Starting /dee2/code/volunteer_pipeline.sh SRR5030982
    current disk space = 160578977792
    free memory = 73922832 
SRR5030982 SRAfilesize
d556f196d2d23c8f055bd776b4135c5d  SRR5030982.sra
SRR5030982.sra file validated
SRR5030982 is single end
SRR5030982 is conventional basespace
SRR5030982 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030982_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	32.30975	33.0	31.0	34.0	31.0	34.0
2	32.56875	34.0	31.0	34.0	31.0	34.0
3	32.61125	34.0	31.0	34.0	31.0	34.0
4	36.1465	37.0	35.0	37.0	35.0	37.0
5	36.05525	37.0	35.0	37.0	35.0	37.0
6	35.85875	37.0	35.0	37.0	35.0	37.0
7	35.802	37.0	35.0	37.0	35.0	37.0
8	35.8785	37.0	35.0	37.0	35.0	37.0
9	37.538	39.0	37.0	39.0	35.0	39.0
10	37.52825	39.0	37.0	39.0	35.0	39.0
11	37.10325	39.0	37.0	39.0	33.0	39.0
12	37.568	39.0	37.0	39.0	35.0	39.0
13	37.56825	39.0	37.0	39.0	35.0	39.0
14	38.901	40.0	38.0	41.0	35.0	41.0
15	38.86625	40.0	38.0	41.0	34.0	41.0
16	38.94375	40.0	38.0	41.0	35.0	41.0
17	39.10975	40.0	38.0	41.0	36.0	41.0
18	38.87875	41.0	38.0	41.0	35.0	41.0
19	38.76375	40.0	38.0	41.0	34.0	41.0
20	38.806	40.0	38.0	41.0	35.0	41.0
21	38.7785	40.0	38.0	41.0	34.0	41.0
22	38.745	40.0	38.0	41.0	34.0	41.0
23	38.488	40.0	38.0	41.0	34.0	41.0
24	38.778	40.0	38.0	41.0	34.0	41.0
25	38.943	40.0	38.0	41.0	35.0	41.0
26	38.7315	40.0	38.0	41.0	34.0	41.0
27	38.87425	40.0	38.0	41.0	35.0	41.0
28	38.5455	40.0	38.0	41.0	34.0	41.0
29	38.20925	40.0	38.0	41.0	33.0	41.0
30	38.16175	40.0	38.0	41.0	33.0	41.0
31	38.48475	40.0	38.0	41.0	34.0	41.0
32	38.50475	40.0	38.0	41.0	34.0	41.0
33	38.1955	40.0	38.0	41.0	33.0	41.0
34	38.078	40.0	38.0	41.0	33.0	41.0
35	37.956	40.0	38.0	41.0	33.0	41.0
36	37.82475	40.0	37.0	41.0	33.0	41.0
37	37.2375	39.0	37.0	41.0	31.0	41.0
38	37.07375	39.0	36.0	40.0	31.0	41.0
39	37.5385	39.0	37.0	41.0	32.0	41.0
40	37.669	40.0	37.0	41.0	33.0	41.0
41	37.951	40.0	37.0	41.0	33.0	41.0
42	37.7985	40.0	37.0	41.0	33.0	41.0
43	37.7415	40.0	37.0	41.0	33.0	41.0
44	37.588	40.0	37.0	41.0	33.0	41.0
45	37.65725	40.0	37.0	41.0	33.0	41.0
46	37.43825	40.0	37.0	41.0	33.0	41.0
47	36.7425	40.0	35.0	41.0	31.0	41.0
48	36.64025	39.0	35.0	41.0	30.0	41.0
49	36.76375	39.0	36.0	41.0	31.0	41.0
50	36.14425	39.0	35.0	41.0	30.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
16	1.0
17	0.0
18	2.0
19	3.0
20	4.0
21	6.0
22	4.0
23	5.0
24	6.0
25	10.0
26	9.0
27	20.0
28	27.0
29	40.0
30	49.0
31	57.0
32	93.0
33	130.0
34	168.0
35	219.0
36	274.0
37	445.0
38	746.0
39	1682.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.7	23.925	50.075	15.299999999999999
2	22.099724379854674	27.662240040090204	19.143071911801552	31.094963668253573
3	25.474999999999998	17.974999999999998	22.125	34.425
4	35.975	28.125	14.7	21.2
5	21.825	37.875	26.35	13.950000000000001
6	28.825	16.525000000000002	39.825	14.825
7	20.225	19.85	19.825	40.1
8	20.724999999999998	29.15	18.4	31.724999999999998
9	25.974999999999998	30.375000000000004	26.55	17.1
10	22.45	18.175	30.8	28.575
11	31.1	13.750000000000002	15.525	39.625
12	16.175	21.0	31.874999999999996	30.95
13	29.175	16.575	32.525	21.725
14	30.825000000000003	31.0	20.025000000000002	18.15
15	38.15	21.325	24.8	15.725
16	17.75	19.5	23.75	39.0
17	26.875	21.375	37.0	14.75
18	26.35	15.675	33.575	24.4
19	37.475	13.750000000000002	31.900000000000002	16.875
20	44.925	15.049999999999999	25.45	14.575
21	23.9	22.925	23.075000000000003	30.099999999999998
22	30.099999999999998	15.875	43.974999999999994	10.05
23	26.05	14.149999999999999	44.025	15.775
24	48.0	15.275	26.974999999999998	9.75
25	49.2	23.325000000000003	17.25	10.225
26	28.349999999999998	43.824999999999996	15.675	12.15
27	17.424999999999997	44.55	23.225	14.799999999999999
28	13.775	24.275	45.2	16.75
29	13.25	14.374999999999998	53.55	18.825
30	10.875	7.375	35.449999999999996	46.300000000000004
31	15.8	5.525	45.324999999999996	33.35
32	27.075	6.1	23.849999999999998	42.975
33	51.800000000000004	8.5	14.625	25.074999999999996
34	57.675	8.225	16.8	17.299999999999997
35	62.475	8.575000000000001	18.25	10.7
36	42.025	8.5	34.9	14.575
37	44.925	11.175	21.3	22.6
38	24.675	16.875	13.475000000000001	44.975
39	17.7	23.575	10.65	48.075
40	16.3	45.95	12.7	25.05
41	23.775	46.650000000000006	10.6	18.975
42	45.7	29.475	12.6	12.225
43	50.275000000000006	28.7	9.4	11.625
44	31.85	44.6	8.15	15.4
45	20.95	47.4	14.124999999999998	17.525
46	16.525000000000002	26.375	16.6	40.5
47	10.625	16.45	37.125	35.8
48	11.65	13.525	21.825	53.0
49	13.575000000000001	19.225	15.925	51.275000000000006
50	17.075000000000003	35.9	14.45	32.574999999999996
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	0.5
28	0.0
29	0.5
30	1.0
31	6.0
32	11.0
33	9.0
34	7.0
35	18.5
36	30.0
37	38.5
38	47.0
39	46.0
40	45.0
41	51.5
42	58.0
43	84.5
44	111.0
45	135.0
46	159.0
47	274.0
48	389.0
49	496.5
50	604.0
51	721.5
52	839.0
53	651.5
54	464.0
55	499.0
56	534.0
57	394.5
58	255.0
59	173.5
60	92.0
61	70.5
62	49.0
63	98.0
64	147.0
65	92.0
66	37.0
67	28.0
68	19.0
69	26.5
70	34.0
71	46.5
72	59.0
73	30.0
74	1.0
75	1.0
76	1.0
77	1.0
78	1.0
79	2.5
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	0.22499999999999998
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	39.1
