.0	31.0	34.0	31.0	34.0
4	36.213	37.0	37.0	37.0	35.0	37.0
5	36.23075	37.0	37.0	37.0	35.0	37.0
6	35.90425	37.0	35.0	37.0	35.0	37.0
7	36.0115	37.0	35.0	37.0	35.0	37.0
8	36.12125	37.0	35.0	37.0	35.0	37.0
9	37.80325	39.0	38.0	39.0	35.0	39.0
10	37.93775	39.0	38.0	39.0	35.0	39.0
11	37.8245	39.0	38.0	39.0	35.0	39.0
12	37.888	39.0	38.0	39.0	35.0	39.0
13	37.90825	39.0	38.0	39.0	35.0	39.0
14	39.2085	41.0	39.0	41.0	36.0	41.0
15	39.32825	41.0	39.0	41.0	36.0	41.0
16	39.101	40.0	39.0	41.0	36.0	41.0
17	39.30575	41.0	39.0	41.0	36.0	41.0
18	39.209	41.0	39.0	41.0	36.0	41.0
19	38.94175	40.0	39.0	41.0	35.0	41.0
20	39.087	40.0	39.0	41.0	36.0	41.0
21	39.1225	40.0	39.0	41.0	36.0	41.0
22	39.132	41.0	39.0	41.0	36.0	41.0
23	39.06	40.0	39.0	41.0	36.0	41.0
24	38.35725	40.0	38.0	41.0	34.0	41.0
25	38.7985	40.0	39.0	41.0	35.0	41.0
26	38.8815	40.0	38.0	41.0	35.0	41.0
27	38.8545	40.0	39.0	41.0	35.0	41.0
28	38.93	40.0	39.0	41.0	35.0	41.0
29	38.87625	40.0	38.0	41.0	35.0	41.0
30	38.607	40.0	38.0	41.0	34.0	41.0
31	38.892	41.0	38.0	41.0	35.0	41.0
32	39.05475	41.0	39.0	41.0	35.0	41.0
33	37.56325	40.0	38.0	41.0	32.0	41.0
34	37.003	40.0	37.0	41.0	30.0	41.0
35	32.5455	38.0	31.0	40.0	15.0	41.0
36	28.82825	36.0	16.0	40.0	8.0	41.0
37	29.0405	35.0	22.0	39.0	6.0	40.0
38	32.164	37.0	30.0	39.0	15.0	40.0
39	31.39525	37.0	30.0	40.0	7.0	41.0
40	32.4605	37.0	31.0	40.0	7.0	41.0
41	30.00225	36.0	25.0	40.0	2.0	41.0
42	31.769	37.0	31.0	40.0	2.0	41.0
43	29.8825	36.0	26.0	40.0	2.0	41.0
44	31.01525	37.0	30.0	40.0	2.0	41.0
45	28.52775	36.0	22.0	40.0	2.0	41.0
46	26.36975	34.0	7.0	39.0	2.0	41.0
47	26.63175	34.0	8.0	39.0	2.0	41.0
48	27.53975	35.0	2.0	40.0	2.0	41.0
49	25.599	34.0	2.0	40.0	2.0	41.0
50	22.27775	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
14	1.0
15	0.0
16	0.0
17	1.0
18	1.0
19	11.0
20	12.0
21	13.0
22	22.0
23	26.0
24	26.0
25	65.0
26	72.0
27	185.0
28	85.0
29	150.0
30	154.0
31	177.0
32	173.0
33	184.0
34	221.0
35	267.0
36	311.0
37	433.0
38	554.0
39	856.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.69438877755511	24.473947895791586	53.056112224448896	12.775551102204407
2	24.925	26.700000000000003	21.325	27.05
3	16.1	20.3	20.150000000000002	43.45
4	25.7	35.575	14.575	24.15
5	23.974999999999998	34.875	30.55	10.6
6	34.4	15.525	39.125	10.95
7	15.625	25.775	24.625	33.975
8	26.25	39.625	14.674999999999999	19.45
9	16.5	39.675	31.6	12.225
10	21.85	19.650000000000002	25.624999999999996	32.875
11	35.099999999999994	13.450000000000001	14.174999999999999	37.275000000000006
12	17.424999999999997	18.775	21.5	42.3
13	19.6	20.724999999999998	39.65	20.025000000000002
14	36.625	22.375	27.775	13.225000000000001
15	37.675	20.65	29.599999999999998	12.075
16	13.200000000000001	25.95	21.875	38.975
17	26.900000000000002	24.325	34.025	14.75
18	28.9	17.625	28.425	25.05
19	32.975	16.650000000000002	32.525	17.849999999999998
20	48.1	16.725	23.474999999999998	11.700000000000001
21	22.725	27.250000000000004	23.849999999999998	26.174999999999997
22	33.900000000000006	12.325	45.175	8.6
23	23.65	14.75	48.6	13.0
24	49.675000000000004	12.725	28.575	9.025
25	55.60000000000001	20.4	14.099999999999998	9.9
26	30.275000000000002	46.475	12.125	11.125
27	13.8	53.55	20.875	11.774999999999999
28	10.975	27.900000000000002	48.949999999999996	12.174999999999999
29	9.875	11.425	60.824999999999996	17.875
30	9.525	5.949999999999999	39.0	45.525
31	12.6	4.9750000000000005	46.425	36.0
32	24.6	5.2749999999999995	25.3	44.824999999999996
33	52.97500000000001	7.7	13.55	25.775
34	67.15	6.825	11.450000000000001	14.575
35	62.7	7.049999999999999	20.525	9.725
36	66.64999999999999	8.275	14.45	10.625
37	39.4	10.25	24.9	25.45
38	26.3	12.975	12.275	48.449999999999996
39	14.875	24.4	8.5	52.225
40	13.375	49.275000000000006	9.825000000000001	27.525
41	25.95	50.6	8.924999999999999	14.524999999999999
42	50.7	32.2	9.025	8.075000000000001
43	52.325	30.7	9.0	7.9750000000000005
44	31.900000000000002	48.275	7.124999999999999	12.7
45	15.475	52.075	10.0	22.45
46	11.075	30.95	23.674999999999997	34.300000000000004
47	9.275	14.099999999999998	33.975	42.65
48	9.825000000000001	10.625	25.0	54.55
49	12.775	23.974999999999998	11.924999999999999	51.324999999999996
50	31.25	25.275	8.924999999999999	34.55
>>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	0.5
10	1.0
11	0.5
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	0.5
22	1.0
23	0.5
24	0.0
25	0.5
26	1.0
27	2.0
28	3.0
29	2.5
30	2.0
31	6.5
32	11.0
33	12.0
34	13.0
35	28.0
36	43.0
37	57.5
38	72.0
39	65.0
40	58.0
41	57.5
42	57.0
43	79.0
44	101.0
45	170.5
46	240.0
47	282.5
48	325.0
49	452.5
50	580.0
51	756.0
52	932.0
53	733.0
54	534.0
55	430.0
56	326.0
57	322.0
58	318.0
59	222.5
60	127.0
61	99.5
62	72.0
63	78.0
64	84.0
65	52.5
66	21.0
67	15.0
68	9.0
69	11.0
70	13.0
71	26.0
72	39.0
73	24.0
74	9.0
75	5.5
76	2.0
77	3.0
78	4.0
79	2.5
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	0.2
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	51.2
