Starting /dee2/code/volunteer_pipeline.sh SRR5030971
    current disk space = 160578486272
    free memory = 73948852 
SRR5030971 SRAfilesize
0dbc92a50cbd5ce8059989e91c63c5db  SRR5030971.sra
SRR5030971.sra file validated
SRR5030971 is single end
SRR5030971 is conventional basespace
SRR5030971 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030971_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	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.491	34.0	31.0	34.0	31.0	34.0
2	32.75475	34.0	31.0	34.0	31.0	34.0
3	32.7765	34.0	31.0	34.0	31.0	34.0
4	36.36375	37.0	37.0	37.0	35.0	37.0
5	36.20275	37.0	37.0	37.0	35.0	37.0
6	35.9535	37.0	35.0	37.0	35.0	37.0
7	36.068	37.0	35.0	37.0	35.0	37.0
8	36.09425	37.0	35.0	37.0	35.0	37.0
9	37.86975	39.0	38.0	39.0	35.0	39.0
10	37.9155	39.0	38.0	39.0	35.0	39.0
11	37.7945	39.0	38.0	39.0	35.0	39.0
12	37.82125	39.0	38.0	39.0	35.0	39.0
13	37.8255	39.0	38.0	39.0	35.0	39.0
14	39.1695	41.0	39.0	41.0	36.0	41.0
15	39.212	41.0	39.0	41.0	36.0	41.0
16	39.34575	41.0	39.0	41.0	36.0	41.0
17	39.27725	41.0	39.0	41.0	36.0	41.0
18	39.30675	41.0	39.0	41.0	36.0	41.0
19	39.03225	40.0	39.0	41.0	35.0	41.0
20	39.031	40.0	39.0	41.0	36.0	41.0
21	39.113	40.0	39.0	41.0	36.0	41.0
22	39.0605	40.0	39.0	41.0	36.0	41.0
23	38.9435	40.0	39.0	41.0	35.0	41.0
24	39.1265	40.0	39.0	41.0	36.0	41.0
25	39.07225	40.0	39.0	41.0	35.0	41.0
26	38.79125	40.0	38.0	41.0	35.0	41.0
27	38.9195	40.0	39.0	41.0	35.0	41.0
28	38.536	40.0	38.0	41.0	34.0	41.0
29	37.787	40.0	38.0	41.0	31.0	41.0
30	38.16725	40.0	38.0	41.0	33.0	41.0
31	38.42	40.0	38.0	41.0	34.0	41.0
32	38.3425	40.0	38.0	41.0	34.0	41.0
33	38.31725	40.0	38.0	41.0	34.0	41.0
34	38.2675	40.0	38.0	41.0	34.0	41.0
35	37.971	40.0	38.0	41.0	33.0	41.0
36	37.55725	40.0	37.0	41.0	32.0	41.0
37	37.1435	39.0	37.0	41.0	31.0	41.0
38	37.37825	39.0	37.0	41.0	31.0	41.0
39	37.73025	39.0	37.0	41.0	33.0	41.0
40	37.691	40.0	37.0	41.0	33.0	41.0
41	37.883	40.0	38.0	41.0	33.0	41.0
42	37.9655	40.0	38.0	41.0	33.0	41.0
43	38.048	40.0	38.0	41.0	33.0	41.0
44	37.92375	40.0	38.0	41.0	33.0	41.0
45	37.677	40.0	37.0	41.0	33.0	41.0
46	37.09375	40.0	37.0	41.0	31.0	41.0
47	36.18375	39.0	35.0	41.0	29.0	41.0
48	35.725	39.0	34.0	40.0	28.0	41.0
49	36.11025	39.0	35.0	40.0	30.0	41.0
50	35.7175	39.0	34.0	40.0	29.0	41.0
>>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
13	1.0
14	2.0
15	1.0
16	3.0
17	1.0
18	1.0
19	1.0
20	1.0
21	5.0
22	4.0
23	6.0
24	5.0
25	10.0
26	14.0
27	16.0
28	26.0
29	29.0
30	48.0
31	55.0
32	78.0
33	90.0
34	160.0
35	173.0
36	289.0
37	457.0
38	893.0
39	1631.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.857393044783588	23.817863397548162	49.76232174130598	16.56242181636227
2	25.374999999999996	25.974999999999998	19.325	29.325000000000003
3	23.875	20.424999999999997	21.75	33.95
4	34.849999999999994	25.874999999999996	15.575	23.7
5	22.725	38.5	27.55	11.225
6	34.1	13.700000000000001	35.225	16.975
7	15.675	22.900000000000002	22.525000000000002	38.9
8	25.05	27.450000000000003	17.7	29.799999999999997
9	23.799999999999997	31.075000000000003	28.125	17.0
10	22.625	22.675	28.875	25.825
11	31.35	9.575	19.5	39.574999999999996
12	16.475	18.525	32.35	32.65
13	30.5	18.35	32.300000000000004	18.85
14	28.725	32.425	20.175	18.675
15	37.55	24.375	24.275	13.8
16	20.925	17.875	25.6	35.6
17	26.650000000000002	22.925	36.125	14.299999999999999
18	25.75	18.2	29.075	26.974999999999998
19	39.550000000000004	14.174999999999999	28.825	17.45
20	44.35	16.125	26.950000000000003	12.575
21	24.275	19.25	26.650000000000002	29.825000000000003
22	28.849999999999998	12.5	47.225	11.425
23	26.25	13.100000000000001	43.85	16.8
24	51.425	13.8	26.3	8.475000000000001
25	49.1	24.625	15.625	10.65
26	28.575	44.45	13.825000000000001	13.15
27	16.8	46.475	23.25	13.475000000000001
28	12.950000000000001	23.625	47.275	16.150000000000002
29	13.975000000000001	12.5	55.375	18.15
30	12.275	6.5	35.65	45.574999999999996
31	14.45	4.7	46.75	34.1
32	28.4	5.075	21.8	44.725
33	52.400000000000006	10.375	13.475000000000001	23.75
34	60.75000000000001	8.5	15.475	15.275
35	64.625	7.124999999999999	18.725	9.525
36	43.775	7.324999999999999	35.375	13.525
37	45.5	11.65	19.825	23.025000000000002
38	24.025	18.6	11.375	46.0
39	15.174999999999999	23.724999999999998	11.075	50.025
40	14.924999999999999	46.800000000000004	13.100000000000001	25.174999999999997
41	22.85	48.725	9.700000000000001	18.725
42	46.725	29.299999999999997	12.425	11.55
43	50.525	28.599999999999998	8.625	12.25
44	31.775	46.35	7.3999999999999995	14.475
45	19.275000000000002	48.725	13.600000000000001	18.4
46	14.549999999999999	24.975	17.299999999999997	43.175000000000004
47	9.9	15.825	39.6	34.675
48	11.275	11.825	20.95	55.95
49	12.725	17.95	13.5	55.825
50	17.0	35.8	14.6	32.6
>>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	0.5
20	1.0
21	0.5
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	1.0
28	2.0
29	1.5
30	1.0
31	4.5
32	8.0
33	7.0
34	6.0
35	18.0
36	30.0
37	24.5
38	19.0
39	23.0
40	27.0
41	32.0
42	37.0
43	65.5
44	94.0
45	140.5
46	187.0
47	315.5
48	444.0
49	540.5
50	637.0
51	709.0
52	781.0
53	605.0
54	429.0
55	510.5
56	592.0
57	436.0
58	280.0
