Starting /dee2/code/volunteer_pipeline.sh SRR5031023
    current disk space = 160536035328
    free memory = 73938644 
SRR5031023 SRAfilesize
a08679f78c7bad81b04cdfc4a9f29309  SRR5031023.sra
SRR5031023.sra file validated
SRR5031023 is single end
SRR5031023 is conventional basespace
SRR5031023 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031023_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	32.35825	33.0	31.0	34.0	31.0	34.0
2	32.613	34.0	31.0	34.0	31.0	34.0
3	32.63525	34.0	31.0	34.0	31.0	34.0
4	36.19425	37.0	35.0	37.0	35.0	37.0
5	36.15325	37.0	35.0	37.0	35.0	37.0
6	35.95275	37.0	35.0	37.0	35.0	37.0
7	35.891	37.0	35.0	37.0	35.0	37.0
8	35.9555	37.0	35.0	37.0	35.0	37.0
9	37.4925	39.0	37.0	39.0	35.0	39.0
10	37.55025	39.0	37.0	39.0	35.0	39.0
11	37.36225	39.0	37.0	39.0	34.0	39.0
12	37.687	39.0	37.0	39.0	35.0	39.0
13	37.651	39.0	37.0	39.0	35.0	39.0
14	39.02175	40.0	38.0	41.0	35.0	41.0
15	38.84675	40.0	38.0	41.0	35.0	41.0
16	39.01125	40.0	38.0	41.0	36.0	41.0
17	39.07375	40.0	38.0	41.0	36.0	41.0
18	39.02775	40.0	38.0	41.0	35.0	41.0
19	38.9005	40.0	38.0	41.0	35.0	41.0
20	38.871	40.0	38.0	41.0	35.0	41.0
21	38.79375	40.0	38.0	41.0	35.0	41.0
22	38.931	40.0	39.0	41.0	35.0	41.0
23	38.684	40.0	38.0	41.0	34.0	41.0
24	38.84875	40.0	38.0	41.0	35.0	41.0
25	38.95475	40.0	38.0	41.0	35.0	41.0
26	38.85125	40.0	38.0	41.0	35.0	41.0
27	38.8805	40.0	38.0	41.0	35.0	41.0
28	38.707	40.0	38.0	41.0	34.0	41.0
29	38.43325	40.0	38.0	41.0	33.0	41.0
30	38.29125	40.0	38.0	41.0	33.0	41.0
31	38.618	40.0	38.0	41.0	34.0	41.0
32	38.47725	40.0	38.0	41.0	34.0	41.0
33	38.03275	40.0	38.0	41.0	33.0	41.0
34	37.95475	40.0	38.0	41.0	33.0	41.0
35	37.70975	40.0	37.0	41.0	33.0	41.0
36	37.786	40.0	37.0	41.0	33.0	41.0
37	37.33025	40.0	37.0	41.0	31.0	41.0
38	37.30875	39.0	37.0	41.0	31.0	41.0
39	37.83175	40.0	37.0	41.0	33.0	41.0
40	37.935	40.0	37.0	41.0	33.0	41.0
41	38.1565	40.0	37.0	41.0	33.0	41.0
42	38.05275	40.0	37.0	41.0	33.0	41.0
43	38.16025	40.0	38.0	41.0	34.0	41.0
44	38.17425	40.0	37.0	41.0	34.0	41.0
45	38.02875	40.0	37.0	41.0	33.0	41.0
46	37.7125	40.0	37.0	41.0	33.0	41.0
47	37.1905	40.0	36.0	41.0	31.0	41.0
48	36.9385	40.0	36.0	41.0	31.0	41.0
49	37.01375	40.0	36.0	41.0	31.0	41.0
50	36.48975	39.0	35.0	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
11	1.0
12	1.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	2.0
21	2.0
22	4.0
23	2.0
24	10.0
25	10.0
26	17.0
27	13.0
28	26.0
29	25.0
30	51.0
31	65.0
32	82.0
33	104.0
34	170.0
35	207.0
36	280.0
37	432.0
38	735.0
39	1761.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.4	24.8	52.1	14.7
2	24.91868901676257	27.070302727045288	18.188641481110835	29.82236677508131
3	24.224999999999998	23.325000000000003	22.25	30.2
4	33.25	27.425	13.5	25.825
5	22.125	42.1	25.0	10.775
6	35.475	16.35	33.300000000000004	14.875
7	15.325	20.225	24.349999999999998	40.1
8	26.474999999999998	27.0	15.225	31.3
9	20.0	34.8	27.950000000000003	17.25
10	20.5	25.45	27.625	26.424999999999997
11	31.225	9.0	17.65	42.125
12	15.275	19.625	30.325000000000003	34.775
13	34.525	16.675	31.424999999999997	17.375
14	33.050000000000004	28.9	20.849999999999998	17.2
15	33.775	22.875	27.725	15.625
16	19.975	16.400000000000002	23.775	39.85
17	23.65	22.45	40.300000000000004	13.600000000000001
18	25.474999999999998	17.95	27.025	29.549999999999997
19	34.849999999999994	14.45	33.925	16.775000000000002
20	42.199999999999996	13.850000000000001	29.299999999999997	14.649999999999999
21	22.225	20.225	30.099999999999998	27.450000000000003
22	30.175	11.15	47.525	11.15
23	29.125	12.3	43.525000000000006	15.049999999999999
24	53.2	13.175	24.7	8.924999999999999
25	50.24999999999999	26.325	14.674999999999999	8.75
26	27.175	47.699999999999996	14.524999999999999	10.6
27	16.25	45.95	25.35	12.45
28	12.275	23.05	49.825	14.85
29	12.425	12.049999999999999	54.825	20.7
30	9.725	6.4	37.4	46.475
31	14.799999999999999	4.9	45.35	34.949999999999996
32	30.5	5.425	20.95	43.125
33	55.675	8.3	12.75	23.275000000000002
34	62.0	7.1	16.225	14.674999999999999
35	63.175000000000004	7.249999999999999	20.674999999999997	8.9
36	43.175000000000004	7.074999999999999	36.199999999999996	13.55
37	44.824999999999996	10.375	18.95	25.85
38	23.625	15.975	11.425	48.975
39	15.049999999999999	25.75	9.675	49.525000000000006
40	15.9	49.475	10.775	23.849999999999998
41	27.075	47.4	7.85	17.675
42	49.925000000000004	28.475	10.424999999999999	11.175
43	49.95	31.75	7.449999999999999	10.85
44	30.049999999999997	49.375	7.074999999999999	13.5
45	17.275	48.4	13.125	21.2
46	13.325000000000001	24.45	19.85	42.375
47	8.6	14.95	38.1	38.35
48	9.700000000000001	13.125	19.725	57.45
49	12.275	21.975	14.374999999999998	51.37500000000001
50	19.925	37.0	13.325000000000001	29.75
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	0.5
26	1.0
27	1.5
28	2.0
29	2.5
30	3.0
31	5.5
32	8.0
33	9.5
34	11.0
35	13.5
36	16.0
37	18.0
38	20.0
39	24.5
40	29.0
41	36.5
42	44.0
43	87.5
44	131.0
45	157.0
46	183.0
47	300.0
48	417.0
49	563.5
50	710.0
51	802.0
52	894.0
53	670.0
54	446.0
55	454.0
56	462.0
57	336.5
58	211.0
59	136.0
60	61.0
61	43.5
62	26.0
63	80.0
64	134.0
65	85.5
66	37.0
67	28.0
68	19.0
69	23.5
70	28.0
71	60.5
72	93.0
73	49.5
74	6.0
75	3.5
76	1.0
77	2.0
78	3.0
79	2.5
80	2.0
81	1.0
82	0.0
83	0.0
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	0.075
