Starting /dee2/code/volunteer_pipeline.sh SRR5031001
    current disk space = 160560300032
    free memory = 1052013172 
SRR5031001 SRAfilesize
d4942d286c9dc5051446efe0a5d6d967  SRR5031001.sra
SRR5031001.sra file validated
SRR5031001 is single end
SRR5031001 is conventional basespace
SRR5031001 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031001_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	32.346	33.0	31.0	34.0	31.0	34.0
2	32.463	34.0	31.0	34.0	31.0	34.0
3	32.497	34.0	31.0	34.0	31.0	34.0
4	36.16575	37.0	35.0	37.0	35.0	37.0
5	36.067	37.0	35.0	37.0	35.0	37.0
6	35.787	37.0	35.0	37.0	33.0	37.0
7	35.80575	37.0	35.0	37.0	35.0	37.0
8	35.95075	37.0	35.0	37.0	35.0	37.0
9	37.62675	39.0	37.0	39.0	35.0	39.0
10	37.533	39.0	37.0	39.0	35.0	39.0
11	37.07625	39.0	37.0	39.0	33.0	39.0
12	37.53125	39.0	37.0	39.0	35.0	39.0
13	37.52825	39.0	37.0	39.0	34.0	39.0
14	38.977	40.0	38.0	41.0	35.0	41.0
15	38.95975	40.0	38.0	41.0	35.0	41.0
16	38.91625	40.0	38.0	41.0	35.0	41.0
17	39.065	40.0	38.0	41.0	35.0	41.0
18	38.9	41.0	38.0	41.0	35.0	41.0
19	38.54625	40.0	38.0	41.0	34.0	41.0
20	38.622	40.0	38.0	41.0	34.0	41.0
21	38.7725	40.0	38.0	41.0	34.0	41.0
22	38.84875	40.0	38.0	41.0	34.0	41.0
23	38.47675	40.0	38.0	41.0	34.0	41.0
24	38.84975	40.0	38.0	41.0	34.0	41.0
25	39.01275	40.0	38.0	41.0	35.0	41.0
26	38.81975	40.0	38.0	41.0	35.0	41.0
27	38.90025	40.0	38.0	41.0	35.0	41.0
28	38.6955	40.0	38.0	41.0	35.0	41.0
29	38.45375	40.0	38.0	41.0	34.0	41.0
30	38.49475	40.0	38.0	41.0	34.0	41.0
31	38.731	40.0	38.0	41.0	35.0	41.0
32	38.72175	40.0	38.0	41.0	35.0	41.0
33	38.3315	40.0	38.0	41.0	34.0	41.0
34	38.24175	40.0	38.0	41.0	34.0	41.0
35	37.90075	40.0	38.0	41.0	33.0	41.0
36	37.75825	40.0	37.0	41.0	33.0	41.0
37	37.5355	40.0	37.0	41.0	32.0	41.0
38	37.55125	40.0	37.0	41.0	32.0	41.0
39	38.003	40.0	38.0	41.0	33.0	41.0
40	38.00425	40.0	38.0	41.0	33.0	41.0
41	38.217	40.0	38.0	41.0	33.0	41.0
42	38.04875	40.0	38.0	41.0	33.0	41.0
43	37.9095	40.0	38.0	41.0	33.0	41.0
44	38.00575	40.0	38.0	41.0	33.0	41.0
45	38.043	40.0	38.0	41.0	33.0	41.0
46	37.652	40.0	37.0	41.0	33.0	41.0
47	37.20725	40.0	37.0	41.0	31.0	41.0
48	37.13975	40.0	37.0	41.0	32.0	41.0
49	37.05275	40.0	37.0	41.0	31.0	41.0
50	36.6595	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
13	1.0
14	0.0
15	0.0
16	1.0
17	0.0
18	1.0
19	3.0
20	3.0
21	3.0
22	4.0
23	5.0
24	10.0
25	10.0
26	13.0
27	18.0
28	29.0
29	34.0
30	51.0
31	52.0
32	87.0
33	107.0
34	151.0
35	180.0
36	293.0
37	406.0
38	707.0
39	1831.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.55	20.5	59.150000000000006	12.8
2	24.84939759036145	25.552208835341368	21.61144578313253	27.986947791164656
3	18.55	19.3	19.35	42.8
4	26.924999999999997	37.3	11.875	23.9
5	20.625	41.05	27.675	10.65
6	36.8	14.2	36.9	12.1
7	12.775	25.424999999999997	25.650000000000002	36.15
8	24.325	39.875	14.025000000000002	21.775
9	18.75	37.574999999999996	30.675	13.0
10	18.025	21.95	27.275	32.75
11	31.374999999999996	10.35	13.850000000000001	44.425
12	16.85	15.85	24.075	43.225
13	21.85	21.875	37.675	18.6
14	37.974999999999994	22.975	26.375	12.675
15	40.45	20.974999999999998	28.249999999999996	10.325
16	11.55	28.225	21.224999999999998	39.0
17	22.6	23.825	39.550000000000004	14.025000000000002
18	27.450000000000003	19.2	27.775	25.575
19	40.5	14.374999999999998	28.299999999999997	16.825000000000003
20	50.824999999999996	15.950000000000001	22.975	10.25
21	22.35	24.175	24.9	28.575
22	31.025000000000002	12.475	49.75	6.75
23	25.674999999999997	12.925	48.85	12.55
24	54.35	12.950000000000001	26.174999999999997	6.525
25	54.275	23.575	14.224999999999998	7.925
26	27.375	50.24999999999999	12.15	10.225
27	12.375	52.825	23.575	11.225
28	8.625	26.224999999999998	52.37500000000001	12.775
29	11.275	10.325	59.9	18.5
30	8.375	5.2	39.275	47.15
31	12.65	4.25	46.925	36.175000000000004
32	26.325	5.3	22.6	45.775
33	57.225	6.7	11.924999999999999	24.15
34	69.85	5.949999999999999	12.85	11.35
35	67.975	5.45	19.125	7.449999999999999
36	42.675000000000004	6.2	40.45	10.674999999999999
37	46.0	8.95	22.35	22.7
38	23.200000000000003	14.224999999999998	10.5	52.075
39	13.425	23.525	8.4	54.65
40	12.275	52.47500000000001	9.4	25.85
41	23.425	53.900000000000006	8.649999999999999	14.025000000000002
42	52.175000000000004	29.549999999999997	8.725	9.55
43	56.474999999999994	27.3	7.95	8.275
44	30.325000000000003	51.24999999999999	5.8999999999999995	12.525
45	16.875	54.35	10.7	18.075
46	10.825	25.85	19.225	44.1
47	7.725	12.575	41.349999999999994	38.35
48	8.325000000000001	10.125	23.400000000000002	58.15
49	12.25	18.45	11.225	58.074999999999996
50	18.25	39.275	11.225	31.25
>>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	0.5
12	1.0
13	0.5
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.5
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	2.0
30	4.0
31	6.0
32	8.0
33	9.0
34	10.0
35	16.5
36	23.0
37	23.5
38	24.0
39	29.0
40	34.0
41	36.5
42	39.0
43	65.5
44	92.0
45	162.0
46	232.0
47	428.0
48	624.0
49	647.0
50	670.0
51	832.5
52	995.0
53	666.0
54	337.0
55	363.0
56	389.0
57	322.0
58	255.0
59	158.0
60	61.0
61	48.5
62	36.0
63	65.0
64	94.0
65	56.0
66	18.0
67	14.0
68	10.0
69	7.5
70	5.0
71	16.0
72	27.0
73	15.5
74	4.0
