Starting /dee2/code/volunteer_pipeline.sh SRR5030988
    current disk space = 160564707328
    free memory = 73932540 
SRR5030988 SRAfilesize
dc822b009cbd34f0febdc2ce93aa62eb  SRR5030988.sra
SRR5030988.sra file validated
SRR5030988 is single end
SRR5030988 is conventional basespace
SRR5030988 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030988_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.29825	33.0	31.0	34.0	31.0	34.0
2	32.49675	34.0	31.0	34.0	31.0	34.0
3	32.4195	34.0	31.0	34.0	30.0	34.0
4	36.146	37.0	35.0	37.0	35.0	37.0
5	36.13525	37.0	35.0	37.0	35.0	37.0
6	35.75675	37.0	35.0	37.0	33.0	37.0
7	35.91	37.0	35.0	37.0	35.0	37.0
8	36.08375	37.0	35.0	37.0	35.0	37.0
9	37.6375	39.0	37.0	39.0	35.0	39.0
10	37.537	39.0	37.0	39.0	35.0	39.0
11	37.16225	39.0	37.0	39.0	33.0	39.0
12	37.6275	39.0	37.0	39.0	35.0	39.0
13	37.52675	39.0	37.0	39.0	35.0	39.0
14	39.065	41.0	38.0	41.0	36.0	41.0
15	39.03225	40.0	38.0	41.0	35.0	41.0
16	38.94425	40.0	38.0	41.0	35.0	41.0
17	39.0025	40.0	38.0	41.0	35.0	41.0
18	38.899	40.0	38.0	41.0	35.0	41.0
19	38.61175	40.0	38.0	41.0	34.0	41.0
20	38.706	40.0	38.0	41.0	34.0	41.0
21	38.84325	40.0	38.0	41.0	35.0	41.0
22	38.718	40.0	38.0	41.0	34.0	41.0
23	38.4165	40.0	38.0	41.0	34.0	41.0
24	38.58725	40.0	38.0	41.0	34.0	41.0
25	38.76125	40.0	38.0	41.0	34.0	41.0
26	38.532	40.0	38.0	41.0	34.0	41.0
27	38.72225	40.0	38.0	41.0	34.0	41.0
28	38.67875	40.0	38.0	41.0	35.0	41.0
29	38.4595	40.0	38.0	41.0	34.0	41.0
30	38.63	40.0	38.0	41.0	34.0	41.0
31	38.754	40.0	38.0	41.0	34.0	41.0
32	38.81175	40.0	38.0	41.0	35.0	41.0
33	38.564	40.0	38.0	41.0	35.0	41.0
34	38.47675	40.0	38.0	41.0	34.0	41.0
35	38.1745	40.0	38.0	41.0	34.0	41.0
36	37.958	40.0	38.0	41.0	33.0	41.0
37	37.5035	40.0	37.0	41.0	31.0	41.0
38	37.51025	40.0	37.0	41.0	32.0	41.0
39	37.86925	40.0	38.0	41.0	33.0	41.0
40	37.8895	40.0	38.0	41.0	33.0	41.0
41	38.21225	40.0	38.0	41.0	33.0	41.0
42	38.00375	40.0	38.0	41.0	33.0	41.0
43	37.73275	40.0	37.0	41.0	33.0	41.0
44	37.83425	40.0	38.0	41.0	33.0	41.0
45	37.72975	40.0	38.0	41.0	33.0	41.0
46	37.50225	40.0	37.0	41.0	33.0	41.0
47	37.14575	40.0	37.0	41.0	31.0	41.0
48	37.0695	40.0	37.0	41.0	31.0	41.0
49	37.187	40.0	37.0	41.0	32.0	41.0
50	36.64875	40.0	36.0	41.0	31.0	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
15	2.0
16	2.0
17	1.0
18	0.0
19	4.0
20	3.0
21	4.0
22	5.0
23	5.0
24	6.0
25	18.0
26	13.0
27	26.0
28	28.0
29	34.0
30	49.0
31	61.0
32	75.0
33	102.0
34	131.0
35	195.0
36	273.0
37	407.0
38	724.0
39	1832.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.074999999999999	24.349999999999998	56.375	12.2
2	26.136078332914884	26.86417273412001	23.022847100175746	23.976901832789355
3	16.875	19.475	21.725	41.925000000000004
4	26.474999999999998	40.550000000000004	13.25	19.725
5	22.35	39.45	28.175	10.025
6	33.725	16.55	38.6	11.125
7	13.875000000000002	23.45	25.0	37.675
8	23.200000000000003	43.275000000000006	13.700000000000001	19.825
9	16.825000000000003	38.224999999999994	32.324999999999996	12.625
10	19.175	20.599999999999998	27.675	32.550000000000004
11	32.475	10.325	15.024999999999999	42.175000000000004
12	15.85	15.55	24.425	44.175
13	20.974999999999998	22.0	37.325	19.7
14	41.575	22.625	23.5	12.3
15	41.225	19.925	28.599999999999998	10.25
16	12.65	24.125	23.225	40.0
17	27.175	21.425	38.975	12.425
18	32.175	19.75	24.6	23.474999999999998
19	39.7	13.375	31.6	15.325
20	51.824999999999996	17.849999999999998	19.475	10.85
21	18.8	28.9	24.275	28.025
22	33.5	11.05	47.225	8.225
23	23.549999999999997	12.85	49.35	14.249999999999998
24	50.449999999999996	13.475000000000001	30.175	5.8999999999999995
25	56.625	21.025	14.7	7.6499999999999995
26	32.375	47.225	12.125	8.275
27	14.549999999999999	54.400000000000006	21.05	10.0
28	8.875	28.575	50.849999999999994	11.700000000000001
29	8.725	12.2	61.9	17.175
30	9.6	5.35	40.575	44.474999999999994
31	12.825000000000001	4.175	46.85	36.15
32	24.0	5.1499999999999995	24.275	46.575
33	54.0	5.45	13.450000000000001	27.1
34	68.175	6.25	12.425	13.15
35	69.8	5.949999999999999	16.275000000000002	7.9750000000000005
36	43.55	6.800000000000001	38.2	11.450000000000001
37	46.475	8.425	24.0	21.099999999999998
38	26.0	13.15	12.025	48.825
39	14.099999999999998	21.95	8.0	55.95
40	12.625	49.625	7.6	30.15
41	21.675	55.875	7.449999999999999	15.0
42	49.525000000000006	33.175	8.799999999999999	8.5
43	57.75	27.425	6.675000000000001	8.15
44	33.85	48.8	6.45	10.9
45	16.45	55.925000000000004	10.424999999999999	17.2
46	9.6	30.65	16.075	43.675000000000004
47	7.1499999999999995	14.35	39.375	39.125
48	7.425	10.75	24.025	57.8
49	9.950000000000001	17.8	13.8	58.45
50	16.2	38.675	11.3	33.825
>>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	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	1.0
20	2.0
21	1.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	0.5
28	0.0
29	1.5
30	3.0
31	8.5
32	14.0
33	11.5
34	9.0
35	16.0
36	23.0
37	24.5
38	26.0
39	28.0
40	30.0
41	42.5
42	55.0
43	88.0