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	36.375
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.25773195876289	27.375
2	10.790378006872853	7.85
3	3.5051546391752577	3.8249999999999997
4	2.542955326460481	3.6999999999999997
5	1.3745704467353952	2.5
6	0.9621993127147767	2.1
7	1.0309278350515463	2.625
8	0.4123711340206186	1.2
9	0.3436426116838488	1.125
>10	3.0927835051546393	22.900000000000002
>50	0.48109965635738833	14.6
>100	0.2061855670103093	10.2
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	162	4.05	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	114	2.85	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	100	2.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	96	2.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	93	2.325	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	79	1.975	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	75	1.875	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	39	0.975	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	38	0.95	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	36	0.8999999999999999	RNA PCR Primer, Index 7 (97% over 35bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	24	0.6	RNA PCR Primer, Index 1 (100% over 33bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	22	0.5499999999999999	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (100% over 30bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTC	21	0.525	RNA PCR Primer, Index 43 (100% over 44bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	19	0.475	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	17	0.42500000000000004	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGC	17	0.42500000000000004	RNA PCR Primer, Index 43 (100% over 50bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	16	0.4	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	14	0.35000000000000003	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	13	0.325	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	10	0.25	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	7	0.17500000000000002	RNA PCR Primer, Index 3 (100% over 34bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAG	7	0.17500000000000002	RNA PCR Primer, Index 43 (100% over 38bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	7	0.17500000000000002	RNA PCR Primer, Index 3 (100% over 34bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAC	6	0.15	RNA PCR Primer, Index 30 (97% over 36bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACA	5	0.125	RNA PCR Primer, Index 43 (100% over 37bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTACAGTACTGTGATAACTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAGGATCACAGAAAAAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.45	0.0	0.0	0.0
2	0.0	0.45	0.0	0.0	0.0
3	0.0	0.55	0.0	0.0	0.0
4	0.0	0.575	0.0	0.0	0.0
5	0.0	0.625	0.0	0.0	0.0
6	0.0	0.725	0.0	0.0	0.0
7	0.0	1.325	0.0	0.0	0.0
8	0.0	1.45	0.0	0.0	0.0
9	0.0	1.5	0.0	0.0	0.0
10	0.0	1.7	0.0	0.0	0.0
11	0.0	1.925	0.0	0.0	0.0
12	0.0	2.125	0.0	0.0	0.0
13	0.0	2.4	0.0	0.0	0.0
14	0.0	2.725	0.0	0.0	0.0
15	0.0	3.175	0.0	0.0	0.0
16	0.0	4.5	0.0	0.0	0.0
17	0.0	5.35	0.0	0.0	0.0
18	0.0	6.775	0.0	0.0	0.0
19	0.0	7.325	0.0	0.0	0.0
20	0.0	8.3	0.0	0.0	0.0
21	0.0	14.05	0.0	0.0	0.0
22	0.0	27.5	0.0	0.0	0.0
23	0.0	56.675	0.0	0.0	0.0
24	0.0	69.275	0.0	0.0	0.0
25	0.0	75.125	0.0	0.0	0.0
26	0.0	76.85	0.0	0.0	0.0
27	0.0	77.725	0.0	0.0	0.0
28	0.0	78.225	0.0	0.0	0.0
29	0.0	78.825	0.0	0.0	0.0
30	0.0	79.4	0.0	0.0	0.0
31	0.0	80.075	0.0	0.0	0.0
32	0.0	81.175	0.0	0.0	0.0
33	0.0	81.95	0.0	0.0	0.0
34	0.0	84.8	0.0	0.0	0.0
35	0.0	85.775	0.0	0.0	0.0
36	0.0	86.475	0.0	0.0	0.0
37	0.0	87.2	0.0	0.0	0.0
38	0.0	87.525	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGATT	20	6.952051E-4	44.000004	8
ACAGTGA	45	2.728484E-10	44.000004	3
ACCGGTC	45	2.728484E-10	44.000004	10
ATCCCAA	20	6.952051E-4	44.000004	8
GTTTGGA	20	6.952051E-4	44.000004	20
AACCGGT	45	2.728484E-10	44.000004	9
AATCCCA	20	6.952051E-4	44.000004	7
TCCCAAA	20	6.952051E-4	44.000004	9
TTGTATA	20	6.952051E-4	44.000004	13
AGTAGAT	20	6.952051E-4	44.000004	7
CCAAAAG	20	6.952051E-4	44.000004	11
GGTCTCT	45	2.728484E-10	44.000004	13
CTCTTTT	40	5.315087E-9	44.000004	16
GATTGTA	20	6.952051E-4	44.000004	11
GTATAGT	20	6.952051E-4	44.000004	15
AGCAGCT	20	6.952051E-4	44.000004	16
CGGAATC	20	6.952051E-4	44.000004	4
GCAGCTG	20	6.952051E-4	44.000004	17
AAAAGCA	20	6.952051E-4	44.000004	13
CCCAAAA	20	6.952051E-4	44.000004	10
>>END_MODULE
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191176 spots for SRR5031023.sra
Written 191176 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
Read 191168 spots for SRR5031023.sra
Written 191168 spots for SRR5031023.sra
SRR ids: ['SRR5031023.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_h2047_lj
SRR5031023.sra spots: 2294024
blocks: [[1, 191168], [191169, 382336], [382337, 573504], [573505, 764672], [764673, 955840], [955841, 1147008], [1147009, 1338176], [1338177, 1529344], [1529345, 1720512], [1720513, 1911680], [1911681, 2102848], [2102849, 2294024]]
SRR5031023 file size 396535
SRR5031023 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031023 SRR5031023_1.fastq
Input file:	SRR5031023_1.fastq
trimmed:	SRR5031023-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 07:08:51 2020 >> started

