Starting /dee2/code/volunteer_pipeline.sh SRR5030928
    current disk space = 160620855296
    free memory = 73951232 
SRR5030928 SRAfilesize
89e73f5f5af98c2f2a44a361f889c3fe  SRR5030928.sra
SRR5030928.sra file validated
SRR5030928 is single end
SRR5030928 is conventional basespace
SRR5030928 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030928_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.39575	33.0	31.0	34.0	31.0	34.0
2	32.725	34.0	31.0	34.0	31.0	34.0
3	32.74275	34.0	31.0	34.0	31.0	34.0
4	36.20675	37.0	37.0	37.0	35.0	37.0
5	36.20825	37.0	37.0	37.0	35.0	37.0
6	35.9355	37.0	35.0	37.0	35.0	37.0
7	36.081	37.0	35.0	37.0	35.0	37.0
8	36.192	37.0	36.0	37.0	35.0	37.0
9	37.9015	39.0	38.0	39.0	35.0	39.0
10	37.90425	39.0	38.0	39.0	35.0	39.0
11	37.92725	39.0	38.0	39.0	35.0	39.0
12	37.8885	39.0	38.0	39.0	35.0	39.0
13	37.86175	39.0	38.0	39.0	35.0	39.0
14	39.30575	41.0	39.0	41.0	36.0	41.0
15	39.34425	41.0	39.0	41.0	36.0	41.0
16	39.03675	40.0	38.0	41.0	36.0	41.0
17	39.2635	41.0	39.0	41.0	36.0	41.0
18	39.30125	41.0	39.0	41.0	36.0	41.0
19	38.979	40.0	39.0	41.0	36.0	41.0
20	39.0845	40.0	39.0	41.0	35.0	41.0
21	39.15	40.0	39.0	41.0	36.0	41.0
22	39.3555	41.0	39.0	41.0	36.0	41.0
23	39.152	40.0	39.0	41.0	36.0	41.0
24	38.23275	40.0	38.0	41.0	33.0	41.0
25	38.74375	40.0	39.0	41.0	34.0	41.0
26	38.7255	40.0	38.0	41.0	34.0	41.0
27	38.72875	40.0	38.0	41.0	34.0	41.0
28	38.857	40.0	39.0	41.0	35.0	41.0
29	38.898	41.0	38.0	41.0	35.0	41.0
30	38.57025	40.0	38.0	41.0	34.0	41.0
31	38.868	41.0	39.0	41.0	35.0	41.0
32	39.05825	41.0	39.0	41.0	35.0	41.0
33	37.6305	40.0	38.0	41.0	32.0	41.0
34	36.89375	40.0	37.0	41.0	30.0	41.0
35	32.20875	38.0	30.0	40.0	8.0	41.0
36	28.09425	36.0	15.0	40.0	8.0	41.0
37	28.31075	35.0	20.0	39.0	6.0	40.0
38	31.3255	36.0	30.0	39.0	2.0	40.0
39	30.74125	36.0	27.0	40.0	2.0	41.0
40	31.75925	37.0	31.0	40.0	2.0	41.0
41	29.5935	36.0	24.0	40.0	2.0	41.0
42	31.4975	37.0	30.0	40.0	2.0	41.0
43	29.6335	36.0	26.0	40.0	2.0	41.0
44	30.828	37.0	30.0	40.0	2.0	41.0
45	28.451	36.0	22.0	40.0	2.0	41.0
46	26.4885	34.0	7.0	39.0	2.0	41.0
47	26.44875	34.0	2.0	39.0	2.0	41.0
48	27.432	35.0	2.0	40.0	2.0	41.0
49	25.36025	34.0	2.0	40.0	2.0	41.0
50	22.133	29.0	2.0	38.0	2.0	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
4	1.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	1.0
13	1.0
14	2.0
15	2.0
16	1.0
17	0.0
18	4.0
19	7.0
20	11.0
21	16.0
22	25.0
23	30.0
24	44.0
25	61.0
26	117.0
27	181.0
28	69.0
29	126.0
30	153.0
31	173.0
32	172.0
33	193.0
34	214.0
35	228.0
36	353.0
37	385.0
38	552.0
39	878.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.614421632448673	21.532298447671508	55.783675513269905	13.069604406609914
2	24.95	25.650000000000002	21.65	27.750000000000004
3	17.025000000000002	18.075	19.925	44.975
4	25.15	36.5	13.65	24.7
5	21.4	38.925	28.475	11.200000000000001
6	35.25	15.575	36.9	12.275
7	14.7	24.875	24.95	35.475
8	25.825	40.475	14.524999999999999	19.175
9	18.099999999999998	39.525	30.325000000000003	12.049999999999999
10	20.125	20.625	26.650000000000002	32.6
11	32.05	12.075	13.950000000000001	41.925000000000004
12	15.325	18.275	22.975	43.425000000000004
13	18.85	23.575	38.95	18.625
14	36.725	23.525	25.7	14.05
15	37.75	21.175	28.525	12.55
16	13.025	28.299999999999997	21.3	37.375
17	24.375	23.724999999999998	38.525	13.375
18	27.625	19.325	27.250000000000004	25.8
19	37.775	14.6	30.7	16.925
20	47.925000000000004	16.5	24.3	11.275
21	21.45	26.05	24.375	28.125
22	33.175	12.075	47.099999999999994	7.6499999999999995
23	24.05	13.05	48.675000000000004	14.224999999999998
24	51.275000000000006	13.525	28.425	6.775
25	54.800000000000004	21.7	15.425	8.075000000000001
26	30.4	47.599999999999994	11.625	10.375
27	13.850000000000001	53.37499999999999	22.075	10.7
28	10.0	27.150000000000002	49.475	13.375
29	10.4	12.1	60.375	17.125
30	8.625	6.1	37.925	47.349999999999994
31	12.55	5.625	48.225	33.6
32	24.425	5.775	23.95	45.85
33	54.2	7.425	14.299999999999999	24.075
34	66.975	6.525	12.525	13.975000000000001
35	65.5	6.9	18.975	8.625
36	66.675	7.7	15.375	10.25
37	40.975	11.15	22.625	25.25
38	24.4	13.725000000000001	13.0	48.875
39	15.475	24.0	9.875	50.64999999999999
40	12.825000000000001	49.15	10.475	27.55
41	26.150000000000002	49.875	9.025	14.95
42	51.37500000000001	31.35	9.049999999999999	8.225
43	50.824999999999996	32.300000000000004	8.075000000000001	8.799999999999999
44	31.624999999999996	50.64999999999999	6.275	11.450000000000001
45	17.25	51.4	9.825000000000001	21.525
46	9.725	30.0	25.3	34.975
47	8.1	14.7	35.5	41.699999999999996
48	9.950000000000001	11.175	22.5	56.375
49	11.425	23.974999999999998	13.4	51.2
50	30.475	26.85	9.275	33.4
>>END_MODULE
>>Per sequence GC content	warn
#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	1.0
14	1.0
15	1.0
16	1.0
17	0.5
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	0.0
28	0.0
29	1.5
30	3.0
31	8.0
32	13.0
33	15.5
34	18.0
35	28.5
36	39.0
37	43.5
38	48.0
39	43.0
40	38.0
41	44.5
42	51.0
43	80.5
44	110.0
45	188.0
46	266.0
47	346.0
48	426.0
49	505.5
50	585.0
51	744.5
52	904.0
53	696.5
54	489.0
55	435.5
56	382.0
57	337.5
58	293.0
59	191.0