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.95703125	41.449999999999996
2	8.251953125	8.450000000000001
3	2.783203125	4.275
4	2.05078125	4.2
5	1.3671875	3.5000000000000004
6	0.537109375	1.6500000000000001
7	0.537109375	1.925
8	0.634765625	2.6
9	0.390625	1.7999999999999998
>10	2.392578125	22.875
>50	0.048828125	2.025
>100	0.048828125	5.25
>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	210	5.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	81	2.025	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	39	0.975	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	39	0.975	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	32	0.8	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	24	0.6	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGC	18	0.44999999999999996	RNA PCR Primer, Index 15 (100% over 50bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	16	0.4	RNA PCR Primer, Index 1 (100% over 35bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	13	0.325	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	13	0.325	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	11	0.27499999999999997	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	11	0.27499999999999997	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	10	0.25	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	10	0.25	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	10	0.25	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	9	0.22499999999999998	No Hit
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	8	0.2	RNA PCR Primer, Index 1 (95% over 23bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTC	8	0.2	RNA PCR Primer, Index 15 (100% over 44bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	8	0.2	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	7	0.17500000000000002	No Hit
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	6	0.15	No Hit
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	6	0.15	No Hit
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	5	0.125	No Hit
CTTTTTGCGGTCTGGGCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
ACGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	5	0.125	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATCCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TTCAAGTAATTCAGGATAGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGC	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.45	0.0	0.0	0.0
2	0.0	0.45	0.0	0.0	0.0
3	0.0	0.525	0.0	0.0	0.0
4	0.0	0.525	0.0	0.0	0.0
5	0.0	0.525	0.0	0.0	0.0
6	0.0	0.525	0.0	0.0	0.0
7	0.0	0.825	0.0	0.0	0.0
8	0.0	0.875	0.0	0.0	0.0
9	0.0	0.925	0.0	0.0	0.0
10	0.0	0.95	0.0	0.0	0.0
11	0.0	1.15	0.0	0.0	0.0
12	0.0	1.25	0.0	0.0	0.0
13	0.0	1.525	0.0	0.0	0.0
14	0.0	1.625	0.0	0.0	0.0
15	0.0	2.05	0.0	0.0	0.0
16	0.0	2.775	0.0	0.0	0.0
17	0.0	3.15	0.0	0.0	0.0
18	0.0	3.95	0.0	0.0	0.0
19	0.0	4.4	0.0	0.0	0.0
20	0.0	5.525	0.0	0.0	0.0
21	0.0	9.325	0.0	0.0	0.0
22	0.0	18.9	0.0	0.0	0.0
23	0.0	50.15	0.0	0.0	0.0
24	0.0	67.15	0.0	0.0	0.0
25	0.0	72.325	0.0	0.0	0.0
26	0.0	73.125	0.0	0.0	0.0
27	0.0	73.575	0.0	0.0	0.0
28	0.0	73.825	0.0	0.0	0.0
29	0.0	74.0	0.0	0.0	0.0
30	0.0	74.4	0.0	0.0	0.0
31	0.0	75.125	0.0	0.0	0.0
32	0.0	76.25	0.0	0.0	0.0
33	0.0	76.825	0.0	0.0	0.0
34	0.0	78.65	0.0	0.0	0.0
35	0.0	79.825	0.0	0.0	0.0
36	0.0	80.325	0.0	0.0	0.0
37	0.0	81.05	0.0	0.0	0.0
38	0.0	81.35	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCCCG	20	6.952051E-4	44.000004	8
AAGTAAT	45	2.728484E-10	44.000004	4
TCAAGTA	45	2.728484E-10	44.000004	2
ATCCAGG	45	2.728484E-10	44.000004	9
TTCAAGT	45	2.728484E-10	44.000004	1
CGGGGGC	90	0.0	44.000004	32
AGGATAG	45	2.728484E-10	44.000004	13
CATCCCC	20	6.952051E-4	44.000004	7
ATAGGCT	40	5.315087E-9	44.000004	16
TCCAGGA	45	2.728484E-10	44.000004	10
ACATCCC	20	6.952051E-4	44.000004	6
GGATAGG	45	2.728484E-10	44.000004	14
CCCCGAC	20	6.952051E-4	44.000004	10
GGGGGCC	80	0.0	44.000004	33
AGTAATC	45	2.728484E-10	44.000004	5
TAATCCA	45	2.728484E-10	44.000004	7
CAGGATA	45	2.728484E-10	44.000004	12
GTAATCC	45	2.728484E-10	44.000004	6
AGTTTGG	20	6.952051E-4	44.000004	19
CCAGGAT	45	2.728484E-10	44.000004	11
>>END_MODULE
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314394 spots for SRR5030898.sra
Written 314394 spots for SRR5030898.sra
Read 314396 spots for SRR5030898.sra
Written 314396 spots for SRR5030898.sra
SRR ids: ['SRR5030898.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6obtszvk
SRR5030898.sra spots: 3772730
blocks: [[1, 314394], [314395, 628788], [628789, 943182], [943183, 1257576], [1257577, 1571970], [1571971, 1886364], [1886365, 2200758], [2200759, 2515152], [2515153, 2829546], [2829547, 3143940], [3143941, 3458334], [3458335, 3772730]]
SRR5030898 file size 652824
SRR5030898 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030898 SRR5030898_1.fastq
Input file:	SRR5030898_1.fastq
trimmed:	SRR5030898-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 06:39:53 2020 >> started