75	3.0
76	2.0
77	1.5
78	1.0
79	2.0
80	3.0
81	2.0
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	0.4
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	35.0
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.64285714285714	26.125
2	10.785714285714286	7.55
3	4.5	4.725
4	1.9285714285714284	2.7
5	1.0714285714285714	1.875
6	1.0	2.1
7	0.7142857142857143	1.7500000000000002
8	0.35714285714285715	1.0
9	0.7142857142857143	2.25
>10	3.7142857142857144	26.200000000000003
>50	0.2857142857142857	6.075
>100	0.2857142857142857	17.65
>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	268	6.7	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	157	3.925	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	155	3.875	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	126	3.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	61	1.525	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	60	1.5	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	54	1.35	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGC	50	1.25	RNA PCR Primer, Index 21 (100% over 50bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	45	1.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	25	0.625	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (97% over 35bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	16	0.4	No Hit
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTC	12	0.3	RNA PCR Primer, Index 21 (100% over 44bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	11	0.27499999999999997	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCA	11	0.27499999999999997	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	11	0.27499999999999997	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	8	0.2	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	7	0.17500000000000002	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	6	0.15	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	5	0.125	RNA PCR Primer, Index 6 (100% over 34bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	1.325	0.0	0.0	0.0
2	0.0	1.35	0.0	0.0	0.0
3	0.0	1.4	0.0	0.0	0.0
4	0.0	1.425	0.0	0.0	0.0
5	0.0	1.45	0.0	0.0	0.0
6	0.0	1.525	0.0	0.0	0.0
7	0.0	1.875	0.0	0.0	0.0
8	0.0	2.1	0.0	0.0	0.0
9	0.0	2.175	0.0	0.0	0.0
10	0.0	2.275	0.0	0.0	0.0
11	0.0	2.475	0.0	0.0	0.0
12	0.0	2.65	0.0	0.0	0.0
13	0.0	2.925	0.0	0.0	0.0
14	0.0	3.1	0.0	0.0	0.0
15	0.0	3.375	0.0	0.0	0.0
16	0.0	4.35	0.0	0.0	0.0
17	0.0	4.975	0.0	0.0	0.0
18	0.0	5.75	0.0	0.0	0.0
19	0.0	6.4	0.0	0.0	0.0
20	0.0	7.575	0.0	0.0	0.0
21	0.0	12.525	0.0	0.0	0.0
22	0.0	25.15	0.0	0.0	0.0
23	0.0	58.8	0.0	0.0	0.0
24	0.0	74.3	0.0	0.0	0.0
25	0.0	79.425	0.0	0.0	0.0
26	0.0	80.425	0.0	0.0	0.0
27	0.0	80.925	0.0	0.0	0.0
28	0.0	81.5	0.0	0.0	0.0
29	0.0	81.825	0.0	0.0	0.0
30	0.0	82.225	0.0	0.0	0.0
31	0.0	82.9	0.0	0.0	0.0
32	0.0	83.925	0.0	0.0	0.0
33	0.0	85.125	0.0	0.0	0.0
34	0.0	87.625	0.0	0.0	0.0
35	0.0	88.875	0.0	0.0	0.0
36	0.0	89.375	0.0	0.0	0.0
37	0.0	89.875	0.0	0.0	0.0
38	0.0	90.15	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	40	5.315087E-9	44.000004	8
AAGTAAT	40	5.315087E-9	44.000004	4
TCAAGTA	40	5.315087E-9	44.000004	2
ACGCTGT	40	5.315087E-9	44.000004	9
AATCCAG	40	5.315087E-9	44.000004	8
TAAACAT	45	2.728484E-10	44.000004	3
TAGTGGT	20	6.952051E-4	44.000004	13
ATCCAGG	40	5.315087E-9	44.000004	9
AAACATC	45	2.728484E-10	44.000004	4
TTCAAGT	40	5.315087E-9	44.000004	1
TTCAACG	40	5.315087E-9	44.000004	5
AGGATAG	40	5.315087E-9	44.000004	13
GAAGCTT	20	6.952051E-4	44.000004	19
AGTGGTT	20	6.952051E-4	44.000004	14
TCAACGC	40	5.315087E-9	44.000004	6
TCCAGGA	40	5.315087E-9	44.000004	10
GGATAGG	40	5.315087E-9	44.000004	14
AGTAATC	40	5.315087E-9	44.000004	5
AGGCTTG	20	6.952051E-4	44.000004	18
GGCTTGG	20	6.952051E-4	44.000004	19
>>END_MODULE
Read 83510 spots for SRR5031001.sra
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SRR ids: ['SRR5031001.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_qsqntvxk
SRR5031001.sra spots: 4008511
blocks: [[1, 83510], [83511, 167020], [167021, 250530], [250531, 334040], [334041, 417550], [417551, 501060], [501061, 584570], [584571, 668080], [668081, 751590], [751591, 835100], [835101, 918610], [918611, 1002120], [1002121, 1085630], [1085631, 1169140], [1169141, 1252650], [1252651, 1336160], [1336161, 1419670], [1419671, 1503180], [1503181, 1586690], [1586691, 1670200], [1670201, 1753710], [1753711, 1837220], [1837221, 1920730], [1920731, 2004240], [2004241, 2087750], [2087751, 2171260], [2171261, 2254770], [2254771, 2338280], [2338281, 2421790], [2421791, 2505300], [2505301, 2588810], [2588811, 2672320], [2672321, 2755830], [2755831, 2839340], [2839341, 2922850], [2922851, 3006360], [3006361, 3089870], [3089871, 3173380], [3173381, 3256890], [3256891, 3340400], [3340401, 3423910], [3423911, 3507420], [3507421, 3590930], [3590931, 3674440], [3674441, 3757950], [3757951, 3841460], [3841461, 3924970], [3924971, 4008511]]
SRR5031001 file size 693704
SRR5031001 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5031001 SRR5031001_1.fastq
Input file:	SRR5031001_1.fastq
trimmed:	SRR5031001-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):	32
Wed Mar  4 07:03:39 2020 >> started

