Starting /dee2/code/volunteer_pipeline.sh SRR5030859
    current disk space = 160662749184
    free memory = 73928656 
SRR5030859 SRAfilesize
0024c8cc54480d61d910d9eb6279de36  SRR5030859.sra
SRR5030859.sra file validated
SRR5030859 is single end
SRR5030859 is conventional basespace
SRR5030859 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030859_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.496	34.0	31.0	34.0	31.0	34.0
2	32.70775	34.0	31.0	34.0	31.0	34.0
3	32.868	34.0	31.0	34.0	31.0	34.0
4	36.259	37.0	37.0	37.0	35.0	37.0
5	36.3305	37.0	37.0	37.0	35.0	37.0
6	36.22425	37.0	37.0	37.0	35.0	37.0
7	36.19925	37.0	36.0	37.0	35.0	37.0
8	36.1695	37.0	37.0	37.0	35.0	37.0
9	38.016	39.0	38.0	39.0	35.0	39.0
10	38.04875	39.0	39.0	39.0	35.0	39.0
11	37.949	39.0	38.0	39.0	35.0	39.0
12	37.97575	39.0	38.0	39.0	35.0	39.0
13	37.9495	39.0	38.0	39.0	35.0	39.0
14	39.3475	41.0	39.0	41.0	36.0	41.0
15	39.25925	41.0	39.0	41.0	36.0	41.0
16	39.27825	41.0	39.0	41.0	36.0	41.0
17	39.4705	41.0	39.0	41.0	37.0	41.0
18	39.4485	41.0	39.0	41.0	36.0	41.0
19	39.3155	41.0	39.0	41.0	36.0	41.0
20	39.36325	41.0	39.0	41.0	36.0	41.0
21	39.41725	41.0	39.0	41.0	36.0	41.0
22	39.34025	41.0	39.0	41.0	36.0	41.0
23	39.26675	41.0	39.0	41.0	36.0	41.0
24	38.9755	41.0	39.0	41.0	36.0	41.0
25	39.2275	41.0	39.0	41.0	36.0	41.0
26	39.2055	41.0	39.0	41.0	36.0	41.0
27	39.2755	41.0	39.0	41.0	36.0	41.0
28	39.0425	41.0	39.0	41.0	35.0	41.0
29	38.49475	40.0	38.0	41.0	34.0	41.0
30	38.6365	40.0	38.0	41.0	34.0	41.0
31	38.9325	41.0	39.0	41.0	35.0	41.0
32	39.11525	41.0	39.0	41.0	35.0	41.0
33	38.3945	40.0	38.0	41.0	34.0	41.0
34	38.214	40.0	38.0	41.0	33.0	41.0
35	38.02425	40.0	38.0	41.0	34.0	41.0
36	34.31225	38.0	31.0	40.0	23.0	41.0
37	35.79675	38.0	35.0	40.0	30.0	41.0
38	37.22275	39.0	37.0	40.0	32.0	41.0
39	37.158	39.0	37.0	40.0	31.0	41.0
40	37.20875	39.0	37.0	41.0	31.0	41.0
41	37.197	39.0	37.0	41.0	31.0	41.0
42	37.47	40.0	37.0	41.0	32.0	41.0
43	37.309	40.0	37.0	41.0	32.0	41.0
44	37.18275	40.0	37.0	41.0	31.0	41.0
45	36.90175	39.0	36.0	41.0	31.0	41.0
46	35.29225	38.0	34.0	40.0	27.0	41.0
47	36.07675	39.0	35.0	40.0	30.0	41.0
48	36.42775	39.0	36.0	41.0	30.0	41.0
49	35.44375	39.0	35.0	40.0	29.0	41.0
50	30.46325	34.0	27.0	38.0	2.0	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
16	2.0
17	0.0
18	0.0
19	3.0
20	7.0
21	7.0
22	3.0
23	10.0
24	5.0
25	9.0
26	13.0
27	23.0
28	30.0
29	35.0
30	54.0
31	56.0
32	96.0
33	101.0
34	127.0
35	187.0
36	306.0
37	495.0
38	1021.0
39	1410.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.75564475664827	21.32463622679378	55.31861515303562	14.601103863522328
2	20.200000000000003	24.875	19.15	35.775
3	27.1	21.475	20.25	31.175000000000004
4	30.55	25.825	13.55	30.075000000000003
5	17.025000000000002	47.5	23.275000000000002	12.2
6	36.175000000000004	15.825	34.125	13.875000000000002
7	16.05	19.425	26.525	38.0
8	25.5	29.4	13.0	32.1
9	24.2	35.125	26.825	13.850000000000001
10	22.8	22.225	31.15	23.825
11	23.849999999999998	12.950000000000001	17.1	46.1
12	13.025	18.099999999999998	33.625	35.25
13	33.900000000000006	20.45	27.025	18.625
14	27.650000000000002	35.975	19.275000000000002	17.1
15	33.708427106776696	25.531382845711427	25.756439109777446	15.003750937734434
16	15.950000000000001	24.175	20.474999999999998	39.4
17	19.85	20.4	44.9	14.85
18	21.4	19.375	32.35	26.875
19	39.225	13.3	29.549999999999997	17.925
20	41.575	13.975000000000001	30.45	14.000000000000002
21	23.0	16.8	30.325000000000003	29.875
22	27.150000000000002	13.125	50.0	9.725
23	29.049999999999997	12.8	43.775	14.374999999999998
24	52.449999999999996	16.1	22.725	8.725
25	47.449999999999996	27.125	15.45	9.975000000000001
26	24.55	49.0	14.674999999999999	11.774999999999999
27	15.375	45.975	27.175	11.475
28	11.35	23.1	50.475	15.075
29	9.375	13.55	56.375	20.7
30	9.1	7.375	35.85	47.675
31	15.725	5.3	46.775	32.2
32	29.775000000000002	7.225	18.4	44.6
33	57.4	8.05	13.475000000000001	21.075
34	60.699999999999996	7.95	16.675	14.674999999999999
35	62.275000000000006	6.825	20.200000000000003	10.7
36	43.175000000000004	8.774999999999999	33.45	14.6
37	45.324999999999996	9.875	17.724999999999998	27.075
38	19.950000000000003	16.85	12.174999999999999	51.025
39	16.1	27.975	8.25	47.675
40	16.1	50.324999999999996	11.15	22.425
41	27.525	46.6	9.3	16.575
42	51.1	29.95	9.825000000000001	9.125
43	47.825	33.85	9.700000000000001	8.625
44	26.025	51.324999999999996	8.3	14.35
45	17.549999999999997	48.3	13.875000000000002	20.275000000000002
46	10.025	26.075	20.724999999999998	43.175000000000004
47	7.475	16.1	40.275	36.15
48	9.15	14.174999999999999	18.85	57.825
49	14.424999999999999	20.75	14.475	50.349999999999994
50	19.85	36.9	14.875	28.375
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.5
4	1.0
5	0.5
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	0.5
18	1.0
19	1.0
20	1.0
21	1.0
22	1.0
23	1.5
24	2.0
25	1.5
26	1.0
27	1.0
28	1.0
29	1.0
30	1.0
31	8.0
32	15.0
33	21.0
34	27.0
35	34.5
36	42.0
37	44.0
38	46.0
39	52.5
40	59.0
41	49.0
42	39.0
43	78.0
44	117.0
45	151.0
46	185.0
47	301.0
48	417.0
49	566.5
50	716.0
51	804.0
52	892.0
53	657.0
54	422.0
55	461.5
56	501.0
57	380.0
58	259.0
59	163.0
60	67.0
61	49.5
62	32.0
63	56.0
64	80.0
65	56.5
66	33.0
67	22.0
68	11.0
69	8.5
70	6.0
71	9.5
72	13.0
73	7.5
74	2.0
75	2.0
76	2.0
77	3.0
78	4.0
79	3.5
80	3.0
81	1.5
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	0.35000000000000003
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	0.025
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	37.974999999999994