60	89.0
61	79.5
62	70.0
63	89.5
64	109.0
65	64.0
66	19.0
67	11.5
68	4.0
69	9.0
70	14.0
71	18.0
72	22.0
73	12.5
74	3.0
75	1.5
76	0.0
77	0.5
78	1.0
79	0.5
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.15
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	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	warn
#Total Deduplicated Percentage	51.425
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.31113271754982	41.3
2	8.167233835683033	8.4
3	4.083616917841517	6.3
4	1.9445794846864366	4.0
5	1.06951871657754	2.75
6	0.53475935828877	1.6500000000000001
7	0.53475935828877	1.925
8	0.53475935828877	2.1999999999999997
9	0.3889158969372873	1.7999999999999998
>10	2.284880894506563	22.3
>50	0.09722897423432182	3.5249999999999995
>100	0.04861448711716091	3.85
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	154	3.85	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	88	2.1999999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	53	1.325	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	40	1.0	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	25	0.625	RNA PCR Primer, Index 1 (96% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	16	0.4	No Hit
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	15	0.375	RNA PCR Primer, Index 1 (96% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	12	0.3	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTC	11	0.27499999999999997	RNA PCR Primer, Index 44 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	10	0.25	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (95% over 23bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 44 (100% over 50bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	9	0.22499999999999998	No Hit
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 32bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	8	0.2	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	8	0.2	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	8	0.2	RNA PCR Primer, Index 7 (97% over 35bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	7	0.17500000000000002	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACTA	7	0.17500000000000002	RNA PCR Primer, Index 10 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	6	0.15	No Hit
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	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
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAATTCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	5	0.125	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	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	0.325	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	0.475	0.0	0.0	0.0
6	0.0	0.575	0.0	0.0	0.0
7	0.0	0.925	0.0	0.0	0.0
8	0.0	1.05	0.0	0.0	0.0
9	0.0	1.15	0.0	0.0	0.0
10	0.0	1.25	0.0	0.0	0.0
11	0.0	1.4	0.0	0.0	0.0
12	0.0	1.625	0.0	0.0	0.0
13	0.0	1.775	0.0	0.0	0.0
14	0.0	2.125	0.0	0.0	0.0
15	0.0	2.35	0.0	0.0	0.0
16	0.0	3.025	0.0	0.0	0.0
17	0.0	3.575	0.0	0.0	0.0
18	0.0	4.15	0.0	0.0	0.0
19	0.0	4.75	0.0	0.0	0.0
20	0.0	5.7	0.0	0.0	0.0
21	0.0	10.125	0.0	0.0	0.0
22	0.0	20.25	0.0	0.0	0.0
23	0.0	52.7	0.0	0.0	0.0
24	0.0	68.125	0.0	0.0	0.0
25	0.0	74.325	0.0	0.0	0.0
26	0.0	75.2	0.0	0.0	0.0
27	0.0	75.85	0.0	0.0	0.0
28	0.0	76.25	0.0	0.0	0.0
29	0.0	76.325	0.0	0.0	0.0
30	0.0	76.65	0.0	0.0	0.0
31	0.0	77.5	0.0	0.0	0.0
32	0.0	78.25	0.0	0.0	0.0
33	0.0	79.375	0.0	0.0	0.0
34	0.0	82.05	0.0	0.0	0.0
35	0.0	82.825	0.0	0.0	0.0
36	0.0	83.325	0.0	0.0	0.0
37	0.0	83.9	0.0	0.0	0.0
38	0.0	84.25	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	45	2.728484E-10	44.000004	5
AAGTAAT	40	5.315087E-9	44.000004	4
TCAAGTA	40	5.315087E-9	44.000004	2
CTGAGAC	45	2.728484E-10	44.000004	4
ATCCAGG	40	5.315087E-9	44.000004	9
CTTTAAC	40	5.315087E-9	44.000004	12
TTCAAGT	40	5.315087E-9	44.000004	1
AATTCCG	20	6.952051E-4	44.000004	44
AGGATAG	40	5.315087E-9	44.000004	13
ATAGGCT	40	5.315087E-9	44.000004	16
AGGAATT	20	6.952051E-4	44.000004	41
CCTGAGA	45	2.728484E-10	44.000004	3
AACCTGT	40	5.315087E-9	44.000004	16
TCCAGGA	40	5.315087E-9	44.000004	10
GTGAGTT	20	6.952051E-4	44.000004	18
ACCTGTT	20	6.952051E-4	44.000004	17
ACCTGTG	20	6.952051E-4	44.000004	17
GAGTTGG	20	6.952051E-4	44.000004	20
GGATAGG	40	5.315087E-9	44.000004	14
TAACCTG	40	5.315087E-9	44.000004	15
>>END_MODULE
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
Read 380841 spots for SRR5030928.sra
Written 380841 spots for SRR5030928.sra
Read 380836 spots for SRR5030928.sra
Written 380836 spots for SRR5030928.sra
SRR ids: ['SRR5030928.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_r70_si9c
SRR5030928.sra spots: 4570037
blocks: [[1, 380836], [380837, 761672], [761673, 1142508], [1142509, 1523344], [1523345, 1904180], [1904181, 2285016], [2285017, 2665852], [2665853, 3046688], [3046689, 3427524], [3427525, 3808360], [3808361, 4189196], [4189197, 4570037]]
SRR5030928 file size 791015
SRR5030928 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030928 SRR5030928_1.fastq
Input file:	SRR5030928_1.fastq
trimmed:	SRR5030928-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 06:47:01 2020 >> started