Wed Mar  4 07:03:42 2020 >> done (2.388s)
4008511 reads processed; of these:
    298 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
4008208 (99.99%) reads available; of these:
 223839 ( 5.58%) trimmed reads available after processing
3784369 (94.42%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     95	  0.00%
 19	    104	  0.00%
 20	    196	  0.00%
 21	    255	  0.01%
 22	    435	  0.01%
 23	    553	  0.01%
 24	    552	  0.01%
 25	    743	  0.02%
 26	    574	  0.01%
 27	    825	  0.02%
 28	    997	  0.02%
 29	   1760	  0.04%
 30	    998	  0.02%
 31	   1043	  0.03%
 32	   1265	  0.03%
 33	   1512	  0.04%
 34	   2104	  0.05%
 35	   4135	  0.10%
 36	   3277	  0.08%
 37	   3890	  0.10%
 38	   3546	  0.09%
 39	   3981	  0.10%
 40	   4850	  0.12%
 41	   4644	  0.12%
 42	   6132	  0.15%
 43	   8780	  0.22%
 44	  12475	  0.31%
 45	  16389	  0.41%
 46	  22307	  0.56%
 47	  26718	  0.67%
 48	  41282	  1.03%
 49	  47422	  1.18%
 50	3784369	 94.42%
4008208 reads passed initial QC


