Starting /dee2/code/volunteer_pipeline.sh SRR5031100
    current disk space = 160475348992
    free memory = 73931596 
SRR5031100 SRAfilesize
bfd3e0a92a1393c888fd2a54cb8ba4ae  SRR5031100.sra
SRR5031100.sra file validated
SRR5031100 is single end
SRR5031100 is conventional basespace
SRR5031100 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031100_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.9205	31.0	31.0	34.0	30.0	34.0
2	32.4325	33.0	31.0	34.0	31.0	34.0
3	32.4175	33.0	31.0	34.0	31.0	34.0
4	36.1525	37.0	35.0	37.0	35.0	37.0
5	36.155	37.0	35.0	37.0	35.0	37.0
6	36.049	37.0	35.0	37.0	35.0	37.0
7	35.8515	37.0	35.0	37.0	35.0	37.0
8	35.69675	37.0	35.0	37.0	35.0	37.0
9	36.89975	39.0	37.0	39.0	33.0	39.0
10	36.524	39.0	35.0	39.0	32.0	39.0
11	37.31975	39.0	37.0	39.0	34.0	39.0
12	37.65425	39.0	37.0	39.0	35.0	39.0
13	37.40225	39.0	37.0	39.0	35.0	39.0
14	38.21775	40.0	38.0	41.0	33.0	41.0
15	36.9075	40.0	36.0	41.0	30.0	41.0
16	36.55	38.0	36.0	40.0	31.0	41.0
17	36.9275	39.0	36.0	41.0	31.0	41.0
18	38.187	40.0	37.0	41.0	34.0	41.0
19	38.708	40.0	38.0	41.0	35.0	41.0
20	38.44175	40.0	38.0	41.0	34.0	41.0
21	38.54475	40.0	38.0	41.0	34.0	41.0
22	37.393	39.0	37.0	40.0	32.0	41.0
23	37.797	39.0	37.0	40.0	34.0	41.0
24	37.079	39.0	36.0	40.0	31.0	41.0
25	38.02	40.0	37.0	41.0	33.0	41.0
26	37.8495	40.0	37.0	41.0	33.0	41.0
27	38.06725	40.0	38.0	41.0	33.0	41.0
28	38.32825	40.0	38.0	41.0	34.0	41.0
29	38.34825	40.0	38.0	41.0	34.0	41.0
30	38.717	40.0	38.0	41.0	35.0	41.0
31	38.7045	40.0	38.0	41.0	35.0	41.0
32	38.645	40.0	38.0	41.0	35.0	41.0
33	38.2745	40.0	38.0	41.0	34.0	41.0
34	37.82825	40.0	38.0	41.0	33.0	41.0
35	37.26325	40.0	36.0	41.0	30.0	41.0
36	33.223	35.0	30.0	39.0	23.0	41.0
37	35.05075	37.0	33.0	39.0	30.0	40.0
38	36.44525	38.0	35.0	39.0	31.0	40.0
39	36.6515	38.0	36.0	40.0	31.0	40.0
40	37.1145	39.0	37.0	40.0	32.0	41.0
41	37.4355	39.0	37.0	40.0	33.0	41.0
42	37.404	40.0	37.0	41.0	33.0	41.0
43	37.66775	40.0	37.0	41.0	33.0	41.0
44	37.041	39.0	36.0	40.0	31.0	41.0
45	37.0555	39.0	37.0	40.0	31.0	41.0
46	36.92	39.0	36.0	40.0	31.0	41.0
47	35.639	38.0	34.0	40.0	28.0	41.0
48	36.65625	39.0	36.0	40.0	31.0	41.0
49	36.871	39.0	37.0	40.0	32.0	41.0
50	35.09125	38.0	34.0	40.0	28.0	40.0
>>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
12	1.0
13	2.0
14	0.0
15	0.0
16	0.0
17	1.0
18	1.0
19	2.0
20	3.0
21	9.0
22	4.0
23	10.0
24	9.0
25	13.0
26	13.0
27	14.0
28	20.0
29	39.0
30	57.0
31	64.0
32	82.0
33	142.0
34	197.0
35	289.0
36	441.0
37	748.0
38	1163.0
39	676.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.65	27.025	52.25	14.075
2	21.146146146146148	28.928928928928926	15.665665665665665	34.25925925925926
3	27.05	18.175	18.8	35.975
4	33.324999999999996	28.9	13.0	24.775
5	21.875	40.1	27.950000000000003	10.075000000000001
6	33.875	13.0	39.025	14.099999999999998
7	13.325000000000001	22.775000000000002	21.175	42.725
8	24.175	29.9	13.875000000000002	32.05
9	25.0	33.550000000000004	26.875	14.575
10	19.275000000000002	19.25	31.25	30.225
11	32.15	9.55	15.975	42.325
12	14.524999999999999	14.899999999999999	33.775	36.8
13	31.7	15.049999999999999	32.9	20.349999999999998
14	31.574999999999996	33.4	19.6	15.425
15	38.0	19.125	26.0	16.875
16	17.925	17.875	20.849999999999998	43.35
17	26.674999999999997	18.75	39.025	15.55
18	25.25	17.25	32.05	25.45
19	39.2	13.575000000000001	29.275000000000002	17.95
20	51.125	11.725	25.1	12.049999999999999
21	22.5	20.674999999999997	25.95	30.875000000000004
22	29.599999999999998	10.125	49.25	11.025
23	26.75	11.575000000000001	49.075	12.6
24	52.825	11.075	26.924999999999997	9.175
25	53.925	23.275000000000002	15.35	7.449999999999999
26	28.299999999999997	49.425000000000004	13.725000000000001	8.55
27	15.725	51.849999999999994	23.0	9.425
28	9.625	26.05	51.075	13.25
29	10.075000000000001	10.8	60.35	18.775
30	8.774999999999999	6.05	38.5	46.675
31	13.075000000000001	4.0	48.925000000000004	34.0
32	26.724999999999998	4.625	22.425	46.225
33	56.625	7.449999999999999	13.05	22.875
34	66.475	5.925	14.075	13.525
35	69.3	4.875	17.974999999999998	7.85
36	45.4	5.375	37.45	11.774999999999999
37	48.85	9.3	19.775000000000002	22.075
38	24.525	14.6	10.575	50.3
39	13.975000000000001	23.625	8.15	54.25
40	15.0	50.55	8.725	25.724999999999998
41	23.925	53.15	7.1499999999999995	15.775
42	50.675000000000004	31.85	8.15	9.325
43	54.725	30.2	5.65	9.425
44	30.9	51.675000000000004	5.1499999999999995	12.275
45	17.2	54.025	10.575	18.2
46	10.875	27.05	16.8	45.275
47	7.825	15.15	39.875	37.15
48	9.15	12.225	20.0	58.62500000000001
49	13.0	17.9	12.35	56.75
50	18.575	38.35	11.35	31.724999999999998
>>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	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	1.0
26	2.0
27	1.0
28	0.0
29	1.5
30	3.0
31	3.0
32	3.0
33	7.5
34	12.0
35	13.0
36	14.0
37	16.5
38	19.0
39	22.5
40	26.0
41	30.0
42	34.0
43	50.5
44	67.0
45	102.0
46	137.0
47	257.0
48	377.0
49	438.5
50	500.0
51	710.0
52	920.0