44	121.0
45	172.5
46	224.0
47	452.0
48	680.0
49	664.0
50	648.0
51	824.0
52	1000.0
53	663.5
54	327.0
55	342.0
56	357.0
57	296.0
58	235.0
59	146.5
60	58.0
61	43.5
62	29.0
63	40.5
64	52.0
65	36.0
66	20.0
67	15.0
68	10.0
69	14.0
70	18.0
71	32.5
72	47.0
73	27.0
74	7.0
75	4.0
76	1.0
77	1.0
78	1.0
79	1.0
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	0.0
2	0.42500000000000004
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	35.099999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.35327635327636	26.8
2	9.544159544159545	6.7
3	3.347578347578348	3.5249999999999995
4	2.207977207977208	3.1
5	1.3532763532763532	2.375
6	0.9259259259259258	1.95
7	0.8547008547008548	2.1
8	0.5698005698005698	1.6
9	0.2849002849002849	0.8999999999999999
>10	3.9886039886039883	27.400000000000002
>50	0.3561253561253561	7.375
>100	0.2136752136752137	16.175
>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	303	7.575	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	198	4.95	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	63	1.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	60	1.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	53	1.325	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	50	1.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	46	1.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	43	1.075	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	27	0.675	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	27	0.675	RNA PCR Primer, Index 5 (100% over 35bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	26	0.65	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTC	15	0.375	RNA PCR Primer, Index 8 (100% over 44bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	13	0.325	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 31bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGC	8	0.2	RNA PCR Primer, Index 8 (100% over 50bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGTGGAATTCTCGGGTGC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
TTATAAAGCAATGAGACTGATTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
CAATAGGATTACGCTGAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTGGAATTC	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCAGGCTCAGTCCCCTCCCGATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	5	0.125	No Hit
>>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	0.225	0.0	0.0	0.0
2	0.0	0.225	0.0	0.0	0.0
3	0.0	0.3	0.0	0.0	0.0
4	0.0	0.35	0.0	0.0	0.0
5	0.0	0.425	0.0	0.0	0.0
6	0.0	0.55	0.0	0.0	0.0
7	0.0	1.025	0.0	0.0	0.0
8	0.0	1.225	0.0	0.0	0.0
9	0.0	1.25	0.0	0.0	0.0
10	0.0	1.5	0.0	0.0	0.0
11	0.0	1.55	0.0	0.0	0.0
12	0.0	1.675	0.0	0.0	0.0
13	0.0	1.925	0.0	0.0	0.0
14	0.0	2.275	0.0	0.0	0.0
15	0.0	2.55	0.0	0.0	0.0
16	0.0	3.65	0.0	0.0	0.0
17	0.0	4.475	0.0	0.0	0.0
18	0.0	5.475	0.0	0.0	0.0
19	0.0	5.9	0.0	0.0	0.0
20	0.0	7.25	0.0	0.0	0.0
21	0.0	11.925	0.0	0.0	0.0
22	0.0	22.825	0.0	0.0	0.0
23	0.0	55.325	0.0	0.0	0.0
24	0.0	73.125	0.0	0.0	0.0
25	0.0	79.825	0.0	0.0	0.0
26	0.0	80.925	0.0	0.0	0.0
27	0.0	81.35	0.0	0.0	0.0
28	0.0	81.875	0.0	0.0	0.0
29	0.0	82.55	0.0	0.0	0.0
30	0.0	82.925	0.0	0.0	0.0
31	0.0	83.575	0.0	0.0	0.0
32	0.0	84.4	0.0	0.0	0.0
33	0.0	85.6	0.0	0.0	0.0
34	0.0	87.275	0.0	0.0	0.0
35	0.0	88.125	0.0	0.0	0.0
36	0.0	88.725	0.0	0.0	0.0
37	0.0	89.45	0.0	0.0	0.0
38	0.0	89.825	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	25	3.4343255E-5	44.531647	2
TCAAGTA	55	0.0	44.531647	2
TTCAAGT	55	0.0	44.531647	1
ACATTCA	30	1.7904422E-6	44.531647	2
TGAGGTA	25	3.4343255E-5	44.531647	1
AACATTC	30	1.7904422E-6	44.531647	1
TGTAAAC	25	3.4343255E-5	44.531647	1
GTAAACA	25	3.4343255E-5	44.531647	2
CTTTGGT	20	6.54202E-4	44.531643	2
TCTTTGG	20	6.54202E-4	44.531643	1
ATCCCCG	25	3.7082697E-5	43.975002	8
AACGCTG	30	1.9592044E-6	43.975002	8
GGTGAGT	30	1.9592044E-6	43.975002	17
ACGCTGT	30	1.9592044E-6	43.975002	9
TAAACAT	25	3.7082697E-5	43.975002	3
AAACATC	25	3.7082697E-5	43.975002	4
TTCAACG	30	1.9592044E-6	43.975002	5
TCGGTGA	30	1.9592044E-6	43.975002	15
CATCCCC	25	3.7082697E-5	43.975002	7
CATTCAA	30	1.9592044E-6	43.975002	3
>>END_MODULE
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471578 spots for SRR5030988.sra
Written 471578 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
Read 471571 spots for SRR5030988.sra
Written 471571 spots for SRR5030988.sra
SRR ids: ['SRR5030988.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_7dkqb1wd
SRR5030988.sra spots: 5658859
blocks: [[1, 471571], [471572, 943142], [943143, 1414713], [1414714, 1886284], [1886285, 2357855], [2357856, 2829426], [2829427, 3300997], [3300998, 3772568], [3772569, 4244139], [4244140, 4715710], [4715711, 5187281], [5187282, 5658859]]
SRR5030988 file size 979754
SRR5030988 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030988 SRR5030988_1.fastq
Input file:	SRR5030988_1.fastq
trimmed:	SRR5030988-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 07:00:51 2020 >> started