59	185.5
60	91.0
61	69.0
62	47.0
63	93.5
64	140.0
65	91.5
66	43.0
67	28.5
68	14.0
69	17.5
70	21.0
71	36.5
72	52.0
73	29.0
74	6.0
75	5.0
76	4.0
77	3.0
78	2.0
79	1.5
80	1.0
81	1.0
82	1.0
83	1.0
84	1.0
85	0.5
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	0.075
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	fail
#Total Deduplicated Percentage	36.95
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.30446549391068	27.825
2	10.013531799729364	7.3999999999999995
3	4.059539918809202	4.5
4	2.3004059539918806	3.4000000000000004
5	1.2855209742895806	2.375
6	1.4208389715832206	3.15
7	0.6089309878213802	1.575
8	0.40595399188092013	1.2
9	0.4736129905277402	1.575
>10	3.450608930987822	23.1
>50	0.4736129905277402	13.425
>100	0.20297699594046006	10.475
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	156	3.9	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	100	2.5	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	91	2.275	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	78	1.95	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	61	1.525	RNA PCR Primer, Index 1 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	57	1.425	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	45	1.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTC	24	0.6	RNA PCR Primer, Index 38 (100% over 44bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	23	0.575	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 31bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	16	0.4	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	16	0.4	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	12	0.3	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGC	10	0.25	RNA PCR Primer, Index 38 (100% over 50bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	9	0.22499999999999998	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	9	0.22499999999999998	No Hit
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	7	0.17500000000000002	RNA PCR Primer, Index 2 (100% over 34bp)
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTTGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAG	6	0.15	RNA PCR Primer, Index 3 (97% over 37bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (100% over 33bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTA	5	0.125	RNA PCR Primer, Index 2 (97% over 36bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGCACTCCAGTCACCT	5	0.125	RNA PCR Primer, Index 12 (97% over 35bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGC	5	0.125	RNA PCR Primer, Index 38 (100% over 38bp)
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	0.25	0.0	0.0	0.0
2	0.0	0.275	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.425	0.0	0.0	0.0
5	0.0	0.425	0.0	0.0	0.0
6	0.0	0.525	0.0	0.0	0.0
7	0.0	1.25	0.0	0.0	0.0
8	0.0	1.475	0.0	0.0	0.0
9	0.0	1.525	0.0	0.0	0.0
10	0.0	1.825	0.0	0.0	0.0
11	0.0	2.125	0.0	0.0	0.0
12	0.0	2.375	0.0	0.0	0.0
13	0.0	2.7	0.0	0.0	0.0
14	0.0	3.025	0.0	0.0	0.0
15	0.0	3.425	0.0	0.0	0.0
16	0.0	5.625	0.0	0.0	0.0
17	0.0	6.55	0.0	0.0	0.0
18	0.0	7.875	0.0	0.0	0.0
19	0.0	8.525	0.0	0.0	0.0
20	0.0	9.85	0.0	0.0	0.0
21	0.0	14.725	0.0	0.0	0.0
22	0.0	25.7	0.0	0.0	0.0
23	0.0	54.8	0.0	0.0	0.0
24	0.0	67.825	0.0	0.0	0.0
25	0.0	73.6	0.0	0.0	0.0
26	0.0	75.2	0.0	0.0	0.0
27	0.0	75.925	0.0	0.0	0.0
28	0.0	76.5	0.0	0.0	0.0
29	0.0	77.3	0.0	0.0	0.0
30	0.0	77.975	0.0	0.0	0.0
31	0.0	78.725	0.0	0.0	0.0
32	0.0	79.5	0.0	0.0	0.0
33	0.0	80.5	0.0	0.0	0.0
34	0.0	84.0	0.0	0.0	0.0
35	0.0	85.675	0.0	0.0	0.0
36	0.0	86.4	0.0	0.0	0.0
37	0.0	87.65	0.0	0.0	0.0
38	0.0	88.175	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
CGCGACC	20	6.952051E-4	44.000004	1
AACGCTG	20	6.952051E-4	44.000004	8
AAGTAAT	40	5.315087E-9	44.000004	4
TCAAGTA	40	5.315087E-9	44.000004	2
ACGCTGT	20	6.952051E-4	44.000004	9
ATCCAGG	40	5.315087E-9	44.000004	9
CTTTAAC	20	6.952051E-4	44.000004	12
GCGACCT	20	6.952051E-4	44.000004	2
TTCAAGT	40	5.315087E-9	44.000004	1
TTCAACG	20	6.952051E-4	44.000004	5
AGGATAG	40	5.315087E-9	44.000004	13
ATAGGCT	40	5.315087E-9	44.000004	16
TCAACGC	20	6.952051E-4	44.000004	6
TCCAGGA	40	5.315087E-9	44.000004	10
GGATAGG	40	5.315087E-9	44.000004	14
TAACCTG	20	6.952051E-4	44.000004	15
AGTAATC	40	5.315087E-9	44.000004	5
TCAGATC	20	6.952051E-4	44.000004	8
ACCCTTT	20	6.952051E-4	44.000004	9
>>END_MODULE
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141731 spots for SRR5030971.sra
Written 141731 spots for SRR5030971.sra
Read 141733 spots for SRR5030971.sra
Written 141733 spots for SRR5030971.sra
SRR ids: ['SRR5030971.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_a86gmthz
SRR5030971.sra spots: 1700774
blocks: [[1, 141731], [141732, 283462], [283463, 425193], [425194, 566924], [566925, 708655], [708656, 850386], [850387, 992117], [992118, 1133848], [1133849, 1275579], [1275580, 1417310], [1417311, 1559041], [1559042, 1700774]]
SRR5030971 file size 293706
SRR5030971 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030971 SRR5030971_1.fastq
Input file:	SRR5030971_1.fastq
trimmed:	SRR5030971-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 06:57:11 2020 >> started