53	712.5
54	505.0
55	559.5
56	614.0
57	510.5
58	407.0
59	264.5
60	122.0
61	86.5
62	51.0
63	69.0
64	87.0
65	64.5
66	42.0
67	32.0
68	22.0
69	18.5
70	15.0
71	15.5
72	16.0
73	9.5
74	3.0
75	1.5
76	0.0
77	1.0
78	2.0
79	1.0
80	0.0
81	0.0
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	0.1
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	39.625
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.96214511041009	30.099999999999998
2	10.157728706624605	8.05
3	4.353312302839116	5.175
4	2.5867507886435335	4.1000000000000005
5	1.5141955835962144	3.0
6	0.8832807570977917	2.1
7	0.31545741324921134	0.8750000000000001
8	0.4416403785488959	1.4000000000000001
9	0.8201892744479496	2.9250000000000003
>10	2.3343848580441637	17.275
>50	0.3785488958990536	10.7
>100	0.2523659305993691	14.299999999999999
>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
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	170	4.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	154	3.85	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	134	3.35	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	114	2.85	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	99	2.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	94	2.35	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	69	1.725	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	63	1.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	52	1.3	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	51	1.275	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGG	32	0.8	RNA PCR Primer, Index 2 (97% over 35bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 30bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGC	17	0.42500000000000004	RNA PCR Primer, Index 24 (100% over 50bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	15	0.375	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTC	9	0.22499999999999998	RNA PCR Primer, Index 24 (100% over 44bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGACTCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	6	0.15	RNA PCR Primer, Index 6 (100% over 34bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGCCCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	5	0.125	RNA PCR Primer, Index 6 (100% over 34bp)
TCACAGTGACCCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTCACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.5	0.0	0.0	0.0
2	0.0	0.5	0.0	0.0	0.0
3	0.0	0.575	0.0	0.0	0.0
4	0.0	0.6	0.0	0.0	0.0
5	0.0	0.675	0.0	0.0	0.0
6	0.0	0.825	0.0	0.0	0.0
7	0.0	1.2	0.0	0.0	0.0
8	0.0	1.35	0.0	0.0	0.0
9	0.0	1.375	0.0	0.0	0.0
10	0.0	1.575	0.0	0.0	0.0
11	0.0	1.625	0.0	0.0	0.0
12	0.0	1.85	0.0	0.0	0.0
13	0.0	2.1	0.0	0.0	0.0
14	0.0	2.175	0.0	0.0	0.0
15	0.0	2.55	0.0	0.0	0.0
16	0.0	3.8	0.0	0.0	0.0
17	0.0	4.425	0.0	0.0	0.0
18	0.0	5.225	0.0	0.0	0.0
19	0.0	5.75	0.0	0.0	0.0
20	0.0	6.925	0.0	0.0	0.0
21	0.0	11.55	0.0	0.0	0.0
22	0.0	23.35	0.0	0.0	0.0
23	0.0	56.775	0.0	0.0	0.0
24	0.0	71.75	0.0	0.0	0.0
25	0.0	77.85	0.0	0.0	0.0
26	0.0	79.675	0.0	0.0	0.0
27	0.0	80.625	0.0	0.0	0.0
28	0.0	81.35	0.0	0.0	0.0
29	0.0	82.125	0.0	0.0	0.0
30	0.0	82.65	0.0	0.0	0.0
31	0.0	83.25	0.0	0.0	0.0
32	0.0	83.85	0.0	0.0	0.0
33	0.0	84.675	0.0	0.0	0.0
34	0.0	87.05	0.0	0.0	0.0
35	0.0	88.15	0.0	0.0	0.0
36	0.0	88.925	0.0	0.0	0.0
37	0.0	89.475	0.0	0.0	0.0
38	0.0	89.7	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTTTAAC	20	6.952051E-4	44.000004	12
GCGACCC	20	6.952051E-4	44.000004	22
CCGCTGA	20	6.952051E-4	44.000004	27
ATAGGCT	20	6.952051E-4	44.000004	16
GGCGACC	20	6.952051E-4	44.000004	21
AACCTGT	20	6.952051E-4	44.000004	16
ACCCGCT	20	6.952051E-4	44.000004	25
GAGTTGG	20	6.952051E-4	44.000004	20
CCCGCTG	20	6.952051E-4	44.000004	26
CGTGGCG	20	6.952051E-4	44.000004	18
TAACCTG	20	6.952051E-4	44.000004	15
GACGTGG	20	6.952051E-4	44.000004	16
AGGCTTG	20	6.952051E-4	44.000004	18
ACCCTTT	20	6.952051E-4	44.000004	9
GGCTTGG	20	6.952051E-4	44.000004	19
CCTTTAA	20	6.952051E-4	44.000004	11
AGTTGGA	20	6.952051E-4	44.000004	21
GATCAGA	20	6.952051E-4	44.000004	11
CAGATCA	20	6.952051E-4	44.000004	9
GTGGCGA	20	6.952051E-4	44.000004	19
>>END_MODULE
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133925 spots for SRR5031100.sra
Written 133925 spots for SRR5031100.sra
Read 133936 spots for SRR5031100.sra
Written 133936 spots for SRR5031100.sra
SRR ids: ['SRR5031100.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_tbn_qj56
SRR5031100.sra spots: 1607111
blocks: [[1, 133925], [133926, 267850], [267851, 401775], [401776, 535700], [535701, 669625], [669626, 803550], [803551, 937475], [937476, 1071400], [1071401, 1205325], [1205326, 1339250], [1339251, 1473175], [1473176, 1607111]]
SRR5031100 file size 277477
SRR5031100 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031100 SRR5031100_1.fastq
Input file:	SRR5031100_1.fastq
trimmed:	SRR5031100-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 07:24:12 2020 >> started

