Starting /dee2/code/volunteer_pipeline.sh SRR5030987
    current disk space = 160564707328
    free memory = 56715392 
SRR5030987 SRAfilesize
991c5f1b6d1c94f328cacf98be171236  SRR5030987.sra
SRR5030987.sra file validated
SRR5030987 is single end
SRR5030987 is conventional basespace
SRR5030987 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030987_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	32.34825	33.0	31.0	34.0	31.0	34.0
2	32.54225	34.0	31.0	34.0	31.0	34.0
3	32.6235	34.0	31.0	34.0	31.0	34.0
4	36.2395	37.0	37.0	37.0	35.0	37.0
5	36.1605	37.0	37.0	37.0	35.0	37.0
6	35.9585	37.0	35.0	37.0	35.0	37.0
7	35.9615	37.0	35.0	37.0	35.0	37.0
8	36.06975	37.0	35.0	37.0	35.0	37.0
9	37.66475	39.0	37.0	39.0	35.0	39.0
10	37.5945	39.0	37.0	39.0	35.0	39.0
11	37.225	39.0	37.0	39.0	33.0	39.0
12	37.65525	39.0	37.0	39.0	35.0	39.0
13	37.6355	39.0	37.0	39.0	35.0	39.0
14	39.119	40.0	38.0	41.0	35.0	41.0
15	38.966	40.0	38.0	41.0	35.0	41.0
16	39.0615	40.0	38.0	41.0	36.0	41.0
17	39.13725	40.0	39.0	41.0	36.0	41.0
18	38.9645	41.0	38.0	41.0	35.0	41.0
19	38.836	40.0	38.0	41.0	35.0	41.0
20	38.7885	40.0	38.0	41.0	35.0	41.0
21	38.8945	40.0	38.0	41.0	35.0	41.0
22	38.8245	40.0	38.0	41.0	35.0	41.0
23	38.44625	40.0	38.0	41.0	34.0	41.0
24	38.72975	40.0	38.0	41.0	34.0	41.0
25	38.7255	40.0	38.0	41.0	34.0	41.0
26	38.39425	40.0	38.0	41.0	34.0	41.0
27	38.6645	40.0	38.0	41.0	34.0	41.0
28	38.45525	40.0	38.0	41.0	34.0	41.0
29	38.2765	40.0	38.0	41.0	33.0	41.0
30	38.379	40.0	38.0	41.0	34.0	41.0
31	38.564	40.0	38.0	41.0	34.0	41.0
32	38.6275	40.0	38.0	41.0	34.0	41.0
33	38.31775	40.0	38.0	41.0	34.0	41.0
34	38.15675	40.0	38.0	41.0	33.0	41.0
35	37.98525	40.0	38.0	41.0	33.0	41.0
36	37.90425	40.0	37.0	41.0	33.0	41.0
37	37.232	40.0	37.0	41.0	31.0	41.0
38	37.35075	39.0	37.0	41.0	31.0	41.0
39	37.85375	40.0	37.0	41.0	33.0	41.0
40	37.87875	40.0	37.0	41.0	33.0	41.0
41	38.023	40.0	37.0	41.0	33.0	41.0
42	37.96	40.0	38.0	41.0	33.0	41.0
43	37.733	40.0	37.0	41.0	33.0	41.0
44	37.828	40.0	37.0	41.0	33.0	41.0
45	37.82575	40.0	37.0	41.0	33.0	41.0
46	37.60175	40.0	37.0	41.0	33.0	41.0
47	37.02325	40.0	36.0	41.0	31.0	41.0
48	36.91425	40.0	36.0	41.0	31.0	41.0
49	37.0	40.0	36.0	41.0	31.0	41.0
50	36.42975	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
5	1.0
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	2.0
17	2.0
18	1.0
19	2.0
20	3.0
21	6.0
22	7.0
23	7.0
24	8.0
25	7.0
26	14.0
27	18.0
28	15.0
29	43.0
30	42.0
31	82.0
32	80.0
33	106.0
34	141.0
35	147.0
36	266.0
37	473.0
38	790.0
39	1737.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.0	25.0	50.0	16.0
2	24.25916624811652	25.96685082872928	19.261677548970365	30.51230537418383
3	23.200000000000003	21.65	24.15	31.0
4	33.025	28.075	14.899999999999999	24.0
5	23.05	39.375	25.525	12.049999999999999
6	36.4	15.950000000000001	32.6	15.049999999999999
7	16.45	21.425	24.775	37.35
8	26.0	27.675	15.8	30.525000000000002
9	20.775	32.725	28.025	18.475
10	22.075	24.224999999999998	26.724999999999998	26.974999999999998
11	30.125	10.274999999999999	19.125	40.475
12	17.875	16.8	30.375000000000004	34.949999999999996
13	34.5	17.675	30.9	16.925
14	33.1	29.775000000000002	20.0	17.125
15	35.0	23.375	28.825	12.8
16	17.549999999999997	18.95	25.924999999999997	37.574999999999996
17	24.8	21.025	39.324999999999996	14.85
18	25.35	18.625	27.175	28.849999999999998
19	35.675000000000004	15.55	31.25	17.525
20	43.275000000000006	15.825	26.650000000000002	14.249999999999998
21	22.5	19.375	29.549999999999997	28.575
22	28.050000000000004	13.475000000000001	45.9	12.575
23	27.6	12.85	43.05	16.5
24	51.74999999999999	14.399999999999999	25.825	8.025
25	50.4	23.7	14.899999999999999	11.0
26	30.099999999999998	45.074999999999996	14.875	9.950000000000001
27	16.575	46.5	22.975	13.950000000000001
28	13.275	23.25	48.825	14.649999999999999
29	11.725	13.65	55.60000000000001	19.025
30	11.35	6.875000000000001	35.0	46.775
31	15.25	5.1	44.95	34.699999999999996
32	28.375	7.025	20.724999999999998	43.875
33	52.425	8.575000000000001	14.025000000000002	24.975
34	59.75	8.35	16.625	15.275
35	63.55	7.124999999999999	19.1	10.225
36	42.3	7.7	36.15	13.850000000000001
37	43.2	12.125	19.775000000000002	24.9
38	23.150000000000002	16.5	13.575000000000001	46.775
39	16.475	23.575	10.075000000000001	49.875
40	15.950000000000001	48.075	11.225	24.75
41	25.5	47.875	9.5	17.125
42	47.475	28.275	11.975	12.275
43	50.475	29.875	8.725	10.925
44	31.324999999999996	46.625	8.525	13.525
45	17.7	47.65	13.725000000000001	20.925
46	13.075000000000001	25.974999999999998	19.0	41.949999999999996
47	9.2	16.475	37.925	36.4
48	10.85	12.15	21.3	55.7
49	13.075000000000001	19.5	15.275	52.15
50	18.7	38.0	13.375	29.925
>>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	2.0
28	4.0
29	4.5
30	5.0
31	12.0
32	19.0
33	15.5
34	12.0
35	14.5
36	17.0
37	24.5
38	32.0
39	36.0
40	40.0
41	40.5
42	41.0
43	74.5
44	108.0
45	158.5
46	209.0
47	325.0
48	441.0
49	556.5
50	672.0
51	754.5
52	837.0
53	636.5
54	436.0
55	466.5
56	497.0
57	356.0
58	215.0
59	145.5
60	76.0
61	58.5
62	41.0
63	64.0
64	87.0
65	56.0
66	25.0
67	17.0
68	9.0
69	24.0
70	39.0
