Starting /dee2/code/volunteer_pipeline.sh SRR5031036
    current disk space = 160526745600
    free memory = 73929424 
SRR5031036 SRAfilesize
0d58aeae0618443bdfa71a09759e0831  SRR5031036.sra
SRR5031036.sra file validated
SRR5031036 is single end
SRR5031036 is conventional basespace
SRR5031036 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031036_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	32.30425	33.0	31.0	34.0	31.0	34.0
2	32.554	34.0	31.0	34.0	31.0	34.0
3	32.605	34.0	31.0	34.0	31.0	34.0
4	36.2345	37.0	35.0	37.0	35.0	37.0
5	35.8545	37.0	35.0	37.0	35.0	37.0
6	35.875	37.0	35.0	37.0	35.0	37.0
7	35.999	37.0	35.0	37.0	35.0	37.0
8	35.8935	37.0	35.0	37.0	35.0	37.0
9	37.6445	39.0	37.0	39.0	35.0	39.0
10	37.836	39.0	37.0	39.0	35.0	39.0
11	37.60375	39.0	37.0	39.0	35.0	39.0
12	37.70075	39.0	37.0	39.0	35.0	39.0
13	37.651	39.0	37.0	39.0	35.0	39.0
14	39.15025	40.0	38.0	41.0	36.0	41.0
15	38.99225	40.0	38.0	41.0	36.0	41.0
16	39.03475	40.0	38.0	41.0	35.0	41.0
17	38.9	40.0	38.0	41.0	35.0	41.0
18	38.9025	40.0	38.0	41.0	35.0	41.0
19	38.664	40.0	38.0	41.0	34.0	41.0
20	38.79425	40.0	38.0	41.0	34.0	41.0
21	38.79675	40.0	38.0	41.0	34.0	41.0
22	39.03025	40.0	39.0	41.0	36.0	41.0
23	38.72	40.0	38.0	41.0	34.0	41.0
24	38.70575	40.0	38.0	41.0	34.0	41.0
25	38.818	40.0	38.0	41.0	34.0	41.0
26	38.53025	40.0	38.0	41.0	34.0	41.0
27	38.592	40.0	38.0	41.0	34.0	41.0
28	38.65425	40.0	38.0	41.0	34.0	41.0
29	38.284	40.0	38.0	41.0	33.0	41.0
30	38.252	40.0	38.0	41.0	33.0	41.0
31	38.5125	40.0	38.0	41.0	34.0	41.0
32	38.53475	40.0	38.0	41.0	34.0	41.0
33	38.5055	40.0	38.0	41.0	34.0	41.0
34	38.6075	40.0	38.0	41.0	35.0	41.0
35	38.42025	40.0	38.0	41.0	34.0	41.0
36	37.98175	40.0	37.0	41.0	33.0	41.0
37	37.52875	40.0	37.0	41.0	31.0	41.0
38	36.9325	39.0	36.0	41.0	30.0	41.0
39	37.46275	40.0	37.0	41.0	32.0	41.0
40	37.72875	40.0	37.0	41.0	33.0	41.0
41	37.85	40.0	37.0	41.0	33.0	41.0
42	38.0985	40.0	38.0	41.0	33.0	41.0
43	38.2925	40.0	38.0	41.0	34.0	41.0
44	38.00975	40.0	38.0	41.0	33.0	41.0
45	37.93075	40.0	38.0	41.0	33.0	41.0
46	37.87825	40.0	37.0	41.0	33.0	41.0
47	37.527	40.0	37.0	41.0	32.0	41.0
48	37.26075	40.0	36.0	41.0	31.0	41.0
49	37.35075	40.0	36.0	41.0	31.0	41.0
50	36.93825	40.0	36.0	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
17	1.0
18	1.0
19	1.0
20	3.0
21	3.0
22	4.0
23	0.0
24	5.0
25	4.0
26	12.0
27	30.0
28	31.0
29	35.0
30	47.0
31	58.0
32	82.0
33	105.0
34	150.0
35	194.0
36	268.0
37	446.0
38	729.0
39	1791.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.15	26.224999999999998	49.925000000000004	15.7
2	25.137706559839764	27.916875312969452	18.052078117175764	28.893340010015024
3	23.599999999999998	19.85	20.7	35.85
4	33.425	27.85	14.05	24.675
5	23.825	37.225	27.85	11.1
6	34.55	14.475	35.5	15.475
7	15.75	22.95	21.875	39.425
8	25.825	28.275	16.5	29.4
9	21.099999999999998	34.599999999999994	27.900000000000002	16.400000000000002
10	20.875	23.1	28.425	27.6
11	33.125	10.375	17.549999999999997	38.95
12	16.125	19.475	30.025000000000002	34.375
13	30.349999999999998	17.525	33.975	18.15
14	31.924999999999997	30.25	22.35	15.475
15	35.825	24.45	25.974999999999998	13.750000000000002
16	21.325	17.925	23.400000000000002	37.35
17	25.174999999999997	25.525	35.949999999999996	13.350000000000001
18	24.325	18.625	30.0	27.05
19	35.15	14.774999999999999	32.925	17.150000000000002
20	45.45	13.875000000000002	27.950000000000003	12.725
21	23.674999999999997	19.875	27.750000000000004	28.7
22	29.549999999999997	11.425	48.175000000000004	10.85
23	25.1	12.825000000000001	47.375	14.7
24	52.5	12.525	27.3	7.675
25	52.800000000000004	23.225	14.924999999999999	9.049999999999999
26	28.975	46.150000000000006	13.375	11.5
27	15.85	49.35	22.425	12.375
28	10.674999999999999	25.575	49.375	14.374999999999998
29	12.275	12.475	56.925000000000004	18.325
30	10.15	6.175	37.775	45.9
31	14.124999999999998	5.65	47.175	33.050000000000004
32	26.5	5.2749999999999995	23.1	45.125
33	53.800000000000004	9.025	13.725000000000001	23.45
34	64.17500000000001	7.2749999999999995	14.774999999999999	13.775
35	65.85	6.425	18.375	9.35
36	42.775	7.3999999999999995	37.3	12.525
37	46.300000000000004	10.299999999999999	21.65	21.75
38	24.025	15.225	12.525	48.225
39	15.4	22.35	10.424999999999999	51.824999999999996
40	14.35	47.8	11.525	26.325
41	23.45	51.225	8.0	17.325
42	49.325	30.25	11.0	9.425
43	54.325	27.450000000000003	7.449999999999999	10.775
44	32.475	48.3	7.249999999999999	11.975
45	18.275	52.55	11.025	18.15
46	13.3	26.875	17.474999999999998	42.35
47	8.450000000000001	14.549999999999999	40.150000000000006	36.85
48	10.5	11.5	21.175	56.825
49	11.325000000000001	18.775	14.174999999999999	55.725
50	17.1	38.175	11.875	32.85
>>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	0.5
26	1.0
27	0.5
28	0.0
29	0.5
30	1.0
31	3.5
32	6.0
33	7.0
34	8.0
35	14.5
36	21.0
37	24.0
38	27.0
39	33.5
40	40.0
41	48.0
42	56.0
43	102.0
44	148.0
45	168.5
46	189.0
47	302.0
48	415.0
49	534.5
50	654.0
51	782.0
52	910.0
53	650.5
54	391.0
55	447.5
56	504.0
57	378.5
58	253.0
59	167.5
60	82.0
61	66.5
62	51.0
63	87.0
64	123.0
65	74.5
66	26.0
67	17.5
68	9.0
69	16.5
70	24.0
71	36.0