Wed Mar  4 07:24:13 2020 >> done (1.172s)
1607111 reads processed; of these:
    127 ( 0.01%) short reads filtered out after trimming by size control
      2 ( 0.00%) empty reads filtered out after trimming by size control
1606982 (99.99%) reads available; of these:
 137929 ( 8.58%) trimmed reads available after processing
1469053 (91.42%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     42	  0.00%
 19	     73	  0.00%
 20	    110	  0.01%
 21	    177	  0.01%
 22	    307	  0.02%
 23	    333	  0.02%
 24	    349	  0.02%
 25	    518	  0.03%
 26	    343	  0.02%
 27	    422	  0.03%
 28	    473	  0.03%
 29	    871	  0.05%
 30	    525	  0.03%
 31	    639	  0.04%
 32	    777	  0.05%
 33	   1309	  0.08%
 34	   1647	  0.10%
 35	   4272	  0.27%
 36	   2386	  0.15%
 37	   2320	  0.14%
 38	   2286	  0.14%
 39	   2605	  0.16%
 40	   3064	  0.19%
 41	   3274	  0.20%
 42	   3874	  0.24%
 43	   6409	  0.40%
 44	   7577	  0.47%
 45	  11020	  0.69%
 46	  12031	  0.75%
 47	  11176	  0.70%
 48	  27262	  1.70%
 49	  29458	  1.83%
 50	1469053	 91.42%
1606982 reads passed initial QC