Wed Mar  4 06:39:55 2020 >> done (2.066s)
3772730 reads processed; of these:
    172 ( 0.00%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3772552 (100.00%) reads available; of these:
 438616 (11.63%) trimmed reads available after processing
3333936 (88.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     47	  0.00%
 19	     54	  0.00%
 20	    128	  0.00%
 21	    184	  0.00%
 22	    351	  0.01%
 23	    425	  0.01%
 24	    362	  0.01%
 25	    518	  0.01%
 26	    455	  0.01%
 27	    608	  0.02%
 28	    839	  0.02%
 29	   1681	  0.04%
 30	   1062	  0.03%
 31	   1372	  0.04%
 32	   3594	  0.10%
 33	  10552	  0.28%
 34	  33035	  0.88%
 35	   7546	  0.20%
 36	   8987	  0.24%
 37	   4177	  0.11%
 38	   8933	  0.24%
 39	   7439	  0.20%
 40	  15830	  0.42%
 41	   8444	  0.22%
 42	  24329	  0.64%
 43	   9131	  0.24%
 44	  45897	  1.22%
 45	  26302	  0.70%
 46	  20791	  0.55%
 47	  24009	  0.64%
 48	  78920	  2.09%
 49	  92614	  2.45%
 50	3333936	 88.37%
3772552 reads passed initial QC