Wed Mar  4 07:08:52 2020 >> done (1.620s)
2294024 reads processed; of these:
    207 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
2293811 (99.99%) reads available; of these:
 129163 ( 5.63%) trimmed reads available after processing
2164648 (94.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     62	  0.00%
 19	     78	  0.00%
 20	    140	  0.01%
 21	    149	  0.01%
 22	    317	  0.01%
 23	    386	  0.02%
 24	    366	  0.02%
 25	    497	  0.02%
 26	    420	  0.02%
 27	    473	  0.02%
 28	    645	  0.03%
 29	   1075	  0.05%
 30	    670	  0.03%
 31	    716	  0.03%
 32	    804	  0.04%
 33	    915	  0.04%
 34	   1134	  0.05%
 35	   1988	  0.09%
 36	   1781	  0.08%
 37	   2074	  0.09%
 38	   2040	  0.09%
 39	   2175	  0.09%
 40	   2514	  0.11%
 41	   2717	  0.12%
 42	   3547	  0.15%
 43	   5469	  0.24%
 44	   7578	  0.33%
 45	   9262	  0.40%
 46	  12401	  0.54%
 47	  14953	  0.65%
 48	  23473	  1.02%
 49	  28344	  1.24%
 50	2164648	 94.37%
2293811 reads passed initial QC