Wed Mar  4 07:00:55 2020 >> done (3.459s)
5658859 reads processed; of these:
    338 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
5658515 (99.99%) reads available; of these:
 305651 ( 5.40%) trimmed reads available after processing
5352864 (94.60%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     83	  0.00%
 19	    135	  0.00%
 20	    239	  0.00%
 21	    378	  0.01%
 22	    690	  0.01%
 23	    755	  0.01%
 24	    701	  0.01%
 25	    962	  0.02%
 26	    764	  0.01%
 27	    969	  0.02%
 28	   1246	  0.02%
 29	   2558	  0.05%
 30	   1300	  0.02%
 31	   1270	  0.02%
 32	   1464	  0.03%
 33	   2034	  0.04%
 34	   2757	  0.05%
 35	   5683	  0.10%
 36	   4835	  0.09%
 37	   5501	  0.10%
 38	   4724	  0.08%
 39	   5172	  0.09%
 40	   5794	  0.10%
 41	   6447	  0.11%
 42	   8336	  0.15%
 43	  11925	  0.21%
 44	  15071	  0.27%
 45	  20282	  0.36%
 46	  27086	  0.48%
 47	  34384	  0.61%
 48	  60399	  1.07%
 49	  71707	  1.27%
 50	5352864	 94.60%
5658515 reads passed initial QC


