Starting /dee2/code/volunteer_pipeline.sh SRR5031012
    current disk space = 160522485760
    free memory = 1054415144 
SRR5031012 SRAfilesize
cf5c5ea47c91b401e063b679a0c570d9  SRR5031012.sra
SRR5031012.sra file validated
SRR5031012 is single end
SRR5031012 is conventional basespace
SRR5031012 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031012_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	32.3245	33.0	31.0	34.0	31.0	34.0
2	32.60125	34.0	31.0	34.0	31.0	34.0
3	32.6325	34.0	31.0	34.0	31.0	34.0
4	36.1985	37.0	35.0	37.0	35.0	37.0
5	36.075	37.0	35.0	37.0	35.0	37.0
6	35.919	37.0	35.0	37.0	35.0	37.0
7	35.93825	37.0	35.0	37.0	35.0	37.0
8	36.048	37.0	35.0	37.0	35.0	37.0
9	37.599	39.0	37.0	39.0	35.0	39.0
10	37.57425	39.0	37.0	39.0	35.0	39.0
11	37.25075	39.0	37.0	39.0	34.0	39.0
12	37.65475	39.0	37.0	39.0	35.0	39.0
13	37.6075	39.0	37.0	39.0	35.0	39.0
14	39.03525	40.0	38.0	41.0	36.0	41.0
15	38.89975	40.0	38.0	41.0	35.0	41.0
16	38.988	40.0	38.0	41.0	36.0	41.0
17	39.10275	40.0	38.0	41.0	36.0	41.0
18	38.9925	40.0	38.0	41.0	35.0	41.0
19	38.84175	40.0	38.0	41.0	35.0	41.0
20	38.6805	40.0	38.0	41.0	34.0	41.0
21	38.832	40.0	38.0	41.0	35.0	41.0
22	38.87325	40.0	38.0	41.0	35.0	41.0
23	38.54075	40.0	38.0	41.0	34.0	41.0
24	38.6875	40.0	38.0	41.0	34.0	41.0
25	38.846	40.0	38.0	41.0	35.0	41.0
26	38.61125	40.0	38.0	41.0	34.0	41.0
27	38.7645	40.0	38.0	41.0	35.0	41.0
28	38.56725	40.0	38.0	41.0	34.0	41.0
29	38.206	40.0	38.0	41.0	33.0	41.0
30	38.218	40.0	38.0	41.0	33.0	41.0
31	38.51475	40.0	38.0	41.0	34.0	41.0
32	38.50625	40.0	38.0	41.0	34.0	41.0
33	38.15825	40.0	38.0	41.0	33.0	41.0
34	38.14275	40.0	38.0	41.0	33.0	41.0
35	37.88875	40.0	38.0	41.0	33.0	41.0
36	37.76775	40.0	37.0	41.0	33.0	41.0
37	36.9965	39.0	36.0	41.0	31.0	41.0
38	37.30025	39.0	37.0	41.0	32.0	41.0
39	37.73675	39.0	37.0	41.0	33.0	41.0
40	37.80675	40.0	37.0	41.0	33.0	41.0
41	37.9595	40.0	37.0	41.0	33.0	41.0
42	37.90325	40.0	37.0	41.0	33.0	41.0
43	37.69775	40.0	37.0	41.0	33.0	41.0
44	37.642	40.0	37.0	41.0	33.0	41.0
45	37.57875	40.0	37.0	41.0	33.0	41.0
46	37.572	40.0	37.0	41.0	33.0	41.0
47	36.946	40.0	35.0	41.0	31.0	41.0
48	36.85375	39.0	35.0	41.0	31.0	41.0
49	36.9315	40.0	35.0	41.0	31.0	41.0
50	36.21025	39.0	35.0	41.0	30.0	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
10	1.0
11	0.0
12	1.0
13	0.0
14	1.0
15	2.0
16	0.0
17	0.0
18	2.0
19	2.0
20	3.0
21	6.0
22	1.0
23	4.0
24	6.0
25	14.0
26	10.0
27	16.0
28	30.0
29	29.0
30	51.0
31	75.0
32	79.0
33	93.0
34	155.0
35	192.0
36	290.0
37	489.0
38	774.0
39	1674.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.85	24.2	47.575	18.375
2	24.210526315789473	26.666666666666668	20.927318295739347	28.195488721804512
3	23.425	19.950000000000003	23.724999999999998	32.9
4	33.900000000000006	26.025	16.525000000000002	23.549999999999997
5	24.925	35.925000000000004	26.625	12.525
6	33.725	14.7	33.25	18.325
7	16.650000000000002	23.65	22.675	37.025000000000006
8	24.925	27.125	17.4	30.55
9	21.175	32.0	28.525	18.3
10	21.8	23.0	26.85	28.349999999999998
11	34.225	10.299999999999999	17.5	37.974999999999994
12	18.025	19.725	30.175	32.074999999999996
13	30.175	17.125	33.225	19.475
14	30.875000000000004	29.725	21.075	18.325
15	35.15	24.425	25.35	15.075
16	20.7	18.075	26.0	35.225
17	27.200000000000003	22.2	35.6	15.0
18	24.975	17.75	28.975	28.299999999999997
19	35.825	14.575	31.4	18.2
20	42.075	15.5	28.349999999999998	14.075
21	23.974999999999998	20.375	27.1	28.549999999999997
22	29.95	12.425	44.35	13.275
23	27.775	13.675	41.449999999999996	17.1
24	51.65	13.900000000000002	25.95	8.5
25	49.5	25.15	15.075	10.274999999999999
26	28.999999999999996	43.55	14.725	12.725
27	15.35	44.925	23.875	15.85
28	11.875	22.900000000000002	47.675	17.549999999999997
29	14.025000000000002	13.0	53.5	19.475
30	11.675	7.625	34.699999999999996	46.0
31	16.325	5.575	44.3	33.800000000000004
32	29.9	6.0249999999999995	22.375	41.699999999999996
33	50.849999999999994	10.375	14.299999999999999	24.474999999999998
34	58.475	8.075000000000001	18.15	15.299999999999999
35	62.125	8.075000000000001	19.125	10.674999999999999
36	42.0	8.125	36.075	13.8
37	42.425000000000004	11.924999999999999	21.2	24.45
38	24.025	17.375	12.6	46.0
39	16.2	23.575	12.5	47.725
40	17.349999999999998	46.25	11.975	24.425
41	24.725	47.025	10.925	17.325
42	46.75	27.825	13.175	12.25
43	50.9	27.125	9.15	12.825000000000001
44	31.525	44.574999999999996	8.85	15.049999999999999
45	18.725	48.25	13.25	19.775000000000002
46	15.174999999999999	25.55	18.2	41.075
47	10.625	14.299999999999999	38.525	36.55
48	12.75	11.899999999999999	21.825	53.525
49	13.3	18.925	15.174999999999999	52.6
50	18.625	36.35	12.9	32.125
>>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	0.5
16	1.0
17	0.5
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	1.0
28	2.0
29	1.5
30	1.0
31	7.5
32	14.0
33	14.5
34	15.0
35	19.0
36	23.0
37	30.5
38	38.0
39	36.5
40	35.0
41	51.5
42	68.0
43	88.5
44	109.0
45	152.0
46	195.0
47	313.0
48	431.0
49	502.5
50	574.0
51	706.5
52	839.0
53	637.0
54	435.0
55	447.0
56	459.0
57	358.5
58	258.0
59	172.0
60	86.0
61	67.5
62	49.0
63	97.0
64	145.0
65	87.5
66	30.0
67	23.5
68	17.0
69	29.5
70	42.0
71	79.5
72	117.0
73	61.5
74	6.0
75	4.0
76	2.0
77	2.0
78	2.0
79	3.0
80	4.0
81	3.5
82	3.0
83	1.5
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	0.25
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	39.425
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.34749524413444	30.099999999999998