Wed Mar  4 06:57:12 2020 >> done (1.185s)
1700774 reads processed; of these:
    122 ( 0.01%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
1700648 (99.99%) reads available; of these:
 119658 ( 7.04%) trimmed reads available after processing
1580990 (92.96%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     26	  0.00%
 19	     61	  0.00%
 20	     90	  0.01%
 21	    119	  0.01%
 22	    239	  0.01%
 23	    271	  0.02%
 24	    281	  0.02%
 25	    394	  0.02%
 26	    303	  0.02%
 27	    388	  0.02%
 28	    508	  0.03%
 29	    673	  0.04%
 30	    448	  0.03%
 31	    552	  0.03%
 32	    611	  0.04%
 33	    771	  0.05%
 34	    938	  0.06%
 35	   1630	  0.10%
 36	   1619	  0.10%
 37	   1699	  0.10%
 38	   1754	  0.10%
 39	   1886	  0.11%
 40	   2068	  0.12%
 41	   2306	  0.14%
 42	   3056	  0.18%
 43	   4349	  0.26%
 44	   6318	  0.37%
 45	   8240	  0.48%
 46	  12352	  0.73%
 47	  13544	  0.80%
 48	  21129	  1.24%
 49	  31035	  1.82%
 50	1580990	 92.96%
1700648 reads passed initial QC