71	83.0
72	127.0
73	66.0
74	5.0
75	2.5
76	0.0
77	0.0
78	0.0
79	2.0
80	4.0
81	2.0
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	0.44999999999999996
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	38.0
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.78947368421053	28.799999999999997
2	9.868421052631579	7.5
3	4.342105263157895	4.95
4	1.9736842105263157	3.0
5	1.513157894736842	2.875
6	1.0526315789473684	2.4
7	0.855263157894737	2.275
8	0.5263157894736842	1.6
9	0.06578947368421052	0.22499999999999998
>10	3.289473684210526	23.45
>50	0.5263157894736842	13.825000000000001
>100	0.19736842105263158	9.1
>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	141	3.5249999999999995	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	121	3.025	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	102	2.55	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	89	2.225	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	86	2.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	68	1.7000000000000002	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	60	1.5	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	51	1.275	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	50	1.25	RNA PCR Primer, Index 7 (100% over 35bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 33bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	28	0.7000000000000001	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGC	24	0.6	RNA PCR Primer, Index 7 (100% over 50bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	24	0.6	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	19	0.475	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	19	0.475	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTC	18	0.44999999999999996	RNA PCR Primer, Index 7 (100% over 44bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	15	0.375	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	10	0.25	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	8	0.2	RNA PCR Primer, Index 7 (100% over 35bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGA	8	0.2	RNA PCR Primer, Index 7 (100% over 37bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACCA	6	0.15	RNA PCR Primer, Index 7 (97% over 35bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	6	0.15	RNA PCR Primer, Index 2 (100% over 34bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (100% over 33bp)
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGGGCTACACATTTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	5	0.125	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.625	0.0	0.0	0.0
2	0.0	0.625	0.0	0.0	0.0
3	0.0	0.725	0.0	0.0	0.0
4	0.0	0.825	0.0	0.0	0.0
5	0.0	0.925	0.0	0.0	0.0
6	0.0	1.05	0.0	0.0	0.0
7	0.0	1.725	0.0	0.0	0.0
8	0.0	1.85	0.0	0.0	0.0
9	0.0	1.925	0.0	0.0	0.0
10	0.0	2.125	0.0	0.0	0.0
11	0.0	2.3	0.0	0.0	0.0
12	0.0	2.55	0.0	0.0	0.0
13	0.0	2.9	0.0	0.0	0.0
14	0.0	3.275	0.0	0.0	0.0
15	0.0	3.75	0.0	0.0	0.0
16	0.0	5.8	0.0	0.0	0.0
17	0.0	6.5	0.0	0.0	0.0
18	0.0	7.775	0.0	0.0	0.0
19	0.0	8.125	0.0	0.0	0.0
20	0.0	9.2	0.0	0.0	0.0
21	0.0	14.175	0.0	0.0	0.0
22	0.0	25.6	0.0	0.0	0.0
23	0.0	53.825	0.0	0.0	0.0
24	0.0	66.2	0.0	0.0	0.0
25	0.0	71.725	0.0	0.0	0.0
26	0.0	73.325	0.0	0.0	0.0
27	0.0	73.925	0.0	0.0	0.0
28	0.0	74.5	0.0	0.0	0.0
29	0.0	75.275	0.0	0.0	0.0
30	0.0	75.625	0.0	0.0	0.0
31	0.0	76.125	0.0	0.0	0.0
32	0.0	77.025	0.0	0.0	0.0
33	0.0	78.05	0.0	0.0	0.0
34	0.0	80.5	0.0	0.0	0.0
35	0.0	81.225	0.0	0.0	0.0
36	0.0	81.925	0.0	0.0	0.0
37	0.0	83.0	0.0	0.0	0.0
38	0.0	83.525	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACTGTTG	20	6.952051E-4	44.000004	18
AACGCTG	20	6.952051E-4	44.000004	8
GTTGAAG	20	6.952051E-4	44.000004	10
ACGCTGT	20	6.952051E-4	44.000004	9
CAGTTGA	20	6.952051E-4	44.000004	8
CTGAGCT	45	2.728484E-10	44.000004	11
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
TTCAACG	20	6.952051E-4	44.000004	5
TCGGTGA	20	6.952051E-4	44.000004	15
GAGCTTG	45	2.728484E-10	44.000004	13
GGATCCG	45	2.728484E-10	44.000004	3
CCGTCTG	45	2.728484E-10	44.000004	7
TCGGATC	45	2.728484E-10	44.000004	1
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
CGGATCC	45	2.728484E-10	44.000004	2
GAAGAAC	20	6.952051E-4	44.000004	13
GCCAGTT	20	6.952051E-4	44.000004	6
GCTGCCA	20	6.952051E-4	44.000004	3
>>END_MODULE
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376587 spots for SRR5030987.sra
Written 376587 spots for SRR5030987.sra
Read 376593 spots for SRR5030987.sra
Written 376593 spots for SRR5030987.sra
SRR ids: ['SRR5030987.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_8l0_04m0
SRR5030987.sra spots: 4519050
blocks: [[1, 376587], [376588, 753174], [753175, 1129761], [1129762, 1506348], [1506349, 1882935], [1882936, 2259522], [2259523, 2636109], [2636110, 3012696], [3012697, 3389283], [3389284, 3765870], [3765871, 4142457], [4142458, 4519050]]
SRR5030987 file size 782193
SRR5030987 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030987 SRR5030987_1.fastq
Input file:	SRR5030987_1.fastq
trimmed:	SRR5030987-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 07:00:43 2020 >> started