2	9.067850348763475	7.1499999999999995
3	4.819277108433735	5.7
4	2.7266962587190866	4.3
5	1.4584654407102093	2.875
6	0.8243500317057704	1.95
7	0.6341154090044389	1.7500000000000002
8	0.2536461636017755	0.8
9	0.507292327203551	1.7999999999999998
>10	2.6632847178186427	18.975
>50	0.3804692454026633	10.075000000000001
>100	0.31705770450221943	14.524999999999999
>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	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	124	3.1	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	122	3.05	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	103	2.5749999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	101	2.5250000000000004	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	94	2.35	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 30bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	66	1.6500000000000001	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	60	1.5	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	58	1.4500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	45	1.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	32	0.8	RNA PCR Primer, Index 7 (100% over 35bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	31	0.775	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	25	0.625	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	19	0.475	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	17	0.42500000000000004	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGC	16	0.4	RNA PCR Primer, Index 32 (100% over 50bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTC	15	0.375	RNA PCR Primer, Index 32 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	14	0.35000000000000003	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	13	0.325	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	11	0.27499999999999997	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	9	0.22499999999999998	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	7	0.17500000000000002	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CTGGGCTACACATTTTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	5	0.125	No Hit
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	5	0.125	No Hit
CTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.425	0.0	0.0	0.0
2	0.0	0.425	0.0	0.0	0.0
3	0.0	0.525	0.0	0.0	0.0
4	0.0	0.575	0.0	0.0	0.0
5	0.0	0.65	0.0	0.0	0.0
6	0.0	0.675	0.0	0.0	0.0
7	0.0	1.175	0.0	0.0	0.0
8	0.0	1.3	0.0	0.0	0.0
9	0.0	1.375	0.0	0.0	0.0
10	0.0	1.475	0.0	0.0	0.0
11	0.0	1.6	0.0	0.0	0.0
12	0.0	1.95	0.0	0.0	0.0
13	0.0	2.25	0.0	0.0	0.0
14	0.0	2.6	0.0	0.0	0.0
15	0.0	2.975	0.0	0.0	0.0
16	0.0	4.325	0.0	0.0	0.0
17	0.0	4.925	0.0	0.0	0.0
18	0.0	6.1	0.0	0.0	0.0
19	0.0	6.55	0.0	0.0	0.0
20	0.0	7.725	0.0	0.0	0.0
21	0.0	12.65	0.0	0.0	0.0
22	0.0	23.275	0.0	0.0	0.0
23	0.0	50.375	0.0	0.0	0.0
24	0.0	63.175	0.0	0.0	0.0
25	0.0	68.25	0.0	0.0	0.0
26	0.0	69.55	0.0	0.0	0.0
27	0.0	70.125	0.0	0.0	0.0
28	0.0	71.075	0.0	0.0	0.0
29	0.0	71.825	0.0	0.0	0.0
30	0.0	72.425	0.0	0.0	0.0
31	0.0	73.375	0.0	0.0	0.0
32	0.0	74.35	0.0	0.0	0.0
33	0.0	75.625	0.0	0.0	0.0
34	0.0	79.4	0.0	0.0	0.0
35	0.0	80.825	0.0	0.0	0.0
36	0.0	81.65	0.0	0.0	0.0
37	0.0	82.775	0.0	0.0	0.0
38	0.0	83.3	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TTTGAAC	25	3.4343255E-5	44.531647	1
TTGAACC	25	3.4343255E-5	44.531647	2
GAGGTAG	20	6.54202E-4	44.531643	2
ACATTCA	40	4.7512003E-9	44.531643	2
TGAGGTA	20	6.54202E-4	44.531643	1
AACATTC	40	4.7512003E-9	44.531643	1
TGTAAAC	20	6.54202E-4	44.531643	1
GGTGAGT	30	1.9592044E-6	43.975002	17
ACTCGAC	25	3.7082697E-5	43.975002	12
TCGACTC	25	3.7082697E-5	43.975002	14
ACCATCA	25	3.7082697E-5	43.975002	6
CATCACT	25	3.7082697E-5	43.975002	8
AACCATC	25	3.7082697E-5	43.975002	5
GAACCAT	25	3.7082697E-5	43.975002	4
CCATCAC	25	3.7082697E-5	43.975002	7
GGCTTGG	25	3.7082697E-5	43.975002	19
CGGTGAG	30	1.9592044E-6	43.975002	16
CACTCGA	25	3.7082697E-5	43.975002	11
ATCACTC	25	3.7082697E-5	43.975002	9
TCACTCG	25	3.7082697E-5	43.975002	10
>>END_MODULE
Read 75785 spots for SRR5031012.sra
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SRR ids: ['SRR5031012.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_3fkrwi3g
SRR5031012.sra spots: 3637715
blocks: [[1, 75785], [75786, 151570], [151571, 227355], [227356, 303140], [303141, 378925], [378926, 454710], [454711, 530495], [530496, 606280], [606281, 682065], [682066, 757850], [757851, 833635], [833636, 909420], [909421, 985205], [985206, 1060990], [1060991, 1136775], [1136776, 1212560], [1212561, 1288345], [1288346, 1364130], [1364131, 1439915], [1439916, 1515700], [1515701, 1591485], [1591486, 1667270], [1667271, 1743055], [1743056, 1818840], [1818841, 1894625], [1894626, 1970410], [1970411, 2046195], [2046196, 2121980], [2121981, 2197765], [2197766, 2273550], [2273551, 2349335], [2349336, 2425120], [2425121, 2500905], [2500906, 2576690], [2576691, 2652475], [2652476, 2728260], [2728261, 2804045], [2804046, 2879830], [2879831, 2955615], [2955616, 3031400], [3031401, 3107185], [3107186, 3182970], [3182971, 3258755], [3258756, 3334540], [3334541, 3410325], [3410326, 3486110], [3486111, 3561895], [3561896, 3637715]]
SRR5031012 file size 629433
SRR5031012 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5031012 SRR5031012_1.fastq
Input file:	SRR5031012_1.fastq
trimmed:	SRR5031012-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 07:06:17 2020 >> started