criterion=sequence-density
sequence-density=80.38
sequence-density-rank=1
fanout-score=19.36
fanout-score-rank=2
prefix-density=82.91
prefix-fanout=18.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC


criterion=fanout-score
sequence-density=4.47
sequence-density-rank=2
fanout-score=54.57
fanout-score-rank=1
prefix-density=83.01
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC -o SRR5030898 -
Input file:	STDIN
trimmed:	SRR5030898-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC
-- 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 06:40:11 2020 >> started

Wed Mar  4 06:40:15 2020 >> done (3.980s)
3679403 reads processed; of these:
 140159 ( 3.81%) short reads filtered out after trimming by size control
  18444 ( 0.50%) empty reads filtered out after trimming by size control
3520800 (95.69%) reads available; of these:
3075584 (87.35%) trimmed reads available after processing
 445216 (12.65%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  19601	  0.56%
 19	  33708	  0.96%
 20	 128077	  3.64%
 21	 357921	 10.17%
 22	1083872	 30.78%
 23	 643480	 18.28%
 24	 211966	  6.02%
 25	  37091	  1.05%
 26	  18952	  0.54%
 27	  17574	  0.50%
 28	  20690	  0.59%
 29	  18206	  0.52%
 30	  30674	  0.87%
 31	  41489	  1.18%
 32	  40684	  1.16%
 33	  78265	  2.22%
 34	  39101	  1.11%
 35	  25422	  0.72%
 36	  35764	  1.02%
 37	  15276	  0.43%
 38	  18516	  0.53%
 39	  16319	  0.46%
 40	  24185	  0.69%
 41	  28350	  0.81%
 42	  35820	  1.02%
 43	  23601	  0.67%
 44	  25614	  0.73%
 45	  26925	  0.76%
 46	  21252	  0.60%
 47	  16564	  0.47%
 48	   7391	  0.21%
 49	  13257	  0.38%
 50	 365193	 10.37%


criterion=sequence-density
sequence-density=5.30
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=19
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.41
sequence-density-rank=33
fanout-score=10.64
fanout-score-rank=1
prefix-density=0.76
prefix-fanout=5.7
sequence=GGAATTCTCGGGGCCCAGGAA
                                 Started job on |	Mar 04 06:40:35
                             Started mapping on |	Mar 04 06:40:36
                                    Finished on |	Mar 04 06:40:58
       Mapping speed, Million of reads per hour |	591.37

                          Number of input reads |	3613949
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1700346
                        Uniquely mapped reads % |	47.05%
                          Average mapped length |	27.49
                       Number of splices: Total |	1969
            Number of splices: Annotated (sjdb) |	242
                       Number of splices: GT/AG |	1819
                       Number of splices: GC/AG |	21
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	129
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.32
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1471511
             % of reads mapped to multiple loci |	40.72%
        Number of reads mapped to too many loci |	78108
             % of reads mapped to too many loci |	2.16%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.45%
                     % of reads unmapped: other |	0.62%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	442092	442092	442092
N_multimapping	1471511	1471511	1471511
N_noFeature	81458	98190	1347989
N_ambiguous	905739	606492	13311
UnstrandedReadsAssigned:713149 PositiveStrandReadsAssigned:995664 NegativeStrandReadsAssigned:339046
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030898 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: SRR5030898-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,613,949 reads, 675,000 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,138 rounds

 109283 SRR5030898.ke.tsv
  52636 SRR5030898.se.tsv
 161919 total
==> SRR5030898.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

==> SRR5030898.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030898 completed mapping pipeline successfully