Wed Mar  4 06:47:04 2020 >> done (2.689s)
4570037 reads processed; of these:
    181 ( 0.00%) short reads filtered out after trimming by size control
      3 ( 0.00%) empty reads filtered out after trimming by size control
4569853 (100.00%) reads available; of these:
 526625 (11.52%) trimmed reads available after processing
4043228 (88.48%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     38	  0.00%
 19	     79	  0.00%
 20	    141	  0.00%
 21	    213	  0.00%
 22	    436	  0.01%
 23	    545	  0.01%
 24	    463	  0.01%
 25	    683	  0.01%
 26	    584	  0.01%
 27	    748	  0.02%
 28	   1099	  0.02%
 29	   2077	  0.05%
 30	   1163	  0.03%
 31	   1647	  0.04%
 32	   4164	  0.09%
 33	  13142	  0.29%
 34	  42867	  0.94%
 35	   9463	  0.21%
 36	  11368	  0.25%
 37	   5164	  0.11%
 38	  10739	  0.23%
 39	   8346	  0.18%
 40	  18648	  0.41%
 41	   9951	  0.22%
 42	  29173	  0.64%
 43	  10673	  0.23%
 44	  55830	  1.22%
 45	  31849	  0.70%
 46	  25915	  0.57%
 47	  28373	  0.62%
 48	  96917	  2.12%
 49	 104127	  2.28%
 50	4043228	 88.48%
4569853 reads passed initial QC


