Starting /dee2/code/volunteer_pipeline.sh SRR5030855
    current disk space = 160653246464
    free memory = 73934000 
SRR5030855 SRAfilesize
c477623708792c4993432dffbd751a66  SRR5030855.sra
SRR5030855.sra file validated
SRR5030855 is single end
SRR5030855 is conventional basespace
SRR5030855 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030855_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	32.46025	34.0	31.0	34.0	31.0	34.0
2	32.705	34.0	31.0	34.0	31.0	34.0
3	32.89	34.0	31.0	34.0	31.0	34.0
4	36.274	37.0	37.0	37.0	35.0	37.0
5	36.30275	37.0	37.0	37.0	35.0	37.0
6	36.198	37.0	37.0	37.0	35.0	37.0
7	36.116	37.0	35.0	37.0	35.0	37.0
8	36.1655	37.0	36.0	37.0	35.0	37.0
9	37.91775	39.0	38.0	39.0	35.0	39.0
10	38.025	39.0	38.0	39.0	35.0	39.0
11	37.91025	39.0	38.0	39.0	35.0	39.0
12	37.8535	39.0	38.0	39.0	35.0	39.0
13	37.8145	39.0	38.0	39.0	35.0	39.0
14	39.303	41.0	39.0	41.0	36.0	41.0
15	39.29475	40.0	39.0	41.0	36.0	41.0
16	39.30575	40.0	39.0	41.0	36.0	41.0
17	39.453	41.0	39.0	41.0	36.0	41.0
18	39.35875	41.0	39.0	41.0	36.0	41.0
19	39.202	41.0	39.0	41.0	36.0	41.0
20	39.1965	41.0	39.0	41.0	36.0	41.0
21	39.2935	41.0	39.0	41.0	36.0	41.0
22	39.2485	41.0	39.0	41.0	36.0	41.0
23	39.154	41.0	39.0	41.0	36.0	41.0
24	38.82975	40.0	38.0	41.0	35.0	41.0
25	39.08775	41.0	39.0	41.0	35.0	41.0
26	39.03075	40.0	39.0	41.0	35.0	41.0
27	39.14175	41.0	39.0	41.0	36.0	41.0
28	38.84525	40.0	39.0	41.0	35.0	41.0
29	38.18525	40.0	38.0	41.0	33.0	41.0
30	38.611	40.0	38.0	41.0	34.0	41.0
31	38.9195	40.0	39.0	41.0	35.0	41.0
32	39.08125	41.0	39.0	41.0	35.0	41.0
33	38.3945	40.0	38.0	41.0	34.0	41.0
34	38.276	40.0	38.0	41.0	33.0	41.0
35	37.91325	40.0	38.0	41.0	33.0	41.0
36	34.2025	38.0	31.0	40.0	23.0	41.0
37	35.8515	38.0	35.0	40.0	30.0	41.0
38	37.182	39.0	37.0	40.0	32.0	41.0
39	37.106	39.0	37.0	40.0	31.0	41.0
40	37.13125	39.0	37.0	41.0	31.0	41.0
41	37.16075	39.0	37.0	41.0	32.0	41.0
42	37.326	40.0	37.0	41.0	32.0	41.0
43	37.0565	40.0	37.0	41.0	31.0	41.0
44	37.06675	40.0	37.0	41.0	31.0	41.0
45	36.84025	39.0	37.0	41.0	31.0	41.0
46	34.94175	38.0	34.0	40.0	26.0	41.0
47	35.79675	39.0	35.0	40.0	29.0	41.0
48	36.16475	39.0	36.0	41.0	30.0	41.0
49	35.17	39.0	35.0	40.0	28.0	41.0
50	30.3	34.0	27.0	39.0	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
11	1.0
12	1.0
13	1.0
14	0.0
15	0.0
16	2.0
17	0.0
18	0.0
19	1.0
20	2.0
21	2.0
22	7.0
23	7.0
24	9.0
25	15.0
26	16.0
27	40.0
28	35.0
29	34.0
30	43.0
31	56.0
32	88.0
33	117.0
34	145.0
35	210.0
36	301.0
37	504.0
38	992.0
39	1371.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.063595393089635	23.15973960941412	53.78067100650976	13.99599399098648
2	20.925	25.95	19.85	33.275
3	25.374999999999996	21.85	22.225	30.55
4	28.575	27.474999999999998	13.900000000000002	30.049999999999997
5	17.925	45.6	24.8	11.675
6	37.775	17.75	31.8	12.675
7	16.400000000000002	18.65	26.85	38.1
8	26.224999999999998	29.349999999999998	15.7	28.725
9	21.9	36.9	28.075	13.125
10	22.0	23.925	29.9	24.175
11	25.025	11.200000000000001	18.8	44.975
12	13.625000000000002	17.65	32.75	35.975
13	32.725	20.325	28.575	18.375
14	31.275	34.525	19.05	15.15
15	34.275	26.174999999999997	25.95	13.600000000000001
16	17.299999999999997	21.475	21.325	39.900000000000006
17	19.650000000000002	21.725	43.5	15.125
18	23.549999999999997	19.025	28.825	28.599999999999998
19	36.8	13.450000000000001	32.625	17.125
20	39.675	15.65	30.125	14.549999999999999
21	22.025	18.025	30.875000000000004	29.075
22	28.7	12.25	49.55	9.5
23	29.849999999999998	13.725000000000001	43.075	13.350000000000001
24	53.675	14.825	23.775	7.725
25	49.425000000000004	27.400000000000002	14.325	8.85
26	25.724999999999998	49.45	14.725	10.100000000000001
27	14.924999999999999	47.099999999999994	27.275	10.7
28	10.225	23.25	51.275000000000006	15.25
29	9.6	12.7	56.474999999999994	21.224999999999998
30	8.799999999999999	6.525	38.25	46.425
31	15.375	5.050000000000001	46.0	33.575
32	31.175000000000004	5.625	19.400000000000002	43.8
33	58.575	7.074999999999999	12.6	21.75
34	63.075	6.7	16.425	13.8
35	62.9	6.9	20.9	9.3
36	44.175	8.175	33.25	14.399999999999999
37	44.324999999999996	8.975	18.675	28.025
38	21.15	16.025	11.95	50.875
39	15.125	28.625	8.25	48.0
40	15.875	50.824999999999996	10.025	23.275000000000002
41	28.299999999999997	47.675	8.825	15.2
42	51.925	30.375000000000004	9.525	8.175
43	49.175000000000004	34.475	6.950000000000001	9.4
44	26.825	51.800000000000004	6.675000000000001	14.7
45	16.1	50.075	13.0	20.825
46	10.575	26.174999999999997	21.3	41.949999999999996
47	7.925	15.4	38.05	38.625
48	8.975	14.075	19.05	57.9
49	14.475	21.6	12.825000000000001	51.1
50	21.2	36.625	13.525	28.65
>>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	1.0
18	2.0
19	1.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	1.5
28	3.0
29	2.5
30	2.0
31	7.5
32	13.0
33	16.0
34	19.0
35	35.0
36	51.0
37	46.0
38	41.0
39	44.0
40	47.0
41	47.5
42	48.0
43	70.0
44	92.0
45	157.5
46	223.0
47	339.5
48	456.0
49	612.5
50	769.0
51	816.0
52	863.0
53	639.5
54	416.0
55	434.5
56	453.0
57	341.5
58	230.0
59	146.0
60	62.0
61	48.0
62	34.0
63	63.5
64	93.0
65	58.5
66	24.0
67	20.0
68	16.0
69	13.0
70	10.0
71	15.5
72	21.0
73	11.5
74	2.0
75	1.0
76	0.0
77	1.5
78	3.0
79	4.0
80	5.0
81	3.0
82	1.0
83	1.0
84	1.0
85	0.5
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	fail