Wed Mar  4 07:06:20 2020 >> done (3.064s)
3637715 reads processed; of these:
    313 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3637396 (99.99%) reads available; of these:
 224953 ( 6.18%) trimmed reads available after processing
3412443 (93.82%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    110	  0.00%
 19	    122	  0.00%
 20	    205	  0.01%
 21	    283	  0.01%
 22	    479	  0.01%
 23	    532	  0.01%
 24	    579	  0.02%
 25	    754	  0.02%
 26	    638	  0.02%
 27	    847	  0.02%
 28	    957	  0.03%
 29	   1592	  0.04%
 30	   1064	  0.03%
 31	   1112	  0.03%
 32	   1391	  0.04%
 33	   1698	  0.05%
 34	   1791	  0.05%
 35	   3454	  0.09%
 36	   3030	  0.08%
 37	   3630	  0.10%
 38	   3690	  0.10%
 39	   4008	  0.11%
 40	   4445	  0.12%
 41	   4813	  0.13%
 42	   6294	  0.17%
 43	   8963	  0.25%
 44	  11432	  0.31%
 45	  14490	  0.40%
 46	  22105	  0.61%
 47	  26417	  0.73%
 48	  42187	  1.16%
 49	  51841	  1.43%
 50	3412443	 93.82%
3637396 reads passed initial QC