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.19354838709677	28.175
2	10.994075049374588	8.35
3	4.081632653061225	4.65
4	2.7649769585253456	4.2
5	1.119157340355497	2.125
6	0.8558262014483212	1.95
7	0.7899934167215273	2.1
8	0.7241606319947334	2.1999999999999997
9	0.32916392363396973	1.125
>10	3.686635944700461	27.950000000000003
>50	0.19749835418038184	5.475
>100	0.26333113890717574	11.700000000000001
>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	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	120	3.0	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	110	2.75	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	106	2.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	100	2.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	52	1.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	50	1.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	48	1.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	47	1.175	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	39	0.975	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	39	0.975	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	30	0.75	RNA PCR Primer, Index 1 (100% over 30bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTC	22	0.5499999999999999	RNA PCR Primer, Index 45 (100% over 44bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGC	21	0.525	RNA PCR Primer, Index 45 (100% over 50bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	20	0.5	RNA PCR Primer, Index 5 (97% over 35bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	19	0.475	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	17	0.42500000000000004	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	17	0.42500000000000004	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	16	0.4	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	12	0.3	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	12	0.3	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	10	0.25	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	9	0.22499999999999998	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	8	0.2	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	8	0.2	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCT	7	0.17500000000000002	RNA PCR Primer, Index 45 (100% over 43bp)
CAACGGAATCCCAAAAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	6	0.15	No Hit
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	6	0.15	No Hit
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	6	0.15	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	6	0.15	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	6	0.15	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	5	0.125	RNA PCR Primer, Index 3 (100% over 34bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	5	0.125	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	5	0.125	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGTACCGTGAGTAATAATGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
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	0.525	0.0	0.0	0.0
2	0.0	0.525	0.0	0.0	0.0
3	0.0	0.6	0.0	0.0	0.0
4	0.0	0.6	0.0	0.0	0.0
5	0.0	0.625	0.0	0.0	0.0
6	0.0	0.7	0.0	0.0	0.0
7	0.0	1.4	0.0	0.0	0.0
8	0.0	1.7	0.0	0.0	0.0
9	0.0	1.75	0.0	0.0	0.0
10	0.0	1.775	0.0	0.0	0.0
11	0.0	2.2	0.0	0.0	0.0
12	0.0	2.525	0.0	0.0	0.0
13	0.0	2.725	0.0	0.0	0.0
14	0.0	2.95	0.0	0.0	0.0
15	0.0	3.525	0.0	0.0	0.0
16	0.0	4.35	0.0	0.0	0.0
17	0.0	5.025	0.0	0.0	0.0
18	0.0	5.975	0.0	0.0	0.0
19	0.0	6.5	0.0	0.0	0.0
20	0.0	7.45	0.0	0.0	0.0
21	0.0	14.25	0.0	0.0	0.0
22	0.0	27.775	0.0	0.0	0.0
23	0.0	57.875	0.0	0.0	0.0
24	0.0	68.175	0.0	0.0	0.0
25	0.0	74.325	0.0	0.0	0.0
26	0.0	75.825	0.0	0.0	0.0
27	0.0	76.375	0.0	0.0	0.0
28	0.0	76.75	0.0	0.0	0.0
29	0.0	77.15	0.0	0.0	0.0
30	0.0	77.35	0.0	0.0	0.0
31	0.0	77.925	0.0	0.0	0.0
32	0.0	78.625	0.0	0.0	0.0
33	0.0	79.4	0.0	0.0	0.0
34	0.0	81.275	0.0	0.0	0.0
35	0.0	82.125	0.0	0.0	0.0
36	0.0	82.425	0.0	0.0	0.0
37	0.0	83.25	0.0	0.0	0.0
38	0.0	83.7	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	20	6.952051E-4	44.000004	8
GGTGAGT	20	6.952051E-4	44.000004	17
ACGCTGT	20	6.952051E-4	44.000004	9
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
TTCAACG	20	6.952051E-4	44.000004	5
CGGGGGC	20	6.952051E-4	44.000004	32
GAAGCTT	20	6.952051E-4	44.000004	19
TCGGTGA	20	6.952051E-4	44.000004	15
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
CTTGGTG	20	6.952051E-4	44.000004	16
GGGGGCC	20	6.952051E-4	44.000004	33
CTGGAAG	20	6.952051E-4	44.000004	16
CGGTGAG	20	6.952051E-4	44.000004	16
GGCCAAG	20	6.952051E-4	44.000004	36
GCTTGGT	20	6.952051E-4	44.000004	15
GACTGGA	20	6.952051E-4	44.000004	14
CTCGGGG	20	6.952051E-4	44.000004	30
TTGGTGG	20	6.952051E-4	44.000004	17
>>END_MODULE
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254838 spots for SRR5030859.sra
Written 254838 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
Read 254836 spots for SRR5030859.sra
Written 254836 spots for SRR5030859.sra
SRR ids: ['SRR5030859.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_n1mnqtio
SRR5030859.sra spots: 3058034
blocks: [[1, 254836], [254837, 509672], [509673, 764508], [764509, 1019344], [1019345, 1274180], [1274181, 1529016], [1529017, 1783852], [1783853, 2038688], [2038689, 2293524], [2293525, 2548360], [2548361, 2803196], [2803197, 3058034]]
SRR5030859 file size 528949
SRR5030859 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030859 SRR5030859_1.fastq
Input file:	SRR5030859_1.fastq
trimmed:	SRR5030859-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 06:30:23 2020 >> started