criterion=sequence-density
sequence-density=87.78
sequence-density-rank=1
fanout-score=20.23
fanout-score-rank=1
prefix-density=90.15
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC


criterion=fanout-score
sequence-density=87.78
sequence-density-rank=1
fanout-score=20.23
fanout-score-rank=1
prefix-density=90.15
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC -o SRR5030971 -
Input file:	STDIN
trimmed:	SRR5030971-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC
-- 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 06:57:22 2020 >> started

Wed Mar  4 06:57:24 2020 >> done (2.168s)
1661997 reads processed; of these:
 128353 ( 7.72%) short reads filtered out after trimming by size control
   5063 ( 0.30%) empty reads filtered out after trimming by size control
1528581 (91.97%) reads available; of these:
1475620 (96.54%) trimmed reads available after processing
  52961 ( 3.46%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  10240	  0.67%
 19	  20728	  1.36%
 20	  89533	  5.86%
 21	 185341	 12.13%
 22	 480428	 31.43%
 23	 218842	 14.32%
 24	  94604	  6.19%
 25	  26227	  1.72%
 26	  14703	  0.96%
 27	  12258	  0.80%
 28	  13507	  0.88%
 29	   9913	  0.65%
 30	  13786	  0.90%
 31	  15305	  1.00%
 32	  18334	  1.20%
 33	  69298	  4.53%
 34	  22480	  1.47%
 35	  18028	  1.18%
 36	  21984	  1.44%
 37	   9621	  0.63%
 38	  10041	  0.66%
 39	   9246	  0.60%
 40	  12531	  0.82%
 41	  17107	  1.12%
 42	  18655	  1.22%
 43	  13761	  0.90%
 44	   9712	  0.64%
 45	  12375	  0.81%
 46	   9554	  0.63%
 47	   6997	  0.46%
 48	    592	  0.04%
 49	    973	  0.06%
 50	  41877	  2.74%


criterion=sequence-density
sequence-density=7.21
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.24
sequence-density-rank=6
fanout-score=19.78
fanout-score-rank=1
prefix-density=2.31
prefix-fanout=19.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGC
                                 Started job on |	Mar 04 06:57:44
                             Started mapping on |	Mar 04 06:57:44
                                    Finished on |	Mar 04 06:58:08
       Mapping speed, Million of reads per hour |	235.08

                          Number of input reads |	1567232
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	795974
                        Uniquely mapped reads % |	50.79%
                          Average mapped length |	24.17
                       Number of splices: Total |	891
            Number of splices: Annotated (sjdb) |	184
                       Number of splices: GT/AG |	843
                       Number of splices: GC/AG |	8
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	39
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.82
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	549870
             % of reads mapped to multiple loci |	35.09%
        Number of reads mapped to too many loci |	35570
             % of reads mapped to too many loci |	2.27%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.11%
                     % of reads unmapped: other |	0.74%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	221388	221388	221388
N_multimapping	549870	549870	549870
N_noFeature	39650	49344	532339
N_ambiguous	455412	227162	9268
UnstrandedReadsAssigned:300912 PositiveStrandReadsAssigned:519468 NegativeStrandReadsAssigned:254367
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030971 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: SRR5030971-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,567,232 reads, 400,501 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,112 rounds

 109283 SRR5030971.ke.tsv
  52636 SRR5030971.se.tsv
 161919 total
==> SRR5030971.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

==> SRR5030971.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030971 completed mapping pipeline successfully