criterion=sequence-density
sequence-density=89.55
sequence-density-rank=1
fanout-score=19.55
fanout-score-rank=2
prefix-density=91.04
prefix-fanout=19.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=3.84
sequence-density-rank=3
fanout-score=70.19
fanout-score-rank=1
prefix-density=90.90
prefix-fanout=3.0
sequence=GAATTCTCGGGGGCCAAGGAACT
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC -o SRR5031100 -
Input file:	STDIN
trimmed:	SRR5031100-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC
-- 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 07:24:24 2020 >> started

Wed Mar  4 07:24:26 2020 >> done (2.119s)
1571271 reads processed; of these:
  84749 ( 5.39%) short reads filtered out after trimming by size control
   8311 ( 0.53%) empty reads filtered out after trimming by size control
1478211 (94.08%) reads available; of these:
1429128 (96.68%) trimmed reads available after processing
  49083 ( 3.32%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   8753	  0.59%
 19	  16876	  1.14%
 20	  97858	  6.62%
 21	 189966	 12.85%
 22	 525740	 35.57%
 23	 233188	 15.78%
 24	 102129	  6.91%
 25	  28933	  1.96%
 26	  14072	  0.95%
 27	  10484	  0.71%
 28	  11329	  0.77%
 29	   8745	  0.59%
 30	  11748	  0.79%
 31	  13757	  0.93%
 32	  13994	  0.95%
 33	  41531	  2.81%
 34	  14490	  0.98%
 35	  11031	  0.75%
 36	  13656	  0.92%
 37	   5783	  0.39%
 38	   6126	  0.41%
 39	   5520	  0.37%
 40	   7991	  0.54%
 41	   9071	  0.61%
 42	   9896	  0.67%
 43	   6508	  0.44%
 44	   4622	  0.31%
 45	   6158	  0.42%
 46	   4321	  0.29%
 47	   3188	  0.22%
 48	    614	  0.04%
 49	   1035	  0.07%
 50	  39098	  2.64%


criterion=sequence-density
sequence-density=8.25
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=10
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=0.51
sequence-density-rank=27
fanout-score=28.81
fanout-score-rank=1
prefix-density=14.62
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:24:59
                             Started mapping on |	Mar 04 07:25:00
                                    Finished on |	Mar 04 07:25:26
       Mapping speed, Million of reads per hour |	209.62

                          Number of input reads |	1513922
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	825197
                        Uniquely mapped reads % |	54.51%
                          Average mapped length |	23.63
                       Number of splices: Total |	3994
            Number of splices: Annotated (sjdb) |	1337
                       Number of splices: GT/AG |	3943
                       Number of splices: GC/AG |	25
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	25
                      Mismatch rate per base, % |	0.36%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.72
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	537223
             % of reads mapped to multiple loci |	35.49%
        Number of reads mapped to too many loci |	21271
             % of reads mapped to too many loci |	1.41%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.11%
                     % of reads unmapped: other |	0.50%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	151502	151502	151502
N_multimapping	537223	537223	537223
N_noFeature	45309	53304	516830
N_ambiguous	496295	223238	6497
UnstrandedReadsAssigned:283593 PositiveStrandReadsAssigned:548655 NegativeStrandReadsAssigned:301870
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031100 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: SRR5031100-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,513,922 reads, 429,123 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,068 rounds

 109283 SRR5031100.ke.tsv
  52636 SRR5031100.se.tsv
 161919 total
==> SRR5031100.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

==> SRR5031100.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031100 completed mapping pipeline successfully