72	48.0
73	26.0
74	4.0
75	2.5
76	1.0
77	1.0
78	1.0
79	2.5
80	4.0
81	3.0
82	2.0
83	1.0
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	0.15
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	36.425000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.39945092656143	27.1
2	10.363761153054222	7.55
3	4.186684969114619	4.575
4	3.0199039121482496	4.3999999999999995
5	1.4413177762525737	2.625
6	1.4413177762525737	3.15
7	0.41180507892930684	1.05
8	0.41180507892930684	1.2
9	0.6863417982155113	2.25
>10	2.8826355525051475	18.65
>50	0.4804392587508579	13.200000000000001
>100	0.27453671928620454	14.249999999999998
>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	176	4.3999999999999995	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	137	3.4250000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	126	3.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	85	2.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	83	2.075	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	80	2.0	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	75	1.875	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	73	1.825	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	70	1.7500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	38	0.95	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	22	0.5499999999999999	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	18	0.44999999999999996	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	17	0.42500000000000004	RNA PCR Primer, Index 5 (100% over 35bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	16	0.4	RNA PCR Primer, Index 1 (100% over 31bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	15	0.375	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	14	0.35000000000000003	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGC	12	0.3	RNA PCR Primer, Index 8 (100% over 50bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTC	9	0.22499999999999998	RNA PCR Primer, Index 8 (100% over 44bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	8	0.2	RNA PCR Primer, Index 1 (100% over 33bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	6	0.15	RNA PCR Primer, Index 5 (100% over 35bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	6	0.15	RNA PCR Primer, Index 1 (100% over 34bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	5	0.125	No Hit
TGCGGGGCTAGGGCTAACAGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	5	0.125	RNA PCR Primer, Index 1 (100% over 24bp)
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	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	0.3	0.0	0.0	0.0
2	0.0	0.325	0.0	0.0	0.0
3	0.0	0.425	0.0	0.0	0.0
4	0.0	0.425	0.0	0.0	0.0
5	0.0	0.5	0.0	0.0	0.0
6	0.0	0.55	0.0	0.0	0.0
7	0.0	0.925	0.0	0.0	0.0
8	0.0	0.975	0.0	0.0	0.0
9	0.0	1.0	0.0	0.0	0.0
10	0.0	1.2	0.0	0.0	0.0
11	0.0	1.45	0.0	0.0	0.0
12	0.0	1.675	0.0	0.0	0.0
13	0.0	1.9	0.0	0.0	0.0
14	0.0	2.325	0.0	0.0	0.0
15	0.0	2.625	0.0	0.0	0.0
16	0.0	3.55	0.0	0.0	0.0
17	0.0	4.25	0.0	0.0	0.0
18	0.0	5.275	0.0	0.0	0.0
19	0.0	5.75	0.0	0.0	0.0
20	0.0	6.975	0.0	0.0	0.0
21	0.0	11.675	0.0	0.0	0.0
22	0.0	22.8	0.0	0.0	0.0
23	0.0	53.6	0.0	0.0	0.0
24	0.0	68.175	0.0	0.0	0.0
25	0.0	74.475	0.0	0.0	0.0
26	0.0	75.775	0.0	0.0	0.0
27	0.0	76.525	0.0	0.0	0.0
28	0.0	77.05	0.0	0.0	0.0
29	0.0	77.875	0.0	0.0	0.0
30	0.0	78.3	0.0	0.0	0.0
31	0.0	79.125	0.0	0.0	0.0
32	0.0	80.275	0.0	0.0	0.0
33	0.0	81.425	0.0	0.0	0.0
34	0.0	84.85	0.0	0.0	0.0
35	0.0	85.975	0.0	0.0	0.0
36	0.0	86.675	0.0	0.0	0.0
37	0.0	87.25	0.0	0.0	0.0
38	0.0	87.825	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGTTGGA	45	2.728484E-10	44.000004	20
GTTTGGA	20	6.952051E-4	44.000004	20
CTTTAAC	20	6.952051E-4	44.000004	12
CCTGTTG	20	6.952051E-4	44.000004	18
AACCTGT	20	6.952051E-4	44.000004	16
ACCTGTT	20	6.952051E-4	44.000004	17
TAACCTG	20	6.952051E-4	44.000004	15
ACCCTTT	20	6.952051E-4	44.000004	9
CCTTTAA	20	6.952051E-4	44.000004	11
GACCCTT	20	6.952051E-4	44.000004	8
CCCTTTA	20	6.952051E-4	44.000004	10
CTGTTGG	45	2.728484E-10	44.000004	19
TTAACCT	20	6.952051E-4	44.000004	14
TTTAACC	20	6.952051E-4	44.000004	13
TGAGACC	25	3.6958358E-5	44.0	5
ACTGTTG	25	3.6958358E-5	44.0	18
GAGGTAG	25	3.6958358E-5	44.0	2
GTTGAAG	25	3.6958358E-5	44.0	10
CAGTTGA	25	3.6958358E-5	44.0	8
CTGAGCT	75	0.0	44.0	11
>>END_MODULE
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
Read 165243 spots for SRR5031036.sra
Written 165243 spots for SRR5031036.sra
Read 165242 spots for SRR5031036.sra
Written 165242 spots for SRR5031036.sra
SRR ids: ['SRR5031036.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_p6szhz9o
SRR5031036.sra spots: 1982905
blocks: [[1, 165242], [165243, 330484], [330485, 495726], [495727, 660968], [660969, 826210], [826211, 991452], [991453, 1156694], [1156695, 1321936], [1321937, 1487178], [1487179, 1652420], [1652421, 1817662], [1817663, 1982905]]
SRR5031036 file size 342611
SRR5031036 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031036 SRR5031036_1.fastq
Input file:	SRR5031036_1.fastq
trimmed:	SRR5031036-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 07:11:03 2020 >> started