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.89514066496163	29.675
2	9.143222506393862	7.1499999999999995
3	4.3478260869565215	5.1
4	3.0051150895140664	4.7
5	1.278772378516624	2.5
6	1.2148337595907928	2.85
7	0.5754475703324808	1.575
8	0.4475703324808184	1.4000000000000001
9	0.5754475703324808	2.025
>10	2.941176470588235	21.4
>50	0.319693094629156	9.475
>100	0.2557544757033248	12.15
>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	154	3.85	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	117	2.9250000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	111	2.775	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	104	2.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	98	2.45	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	77	1.925	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	75	1.875	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	72	1.7999999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	57	1.425	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	36	0.8999999999999999	No Hit
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	34	0.8500000000000001	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	25	0.625	RNA PCR Primer, Index 1 (100% over 35bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGC	21	0.525	RNA PCR Primer, Index 1 (100% over 50bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	17	0.42500000000000004	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	17	0.42500000000000004	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	12	0.3	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	11	0.27499999999999997	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 44bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	10	0.25	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	10	0.25	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	9	0.22499999999999998	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	6	0.15	No Hit
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TCCCTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTGCC	6	0.15	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	6	0.15	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	6	0.15	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	5	0.125	RNA PCR Primer, Index 1 (100% over 34bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATC	5	0.125	RNA PCR Primer, Index 1 (100% over 36bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	5	0.125	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>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	0.575	0.0	0.0	0.0
2	0.0	0.625	0.0	0.0	0.0
3	0.0	0.8	0.0	0.0	0.0
4	0.0	0.875	0.0	0.0	0.0
5	0.0	0.9	0.0	0.0	0.0
6	0.0	0.95	0.0	0.0	0.0
7	0.0	1.325	0.0	0.0	0.0
8	0.0	1.525	0.0	0.0	0.0
9	0.0	1.625	0.0	0.0	0.0
10	0.0	1.75	0.0	0.0	0.0
11	0.0	1.85	0.0	0.0	0.0
12	0.0	2.125	0.0	0.0	0.0
13	0.0	2.375	0.0	0.0	0.0
14	0.0	2.55	0.0	0.0	0.0
15	0.0	2.9	0.0	0.0	0.0
16	0.0	3.95	0.0	0.0	0.0
17	0.0	4.7	0.0	0.0	0.0
18	0.0	5.875	0.0	0.0	0.0
19	0.0	6.45	0.0	0.0	0.0
20	0.0	7.525	0.0	0.0	0.0
21	0.0	12.95	0.0	0.0	0.0
22	0.0	22.75	0.0	0.0	0.0
23	0.0	49.95	0.0	0.0	0.0
24	0.0	62.775	0.0	0.0	0.0
25	0.0	69.2	0.0	0.0	0.0
26	0.0	71.1	0.0	0.0	0.0
27	0.0	71.825	0.0	0.0	0.0
28	0.0	72.55	0.0	0.0	0.0
29	0.0	73.3	0.0	0.0	0.0
30	0.0	73.8	0.0	0.0	0.0
31	0.0	74.75	0.0	0.0	0.0
32	0.0	76.625	0.0	0.0	0.0
33	0.0	77.5	0.0	0.0	0.0
34	0.0	80.775	0.0	0.0	0.0
35	0.0	82.6	0.0	0.0	0.0
36	0.0	83.675	0.0	0.0	0.0
37	0.0	85.025	0.0	0.0	0.0
38	0.0	85.35	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TAGAACC	20	6.952051E-4	44.000004	8
GAGGTAG	20	6.952051E-4	44.000004	2
AACCGAA	20	6.952051E-4	44.000004	11
AATTTGT	20	6.952051E-4	44.000004	16
CCTGTAG	20	6.952051E-4	44.000004	4
GTGAGTT	20	6.952051E-4	44.000004	18
ACATTCA	40	5.315087E-9	44.000004	2
AGAACCG	20	6.952051E-4	44.000004	9
ACCGAAT	20	6.952051E-4	44.000004	12
GCTGTCG	40	5.315087E-9	44.000004	11
GAACCGA	20	6.952051E-4	44.000004	10
CGAATTT	20	6.952051E-4	44.000004	14
CCCTGTA	20	6.952051E-4	44.000004	3
GAATTTG	20	6.952051E-4	44.000004	15
GGTAGTA	20	6.952051E-4	44.000004	4
TGTAGAA	20	6.952051E-4	44.000004	6
TTGGCTT	20	6.952051E-4	44.000004	17
AGGTAGT	20	6.952051E-4	44.000004	3
CTGTCGG	40	5.315087E-9	44.000004	12
TGAGTTG	20	6.952051E-4	44.000004	19
>>END_MODULE
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194147 spots for SRR5030982.sra
Written 194147 spots for SRR5030982.sra
Read 194156 spots for SRR5030982.sra
Written 194156 spots for SRR5030982.sra
SRR ids: ['SRR5030982.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_b69r2prw
SRR5030982.sra spots: 2329773
blocks: [[1, 194147], [194148, 388294], [388295, 582441], [582442, 776588], [776589, 970735], [970736, 1164882], [1164883, 1359029], [1359030, 1553176], [1553177, 1747323], [1747324, 1941470], [1941471, 2135617], [2135618, 2329773]]
SRR5030982 file size 402729
SRR5030982 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030982 SRR5030982_1.fastq
Input file:	SRR5030982_1.fastq
trimmed:	SRR5030982-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 06:59:22 2020 >> started