criterion=sequence-density
sequence-density=83.56
sequence-density-rank=1
fanout-score=22.07
fanout-score-rank=1
prefix-density=85.89
prefix-fanout=21.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCC


criterion=fanout-score
sequence-density=83.56
sequence-density-rank=1
fanout-score=22.07
fanout-score-rank=1
prefix-density=85.89
prefix-fanout=21.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCC -o SRR5031012 -
Input file:	STDIN
trimmed:	SRR5031012-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACTCAATCTCGTATGCC
-- 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 07:06:38 2020 >> started

Wed Mar  4 07:06:43 2020 >> done (5.275s)
3550791 reads processed; of these:
 218073 ( 6.14%) short reads filtered out after trimming by size control
  18013 ( 0.51%) empty reads filtered out after trimming by size control
3314705 (93.35%) reads available; of these:
3094093 (93.34%) trimmed reads available after processing
 220612 ( 6.66%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18385	  0.55%
 19	  40978	  1.24%
 20	 179246	  5.41%
 21	 382867	 11.55%
 22	 976942	 29.47%
 23	 449536	 13.56%
 24	 192162	  5.80%
 25	  51142	  1.54%
 26	  29059	  0.88%
 27	  25189	  0.76%
 28	  28598	  0.86%
 29	  23232	  0.70%
 30	  33513	  1.01%
 31	  39254	  1.18%
 32	  45458	  1.37%
 33	 132262	  3.99%
 34	  48115	  1.45%
 35	  37320	  1.13%
 36	  42750	  1.29%
 37	  21713	  0.66%
 38	  24434	  0.74%
 39	  22632	  0.68%
 40	  38480	  1.16%
 41	  43290	  1.31%
 42	  49771	  1.50%
 43	  36154	  1.09%
 44	  25490	  0.77%
 45	  34970	  1.05%
 46	  27795	  0.84%
 47	  20556	  0.62%
 48	   2522	  0.08%
 49	   4217	  0.13%
 50	 186673	  5.63%


criterion=sequence-density
sequence-density=7.00
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.44
sequence-density-rank=31
fanout-score=14.80
fanout-score-rank=1
prefix-density=6.49
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:07:24
                             Started mapping on |	Mar 04 07:07:25
                                    Finished on |	Mar 04 07:07:56
       Mapping speed, Million of reads per hour |	394.99

                          Number of input reads |	3401310
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1712901
                        Uniquely mapped reads % |	50.36%
                          Average mapped length |	25.22
                       Number of splices: Total |	2162
            Number of splices: Annotated (sjdb) |	499
                       Number of splices: GT/AG |	2033
                       Number of splices: GC/AG |	20
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	106
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.73
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1147264
             % of reads mapped to multiple loci |	33.73%
        Number of reads mapped to too many loci |	94243
             % of reads mapped to too many loci |	2.77%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.51%
                     % of reads unmapped: other |	0.62%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	541145	541145	541145
N_multimapping	1147264	1147264	1147264
N_noFeature	97098	120435	1199860
N_ambiguous	938169	500364	21442
UnstrandedReadsAssigned:677634 PositiveStrandReadsAssigned:1092102 NegativeStrandReadsAssigned:491599
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031012 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: SRR5031012-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,401,310 reads, 811,486 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,152 rounds

 109283 SRR5031012.ke.tsv
  52636 SRR5031012.se.tsv
 161919 total
==> SRR5031012.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

==> SRR5031012.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031012 completed mapping pipeline successfully