Wed Mar  4 07:11:04 2020 >> done (1.514s)
1982905 reads processed; of these:
    132 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
1982764 (99.99%) reads available; of these:
  95111 ( 4.80%) trimmed reads available after processing
1887653 (95.20%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     38	  0.00%
 19	     56	  0.00%
 20	    113	  0.01%
 21	    137	  0.01%
 22	    266	  0.01%
 23	    319	  0.02%
 24	    314	  0.02%
 25	    388	  0.02%
 26	    324	  0.02%
 27	    405	  0.02%
 28	    485	  0.02%
 29	    738	  0.04%
 30	    442	  0.02%
 31	    514	  0.03%
 32	    575	  0.03%
 33	    756	  0.04%
 34	    946	  0.05%
 35	   1916	  0.10%
 36	   1561	  0.08%
 37	   1891	  0.10%
 38	   1725	  0.09%
 39	   1816	  0.09%
 40	   2093	  0.11%
 41	   2026	  0.10%
 42	   2575	  0.13%
 43	   3836	  0.19%
 44	   4882	  0.25%
 45	   6339	  0.32%
 46	   9333	  0.47%
 47	  11396	  0.57%
 48	  18299	  0.92%
 49	  18607	  0.94%
 50	1887653	 95.20%
1982764 reads passed initial QC