Wed Mar  4 06:59:24 2020 >> done (1.630s)
2329773 reads processed; of these:
    372 ( 0.02%) short reads filtered out after trimming by size control
     17 ( 0.00%) empty reads filtered out after trimming by size control
2329384 (99.98%) reads available; of these:
 146594 ( 6.29%) trimmed reads available after processing
2182790 (93.71%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     94	  0.00%
 19	     89	  0.00%
 20	    154	  0.01%
 21	    208	  0.01%
 22	    347	  0.01%
 23	    425	  0.02%
 24	    409	  0.02%
 25	    531	  0.02%
 26	    415	  0.02%
 27	    514	  0.02%
 28	    699	  0.03%
 29	   1019	  0.04%
 30	    675	  0.03%
 31	    730	  0.03%
 32	    796	  0.03%
 33	   1018	  0.04%
 34	   1227	  0.05%
 35	   2287	  0.10%
 36	   2060	  0.09%
 37	   2432	  0.10%
 38	   2440	  0.10%
 39	   2626	  0.11%
 40	   2962	  0.13%
 41	   3167	  0.14%
 42	   4302	  0.18%
 43	   6112	  0.26%
 44	   7953	  0.34%
 45	   9927	  0.43%
 46	  14723	  0.63%
 47	  17735	  0.76%
 48	  25804	  1.11%
 49	  32714	  1.40%
 50	2182790	 93.71%
2329384 reads passed initial QC