criterion=sequence-density
sequence-density=87.61
sequence-density-rank=1
fanout-score=20.63
fanout-score-rank=1
prefix-density=89.15
prefix-fanout=20.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=87.61
sequence-density-rank=1
fanout-score=20.63
fanout-score-rank=1
prefix-density=89.15
prefix-fanout=20.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC -o SRR5031023 -
Input file:	STDIN
trimmed:	SRR5031023-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC
-- 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 07:09:06 2020 >> started

Wed Mar  4 07:09:09 2020 >> done (3.064s)
2241679 reads processed; of these:
 146837 ( 6.55%) short reads filtered out after trimming by size control
  12336 ( 0.55%) empty reads filtered out after trimming by size control
2082506 (92.90%) reads available; of these:
1987998 (95.46%) trimmed reads available after processing
  94508 ( 4.54%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11892	  0.57%
 19	  24587	  1.18%
 20	 120430	  5.78%
 21	 290638	 13.96%
 22	 666569	 32.01%
 23	 311589	 14.96%
 24	 142772	  6.86%
 25	  33545	  1.61%
 26	  17586	  0.84%
 27	  13666	  0.66%
 28	  13414	  0.64%
 29	  11656	  0.56%
 30	  16565	  0.80%
 31	  26715	  1.28%
 32	  21708	  1.04%
 33	  65986	  3.17%
 34	  20249	  0.97%
 35	  14881	  0.71%
 36	  18051	  0.87%
 37	   9700	  0.47%
 38	  10183	  0.49%
 39	   9613	  0.46%
 40	  13855	  0.67%
 41	  18765	  0.90%
 42	  23664	  1.14%
 43	  16564	  0.80%
 44	  12107	  0.58%
 45	  18454	  0.89%
 46	  14281	  0.69%
 47	  10706	  0.51%
 48	    929	  0.04%
 49	   1447	  0.07%
 50	  79739	  3.83%


criterion=sequence-density
sequence-density=8.39
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=38
fanout-score=130.50
fanout-score-rank=1
prefix-density=2.64
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:09:29
                             Started mapping on |	Mar 04 07:09:30
                                    Finished on |	Mar 04 07:09:56
       Mapping speed, Million of reads per hour |	295.57

                          Number of input reads |	2134638
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1081134
                        Uniquely mapped reads % |	50.65%
                          Average mapped length |	24.08
                       Number of splices: Total |	1057
            Number of splices: Annotated (sjdb) |	243
                       Number of splices: GT/AG |	984
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	56
                      Mismatch rate per base, % |	0.18%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.92
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	774423
             % of reads mapped to multiple loci |	36.28%
        Number of reads mapped to too many loci |	42154
             % of reads mapped to too many loci |	1.97%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.46%
                     % of reads unmapped: other |	0.64%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	279081	279081	279081
N_multimapping	774423	774423	774423
N_noFeature	57809	69218	753395
N_ambiguous	590509	301200	9575
UnstrandedReadsAssigned:432816 PositiveStrandReadsAssigned:710716 NegativeStrandReadsAssigned:318164
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031023 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: SRR5031023-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,134,638 reads, 528,796 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,075 rounds

 109283 SRR5031023.ke.tsv
  52636 SRR5031023.se.tsv
 161919 total
==> SRR5031023.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

==> SRR5031023.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031023 completed mapping pipeline successfully