criterion=sequence-density
sequence-density=86.67
sequence-density-rank=1
fanout-score=21.01
fanout-score-rank=1
prefix-density=88.62
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC


criterion=fanout-score
sequence-density=86.67
sequence-density-rank=1
fanout-score=21.01
fanout-score-rank=1
prefix-density=88.62
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC -o SRR5031036 -
Input file:	STDIN
trimmed:	SRR5031036-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC
-- 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 07:11:17 2020 >> started

Wed Mar  4 07:11:20 2020 >> done (3.072s)
1937183 reads processed; of these:
  93427 ( 4.82%) short reads filtered out after trimming by size control
  10541 ( 0.54%) empty reads filtered out after trimming by size control
1833215 (94.63%) reads available; of these:
1746661 (95.28%) trimmed reads available after processing
  86554 ( 4.72%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  10522	  0.57%
 19	  19366	  1.06%
 20	  96966	  5.29%
 21	 230688	 12.58%
 22	 611147	 33.34%
 23	 273479	 14.92%
 24	 114052	  6.22%
 25	  29774	  1.62%
 26	  16050	  0.88%
 27	  13973	  0.76%
 28	  15425	  0.84%
 29	  13230	  0.72%
 30	  16776	  0.92%
 31	  18925	  1.03%
 32	  22708	  1.24%
 33	  64024	  3.49%
 34	  19757	  1.08%
 35	  15103	  0.82%
 36	  16783	  0.92%
 37	   9207	  0.50%
 38	  10699	  0.58%
 39	   9901	  0.54%
 40	  17183	  0.94%
 41	  18083	  0.99%
 42	  20180	  1.10%
 43	  14179	  0.77%
 44	   9824	  0.54%
 45	  12799	  0.70%
 46	   9609	  0.52%
 47	   8027	  0.44%
 48	    857	  0.05%
 49	   1128	  0.06%
 50	  72791	  3.97%


criterion=sequence-density
sequence-density=7.52
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=2.18
sequence-density-rank=7
fanout-score=21.18
fanout-score-rank=1
prefix-density=2.24
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGC
                                 Started job on |	Mar 04 07:11:43
                             Started mapping on |	Mar 04 07:11:43
                                    Finished on |	Mar 04 07:12:08
       Mapping speed, Million of reads per hour |	270.55

                          Number of input reads |	1878796
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	964728
                        Uniquely mapped reads % |	51.35%
                          Average mapped length |	24.41
                       Number of splices: Total |	1160
            Number of splices: Annotated (sjdb) |	214
                       Number of splices: GT/AG |	1077
                       Number of splices: GC/AG |	20
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	63
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.83
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	670541
             % of reads mapped to multiple loci |	35.69%
        Number of reads mapped to too many loci |	36541
             % of reads mapped to too many loci |	1.94%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.46%
                     % of reads unmapped: other |	0.56%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	243527	243527	243527
N_multimapping	670541	670541	670541
N_noFeature	48594	59430	666540
N_ambiguous	552558	294040	9836
UnstrandedReadsAssigned:363576 PositiveStrandReadsAssigned:611258 NegativeStrandReadsAssigned:288352
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031036 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: SRR5031036-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,878,796 reads, 486,325 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,072 rounds

 109283 SRR5031036.ke.tsv
  52636 SRR5031036.se.tsv
 161919 total
==> SRR5031036.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

==> SRR5031036.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031036 completed mapping pipeline successfully