#Total Deduplicated Percentage	39.35
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.23888182973316	30.0
2	9.339263024142312	7.35
3	4.193138500635324	4.95
4	2.5412960609911055	4.0
5	1.3977128335451081	2.75
6	0.7623888182973316	1.7999999999999998
7	1.1435832274459974	3.15
8	0.3811944091486658	1.2
9	0.44472681067344344	1.575
>10	2.9860228716645487	22.650000000000002
>50	0.3811944091486658	10.9
>100	0.1905972045743329	9.675
>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	146	3.65	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	125	3.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	116	2.9000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	92	2.3	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	72	1.7999999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	60	1.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	55	1.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	49	1.225	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	48	1.2	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	45	1.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	42	1.05	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	25	0.625	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	23	0.575	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (96% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTC	17	0.42500000000000004	RNA PCR Primer, Index 4 (100% over 44bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGC	16	0.4	RNA PCR Primer, Index 4 (100% over 50bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	14	0.35000000000000003	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTG	14	0.35000000000000003	RNA PCR Primer, Index 2 (97% over 35bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	10	0.25	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	9	0.22499999999999998	RNA PCR Primer, Index 3 (100% over 34bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	9	0.22499999999999998	No Hit
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	8	0.2	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	8	0.2	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	7	0.17500000000000002	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
CATCATCGTCTCAAATGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	7	0.17500000000000002	No Hit
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
CAGGATCACAGAAAAAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	5	0.125	No Hit
CTAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TTGTGCTTGATCTAACCATGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	5	0.125	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTAT	5	0.125	RNA PCR Primer, Index 4 (100% over 48bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.475	0.0	0.0	0.0
2	0.0	0.475	0.0	0.0	0.0
3	0.0	0.625	0.0	0.0	0.0
4	0.0	0.65	0.0	0.0	0.0
5	0.0	0.75	0.0	0.0	0.0
6	0.0	0.825	0.0	0.0	0.0
7	0.0	1.325	0.0	0.0	0.0
8	0.0	1.575	0.0	0.0	0.0
9	0.0	1.65	0.0	0.0	0.0
10	0.0	1.775	0.0	0.0	0.0
11	0.0	1.95	0.0	0.0	0.0
12	0.0	2.35	0.0	0.0	0.0
13	0.0	2.825	0.0	0.0	0.0
14	0.0	3.125	0.0	0.0	0.0
15	0.0	3.5	0.0	0.0	0.0
16	0.0	4.225	0.0	0.0	0.0
17	0.0	4.875	0.0	0.0	0.0
18	0.0	5.95	0.0	0.0	0.0
19	0.0	6.55	0.0	0.0	0.0
20	0.0	7.65	0.0	0.0	0.0
21	0.0	14.5	0.0	0.0	0.0
22	0.0	28.775	0.0	0.0	0.0
23	0.0	58.8	0.0	0.0	0.0
24	0.0	70.8	0.0	0.0	0.0
25	0.0	76.775	0.0	0.0	0.0
26	0.0	78.05	0.0	0.0	0.0
27	0.0	78.625	0.0	0.0	0.0
28	0.0	79.05	0.0	0.0	0.0
29	0.0	79.5	0.0	0.0	0.0
30	0.0	79.95	0.0	0.0	0.0
31	0.0	80.4	0.0	0.0	0.0
32	0.0	81.125	0.0	0.0	0.0
33	0.0	82.0	0.0	0.0	0.0
34	0.0	84.025	0.0	0.0	0.0
35	0.0	84.625	0.0	0.0	0.0
36	0.0	85.225	0.0	0.0	0.0
37	0.0	85.725	0.0	0.0	0.0
38	0.0	85.95	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
TGGTTAT	20	6.952051E-4	44.000004	5
GTATGAT	20	6.952051E-4	44.000004	18
GGTGAGT	20	6.952051E-4	44.000004	17
ACGCTGT	20	6.952051E-4	44.000004	9
CTGAGCT	40	5.315087E-9	44.000004	11
TAAACAT	20	6.952051E-4	44.000004	3
TCTAGCT	20	6.952051E-4	44.000004	11
AAACATC	20	6.952051E-4	44.000004	4
TTCAACG	20	6.952051E-4	44.000004	5
TTATCTA	20	6.952051E-4	44.000004	8
TCGGTGA	20	6.952051E-4	44.000004	15
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TATGATG	20	6.952051E-4	44.000004	19
TCGGATC	40	5.315087E-9	44.000004	1
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
CGGATCC	40	5.315087E-9	44.000004	2
CTTGGTG	20	6.952051E-4	44.000004	16
>>END_MODULE
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308126 spots for SRR5030855.sra
Written 308126 spots for SRR5030855.sra
Read 308129 spots for SRR5030855.sra
Written 308129 spots for SRR5030855.sra
SRR ids: ['SRR5030855.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ly6ba1pa
SRR5030855.sra spots: 3697515
blocks: [[1, 308126], [308127, 616252], [616253, 924378], [924379, 1232504], [1232505, 1540630], [1540631, 1848756], [1848757, 2156882], [2156883, 2465008], [2465009, 2773134], [2773135, 3081260], [3081261, 3389386], [3389387, 3697515]]
SRR5030855 file size 639787
SRR5030855 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030855 SRR5030855_1.fastq
Input file:	SRR5030855_1.fastq
trimmed:	SRR5030855-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 06:29:23 2020 >> started