Wed Mar  4 06:30:25 2020 >> done (1.727s)
3058034 reads processed; of these:
    101 ( 0.00%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
3057927 (100.00%) reads available; of these:
 164948 ( 5.39%) trimmed reads available after processing
2892979 (94.61%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     43	  0.00%
 19	     55	  0.00%
 20	    130	  0.00%
 21	    163	  0.01%
 22	    254	  0.01%
 23	    302	  0.01%
 24	    340	  0.01%
 25	    424	  0.01%
 26	    377	  0.01%
 27	    475	  0.02%
 28	    640	  0.02%
 29	    929	  0.03%
 30	    667	  0.02%
 31	    769	  0.03%
 32	    740	  0.02%
 33	   1137	  0.04%
 34	   2839	  0.09%
 35	   2617	  0.09%
 36	   1993	  0.07%
 37	   2171	  0.07%
 38	   2408	  0.08%
 39	   2443	  0.08%
 40	   2608	  0.09%
 41	   2986	  0.10%
 42	   3856	  0.13%
 43	   5155	  0.17%
 44	   9865	  0.32%
 45	  10477	  0.34%
 46	   9974	  0.33%
 47	  14412	  0.47%
 48	  34041	  1.11%
 49	  49658	  1.62%
 50	2892979	 94.61%
3057927 reads passed initial QC