Wed Mar  4 07:00:46 2020 >> done (2.752s)
4519050 reads processed; of these:
    379 ( 0.01%) short reads filtered out after trimming by size control
      3 ( 0.00%) empty reads filtered out after trimming by size control
4518668 (99.99%) reads available; of these:
 251445 ( 5.56%) trimmed reads available after processing
4267223 (94.44%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    132	  0.00%
 19	    143	  0.00%
 20	    267	  0.01%
 21	    326	  0.01%
 22	    639	  0.01%
 23	    722	  0.02%
 24	    747	  0.02%
 25	   1093	  0.02%
 26	    829	  0.02%
 27	   1048	  0.02%
 28	   1232	  0.03%
 29	   1799	  0.04%
 30	   1264	  0.03%
 31	   1296	  0.03%
 32	   1586	  0.04%
 33	   1936	  0.04%
 34	   2155	  0.05%
 35	   3919	  0.09%
 36	   3706	  0.08%
 37	   4339	  0.10%
 38	   4307	  0.10%
 39	   4720	  0.10%
 40	   5377	  0.12%
 41	   5643	  0.12%
 42	   7399	  0.16%
 43	  10355	  0.23%
 44	  13823	  0.31%
 45	  17008	  0.38%
 46	  24451	  0.54%
 47	  29493	  0.65%
 48	  46320	  1.03%
 49	  53371	  1.18%
 50	4267223	 94.44%
4518668 reads passed initial QC