Wed Mar  4 06:29:26 2020 >> done (3.529s)
3697515 reads processed; of these:
    128 ( 0.00%) short reads filtered out after trimming by size control
      8 ( 0.00%) empty reads filtered out after trimming by size control
3697379 (100.00%) reads available; of these:
 214736 ( 5.81%) trimmed reads available after processing
3482643 (94.19%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     48	  0.00%
 19	     72	  0.00%
 20	    193	  0.01%
 21	    169	  0.00%
 22	    330	  0.01%
 23	    389	  0.01%
 24	    425	  0.01%
 25	    491	  0.01%
 26	    404	  0.01%
 27	    627	  0.02%
 28	    839	  0.02%
 29	   1109	  0.03%
 30	    872	  0.02%
 31	   1065	  0.03%
 32	   1072	  0.03%
 33	   1558	  0.04%
 34	   3807	  0.10%
 35	   3243	  0.09%
 36	   2459	  0.07%
 37	   2573	  0.07%
 38	   2851	  0.08%
 39	   3188	  0.09%
 40	   3604	  0.10%
 41	   3923	  0.11%
 42	   5196	  0.14%
 43	   6750	  0.18%
 44	  13049	  0.35%
 45	  14416	  0.39%
 46	  14088	  0.38%
 47	  20720	  0.56%
 48	  43485	  1.18%
 49	  61721	  1.67%
 50	3482643	 94.19%
3697379 reads passed initial QC