criterion=sequence-density
sequence-density=84.77
sequence-density-rank=1
fanout-score=18.55
fanout-score-rank=1
prefix-density=86.10
prefix-fanout=18.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC


criterion=fanout-score
sequence-density=84.77
sequence-density-rank=1
fanout-score=18.55
fanout-score-rank=1
prefix-density=86.10
prefix-fanout=18.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC -o SRR5030859 -
Input file:	STDIN
trimmed:	SRR5030859-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCATTCATCTCGTATGCC
-- 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 06:30:40 2020 >> started

Wed Mar  4 06:30:45 2020 >> done (4.566s)
2985976 reads processed; of these:
 167275 ( 5.60%) short reads filtered out after trimming by size control
  15918 ( 0.53%) empty reads filtered out after trimming by size control
2802783 (93.86%) reads available; of these:
2565515 (91.53%) trimmed reads available after processing
 237268 ( 8.47%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16720	  0.60%
 19	  29773	  1.06%
 20	 197792	  7.06%
 21	 398484	 14.22%
 22	 919855	 32.82%
 23	 343985	 12.27%
 24	 184171	  6.57%
 25	  45005	  1.61%
 26	  21428	  0.76%
 27	  15860	  0.57%
 28	  16908	  0.60%
 29	  11974	  0.43%
 30	  17078	  0.61%
 31	  21432	  0.76%
 32	  22745	  0.81%
 33	  60016	  2.14%
 34	  23267	  0.83%
 35	  19282	  0.69%
 36	  20184	  0.72%
 37	  10834	  0.39%
 38	  11877	  0.42%
 39	  12992	  0.46%
 40	  19423	  0.69%
 41	  26340	  0.94%
 42	  30785	  1.10%
 43	  20430	  0.73%
 44	  17160	  0.61%
 45	  20715	  0.74%
 46	  14477	  0.52%
 47	  10922	  0.39%
 48	   2488	  0.09%
 49	   9207	  0.33%
 50	 209174	  7.46%


criterion=sequence-density
sequence-density=4.69
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=38
fanout-score=49.44
fanout-score-rank=1
prefix-density=0.99
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:31:07
                             Started mapping on |	Mar 04 06:31:07
                                    Finished on |	Mar 04 06:31:32
       Mapping speed, Million of reads per hour |	413.96

                          Number of input reads |	2874734
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1741364
                        Uniquely mapped reads % |	60.57%
                          Average mapped length |	25.96
                       Number of splices: Total |	1040
            Number of splices: Annotated (sjdb) |	169
                       Number of splices: GT/AG |	946
                       Number of splices: GC/AG |	12
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	81
                      Mismatch rate per base, % |	0.15%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.47
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	866709
             % of reads mapped to multiple loci |	30.15%
        Number of reads mapped to too many loci |	49535
             % of reads mapped to too many loci |	1.72%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.08%
                     % of reads unmapped: other |	0.47%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	266661	266661	266661
N_multimapping	866709	866709	866709
N_noFeature	58278	72847	1186734
N_ambiguous	1000722	523536	15542
UnstrandedReadsAssigned:682364 PositiveStrandReadsAssigned:1144981 NegativeStrandReadsAssigned:539088
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030859 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: SRR5030859-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,874,734 reads, 828,201 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,146 rounds

 109283 SRR5030859.ke.tsv
  52636 SRR5030859.se.tsv
 161919 total
==> SRR5030859.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

==> SRR5030859.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030859 completed mapping pipeline successfully