criterion=sequence-density
sequence-density=84.46
sequence-density-rank=1
fanout-score=20.45
fanout-score-rank=1
prefix-density=85.87
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC


criterion=fanout-score
sequence-density=84.46
sequence-density-rank=1
fanout-score=20.45
fanout-score-rank=1
prefix-density=85.87
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC -o SRR5030987 -
Input file:	STDIN
trimmed:	SRR5030987-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 07:01:06 2020 >> started

Wed Mar  4 07:01:13 2020 >> done (7.189s)
4412347 reads processed; of these:
 318426 ( 7.22%) short reads filtered out after trimming by size control
  35875 ( 0.81%) empty reads filtered out after trimming by size control
4058046 (91.97%) reads available; of these:
3799177 (93.62%) trimmed reads available after processing
 258869 ( 6.38%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  23017	  0.57%
 19	  49289	  1.21%
 20	 223174	  5.50%
 21	 510939	 12.59%
 22	1222108	 30.12%
 23	 573247	 14.13%
 24	 267376	  6.59%
 25	  69692	  1.72%
 26	  36731	  0.91%
 27	  28744	  0.71%
 28	  31045	  0.77%
 29	  24059	  0.59%
 30	  36553	  0.90%
 31	  46140	  1.14%
 32	  52901	  1.30%
 33	 124294	  3.06%
 34	  46041	  1.13%
 35	  36068	  0.89%
 36	  40067	  0.99%
 37	  23421	  0.58%
 38	  25974	  0.64%
 39	  24494	  0.60%
 40	  34861	  0.86%
 41	  46880	  1.16%
 42	  54453	  1.34%
 43	  38804	  0.96%
 44	  29002	  0.71%
 45	  47489	  1.17%
 46	  40257	  0.99%
 47	  28661	  0.71%
 48	   3047	  0.08%
 49	   3696	  0.09%
 50	 215522	  5.31%


criterion=sequence-density
sequence-density=6.98
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=40
fanout-score=97.62
fanout-score-rank=1
prefix-density=1.86
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:01:34
                             Started mapping on |	Mar 04 07:01:34
                                    Finished on |	Mar 04 07:02:09
       Mapping speed, Million of reads per hour |	428.33

                          Number of input reads |	4164367
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2119925
                        Uniquely mapped reads % |	50.91%
                          Average mapped length |	24.66
                       Number of splices: Total |	2980
            Number of splices: Annotated (sjdb) |	610
                       Number of splices: GT/AG |	2816
                       Number of splices: GC/AG |	25
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	137
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.89
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.09
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1416851
             % of reads mapped to multiple loci |	34.02%
        Number of reads mapped to too many loci |	97569
             % of reads mapped to too many loci |	2.34%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.04%
                     % of reads unmapped: other |	0.69%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	627591	627591	627591
N_multimapping	1416851	1416851	1416851
N_noFeature	106548	135860	1485544
N_ambiguous	1143953	601410	22510
UnstrandedReadsAssigned:869424 PositiveStrandReadsAssigned:1382655 NegativeStrandReadsAssigned:611871
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030987 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: SRR5030987-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,164,367 reads, 987,224 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 704 rounds

 109283 SRR5030987.ke.tsv
  52636 SRR5030987.se.tsv
 161919 total
==> SRR5030987.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

==> SRR5030987.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030987 completed mapping pipeline successfully