criterion=sequence-density
sequence-density=84.69
sequence-density-rank=1
fanout-score=22.44
fanout-score-rank=1
prefix-density=87.11
prefix-fanout=21.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC


criterion=fanout-score
sequence-density=84.69
sequence-density-rank=1
fanout-score=22.44
fanout-score-rank=1
prefix-density=87.11
prefix-fanout=21.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC -o SRR5030982 -
Input file:	STDIN
trimmed:	SRR5030982-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC
-- 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 06:59:37 2020 >> started

Wed Mar  4 06:59:40 2020 >> done (2.909s)
2274575 reads processed; of these:
 135952 ( 5.98%) short reads filtered out after trimming by size control
  11471 ( 0.50%) empty reads filtered out after trimming by size control
2127152 (93.52%) reads available; of these:
2015489 (94.75%) trimmed reads available after processing
 111663 ( 5.25%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11967	  0.56%
 19	  21322	  1.00%
 20	 121669	  5.72%
 21	 234684	 11.03%
 22	 619059	 29.10%
 23	 281999	 13.26%
 24	 137124	  6.45%
 25	  40682	  1.91%
 26	  20760	  0.98%
 27	  16400	  0.77%
 28	  17627	  0.83%
 29	  14064	  0.66%
 30	  21782	  1.02%
 31	  48698	  2.29%
 32	  28506	  1.34%
 33	  80442	  3.78%
 34	  33535	  1.58%
 35	  29864	  1.40%
 36	  33416	  1.57%
 37	  14347	  0.67%
 38	  17115	  0.80%
 39	  14532	  0.68%
 40	  22493	  1.06%
 41	  26377	  1.24%
 42	  31862	  1.50%
 43	  22707	  1.07%
 44	  16073	  0.76%
 45	  22229	  1.05%
 46	  16378	  0.77%
 47	  12041	  0.57%
 48	   1201	  0.06%
 49	   2394	  0.11%
 50	  93803	  4.41%


criterion=sequence-density
sequence-density=7.67
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.49
sequence-density-rank=31
fanout-score=17.25
fanout-score-rank=1
prefix-density=8.49
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:00:01
                             Started mapping on |	Mar 04 07:00:01
                                    Finished on |	Mar 04 07:00:25
       Mapping speed, Million of reads per hour |	327.29

                          Number of input reads |	2181961
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1178664
                        Uniquely mapped reads % |	54.02%
                          Average mapped length |	24.96
                       Number of splices: Total |	1419
            Number of splices: Annotated (sjdb) |	280
                       Number of splices: GT/AG |	1334
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	68
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.77
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	689472
             % of reads mapped to multiple loci |	31.60%
        Number of reads mapped to too many loci |	57289
             % of reads mapped to too many loci |	2.63%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.70%
                     % of reads unmapped: other |	1.06%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	313825	313825	313825
N_multimapping	689472	689472	689472
N_noFeature	83697	99535	782496
N_ambiguous	632222	281087	10609
UnstrandedReadsAssigned:462745 PositiveStrandReadsAssigned:798042 NegativeStrandReadsAssigned:385559
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030982 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: SRR5030982-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,181,961 reads, 547,078 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,137 rounds

 109283 SRR5030982.ke.tsv
  52636 SRR5030982.se.tsv
 161919 total
==> SRR5030982.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

==> SRR5030982.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030982 completed mapping pipeline successfully