criterion=sequence-density
sequence-density=88.77
sequence-density-rank=1
fanout-score=17.46
fanout-score-rank=1
prefix-density=90.29
prefix-fanout=17.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC


criterion=fanout-score
sequence-density=88.77
sequence-density-rank=1
fanout-score=17.46
fanout-score-rank=1
prefix-density=90.29
prefix-fanout=17.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC -o SRR5030988 -
Input file:	STDIN
trimmed:	SRR5030988-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC
-- 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 07:01:18 2020 >> started

Wed Mar  4 07:01:28 2020 >> done (9.490s)
5531357 reads processed; of these:
 287272 ( 5.19%) short reads filtered out after trimming by size control
  16967 ( 0.31%) empty reads filtered out after trimming by size control
5227118 (94.50%) reads available; of these:
5012021 (95.88%) trimmed reads available after processing
 215097 ( 4.12%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  27486	  0.53%
 19	  66213	  1.27%
 20	 265401	  5.08%
 21	 634573	 12.14%
 22	1818653	 34.79%
 23	 984594	 18.84%
 24	 346282	  6.62%
 25	  55924	  1.07%
 26	  28600	  0.55%
 27	  27923	  0.53%
 28	  31665	  0.61%
 29	  24134	  0.46%
 30	  42251	  0.81%
 31	  51406	  0.98%
 32	  57437	  1.10%
 33	 105143	  2.01%
 34	  46447	  0.89%
 35	  30423	  0.58%
 36	  32222	  0.62%
 37	  23618	  0.45%
 38	  25013	  0.48%
 39	  24669	  0.47%
 40	  31457	  0.60%
 41	  45932	  0.88%
 42	  50597	  0.97%
 43	  40799	  0.78%
 44	  31835	  0.61%
 45	  38576	  0.74%
 46	  30758	  0.59%
 47	  21701	  0.42%
 48	   2301	  0.04%
 49	   3723	  0.07%
 50	 179362	  3.43%


criterion=sequence-density
sequence-density=4.46
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=10
prefix-density=0.01
prefix-fanout=1.0
sequence=TGTAAACATCCTCGACTGGAAGC


criterion=fanout-score
sequence-density=0.39
sequence-density-rank=31
fanout-score=8.52
fanout-score-rank=1
prefix-density=3.34
prefix-fanout=1.0
sequence=TAGTAGGTTGTGTGGTTTT
                                 Started job on |	Mar 04 07:02:36
                             Started mapping on |	Mar 04 07:02:37
                                    Finished on |	Mar 04 07:03:24
       Mapping speed, Million of reads per hour |	410.11

                          Number of input reads |	5354276
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2475847
                        Uniquely mapped reads % |	46.24%
                          Average mapped length |	24.21
                       Number of splices: Total |	2663
            Number of splices: Annotated (sjdb) |	337
                       Number of splices: GT/AG |	2405
                       Number of splices: GC/AG |	26
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	229
                      Mismatch rate per base, % |	0.15%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.80
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	2304181
             % of reads mapped to multiple loci |	43.03%
        Number of reads mapped to too many loci |	109183
             % of reads mapped to too many loci |	2.04%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.90%
                     % of reads unmapped: other |	0.79%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	574248	574248	574248
N_multimapping	2304181	2304181	2304181
N_noFeature	110639	135518	1884277
N_ambiguous	1283892	779773	17818
UnstrandedReadsAssigned:1081316 PositiveStrandReadsAssigned:1560556 NegativeStrandReadsAssigned:573752
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5030988 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: SRR5030988-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 5,354,276 reads, 952,875 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,152 rounds

 109283 SRR5030988.ke.tsv
  52636 SRR5030988.se.tsv
 161919 total
==> SRR5030988.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

==> SRR5030988.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030988 completed mapping pipeline successfully