criterion=sequence-density
sequence-density=89.85
sequence-density-rank=1
fanout-score=17.99
fanout-score-rank=1
prefix-density=90.22
prefix-fanout=17.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC


criterion=fanout-score
sequence-density=89.85
sequence-density-rank=1
fanout-score=17.99
fanout-score-rank=1
prefix-density=90.22
prefix-fanout=17.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC -o SRR5031001 -
Input file:	STDIN
trimmed:	SRR5031001-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTTTCGATCTCGTATGCC
-- 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):	32
Wed Mar  4 07:04:00 2020 >> started

Wed Mar  4 07:04:06 2020 >> done (6.039s)
3919137 reads processed; of these:
 166152 ( 4.24%) short reads filtered out after trimming by size control
  67197 ( 1.71%) empty reads filtered out after trimming by size control
3685788 (94.05%) reads available; of these:
3564454 (96.71%) trimmed reads available after processing
 121334 ( 3.29%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17721	  0.48%
 19	  43246	  1.17%
 20	 188866	  5.12%
 21	 460299	 12.49%
 22	1357229	 36.82%
 23	 619042	 16.80%
 24	 224520	  6.09%
 25	  38926	  1.06%
 26	  19620	  0.53%
 27	  19059	  0.52%
 28	  21170	  0.57%
 29	  17236	  0.47%
 30	  33189	  0.90%
 31	  45357	  1.23%
 32	  47120	  1.28%
 33	  99885	  2.71%
 34	  39820	  1.08%
 35	  21737	  0.59%
 36	  23105	  0.63%
 37	  17527	  0.48%
 38	  19286	  0.52%
 39	  17912	  0.49%
 40	  23900	  0.65%
 41	  32970	  0.89%
 42	  33959	  0.92%
 43	  25439	  0.69%
 44	  22648	  0.61%
 45	  21644	  0.59%
 46	  16184	  0.44%
 47	  12954	  0.35%
 48	   1430	  0.04%
 49	   3174	  0.09%
 50	  99614	  2.70%


criterion=sequence-density
sequence-density=8.50
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=25
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.42
sequence-density-rank=32
fanout-score=15.61
fanout-score-rank=1
prefix-density=6.57
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:04:48
                             Started mapping on |	Mar 04 07:04:48
                                    Finished on |	Mar 04 07:05:19
       Mapping speed, Million of reads per hour |	438.37

                          Number of input reads |	3774859
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1839376
                        Uniquely mapped reads % |	48.73%
                          Average mapped length |	24.27
                       Number of splices: Total |	1625
            Number of splices: Annotated (sjdb) |	232
                       Number of splices: GT/AG |	1458
                       Number of splices: GC/AG |	22
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	143
                      Mismatch rate per base, % |	0.14%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.74
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1544831
             % of reads mapped to multiple loci |	40.92%
        Number of reads mapped to too many loci |	87207
             % of reads mapped to too many loci |	2.31%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.32%
                     % of reads unmapped: other |	0.72%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	390652	390652	390652
N_multimapping	1544831	1544831	1544831
N_noFeature	76905	94154	1399752
N_ambiguous	991637	616368	13588
UnstrandedReadsAssigned:770834 PositiveStrandReadsAssigned:1128854 NegativeStrandReadsAssigned:426036
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031001 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: SRR5031001-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,774,859 reads, 755,681 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,150 rounds

 109283 SRR5031001.ke.tsv
  52636 SRR5031001.se.tsv
 161919 total
==> SRR5031001.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

==> SRR5031001.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031001 completed mapping pipeline successfully