criterion=sequence-density
sequence-density=82.00
sequence-density-rank=1
fanout-score=18.62
fanout-score-rank=3
prefix-density=84.55
prefix-fanout=18.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC


criterion=fanout-score
sequence-density=1.38
sequence-density-rank=11
fanout-score=550.10
fanout-score-rank=1
prefix-density=83.85
prefix-fanout=9.0
sequence=GGAATTCTCGGTGCCAAGGA
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC -o SRR5030928 -
Input file:	STDIN
trimmed:	SRR5030928-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTATAATATCTCGTATGCC
-- 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 06:47:27 2020 >> started

Wed Mar  4 06:47:33 2020 >> done (6.107s)
4458393 reads processed; of these:
 158870 ( 3.56%) short reads filtered out after trimming by size control
  20648 ( 0.46%) empty reads filtered out after trimming by size control
4278875 (95.97%) reads available; of these:
3799471 (88.80%) trimmed reads available after processing
 479404 (11.20%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  30991	  0.72%
 19	  42803	  1.00%
 20	 175767	  4.11%
 21	 450316	 10.52%
 22	1387495	 32.43%
 23	 727550	 17.00%
 24	 264684	  6.19%
 25	  45310	  1.06%
 26	  22913	  0.54%
 27	  22712	  0.53%
 28	  24698	  0.58%
 29	  20755	  0.49%
 30	  33372	  0.78%
 31	  43359	  1.01%
 32	  48896	  1.14%
 33	 124549	  2.91%
 34	  44185	  1.03%
 35	  26773	  0.63%
 36	  37470	  0.88%
 37	  17663	  0.41%
 38	  21928	  0.51%
 39	  19953	  0.47%
 40	  29791	  0.70%
 41	  34453	  0.81%
 42	  42292	  0.99%
 43	  27584	  0.64%
 44	  31163	  0.73%
 45	  27461	  0.64%
 46	  22354	  0.52%
 47	  18708	  0.44%
 48	   7965	  0.19%
 49	  14485	  0.34%
 50	 388477	  9.08%


criterion=sequence-density
sequence-density=5.96
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=0.50
sequence-density-rank=28
fanout-score=3.39
fanout-score-rank=1
prefix-density=0.47
prefix-fanout=3.4
sequence=TTGGAATTCTCGG
                                 Started job on |	Mar 04 06:47:59
                             Started mapping on |	Mar 04 06:47:59
                                    Finished on |	Mar 04 06:48:49
       Mapping speed, Million of reads per hour |	316.10

                          Number of input reads |	4390335
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2149217
                        Uniquely mapped reads % |	48.95%
                          Average mapped length |	27.06
                       Number of splices: Total |	2177
            Number of splices: Annotated (sjdb) |	268
                       Number of splices: GT/AG |	1995
                       Number of splices: GC/AG |	33
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	147
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.28
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1720686
             % of reads mapped to multiple loci |	39.19%
        Number of reads mapped to too many loci |	104597
             % of reads mapped to too many loci |	2.38%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.87%
                     % of reads unmapped: other |	0.61%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	520432	520432	520432
N_multimapping	1720686	1720686	1720686
N_noFeature	89050	108160	1692755
N_ambiguous	1162166	774597	15501
UnstrandedReadsAssigned:898001 PositiveStrandReadsAssigned:1266460 NegativeStrandReadsAssigned:440961
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030928 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: SRR5030928-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,390,335 reads, 888,405 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,161 rounds

 109283 SRR5030928.ke.tsv
  52636 SRR5030928.se.tsv
 161919 total
==> SRR5030928.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

==> SRR5030928.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030928 completed mapping pipeline successfully