criterion=sequence-density
sequence-density=85.89
sequence-density-rank=1
fanout-score=19.17
fanout-score-rank=1
prefix-density=87.31
prefix-fanout=18.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC


criterion=fanout-score
sequence-density=85.89
sequence-density-rank=1
fanout-score=19.17
fanout-score-rank=1
prefix-density=87.31
prefix-fanout=18.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC -o SRR5030855 -
Input file:	STDIN
trimmed:	SRR5030855-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCC
-- 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 06:29:46 2020 >> started

Wed Mar  4 06:29:55 2020 >> done (8.628s)
3611394 reads processed; of these:
 192375 ( 5.33%) short reads filtered out after trimming by size control
  13567 ( 0.38%) empty reads filtered out after trimming by size control
3405452 (94.30%) reads available; of these:
3139948 (92.20%) trimmed reads available after processing
 265504 ( 7.80%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  20022	  0.59%
 19	  39543	  1.16%
 20	 244003	  7.17%
 21	 522247	 15.34%
 22	1139540	 33.46%
 23	 427903	 12.57%
 24	 216101	  6.35%
 25	  48129	  1.41%
 26	  23561	  0.69%
 27	  18510	  0.54%
 28	  19230	  0.56%
 29	  13987	  0.41%
 30	  18561	  0.55%
 31	  22797	  0.67%
 32	  24916	  0.73%
 33	  66399	  1.95%
 34	  28081	  0.82%
 35	  22846	  0.67%
 36	  26953	  0.79%
 37	  12222	  0.36%
 38	  13303	  0.39%
 39	  13956	  0.41%
 40	  20982	  0.62%
 41	  27918	  0.82%
 42	  33083	  0.97%
 43	  23269	  0.68%
 44	  18403	  0.54%
 45	  23457	  0.69%
 46	  16912	  0.50%
 47	  13442	  0.39%
 48	   2784	  0.08%
 49	   9681	  0.28%
 50	 232711	  6.83%


criterion=sequence-density
sequence-density=4.85
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AAGCTGCCAGTTGAAGAACTGT


criterion=fanout-score
sequence-density=0.03
sequence-density-rank=39
fanout-score=41.99
fanout-score-rank=1
prefix-density=1.20
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:30:29
                             Started mapping on |	Mar 04 06:30:30
                                    Finished on |	Mar 04 06:30:56
       Mapping speed, Million of reads per hour |	483.43

                          Number of input reads |	3491437
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2033916
                        Uniquely mapped reads % |	58.25%
                          Average mapped length |	25.40
                       Number of splices: Total |	1428
            Number of splices: Annotated (sjdb) |	226
                       Number of splices: GT/AG |	1330
                       Number of splices: GC/AG |	14
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	81
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.52
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1130207
             % of reads mapped to multiple loci |	32.37%
        Number of reads mapped to too many loci |	55801
             % of reads mapped to too many loci |	1.60%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.36%
                     % of reads unmapped: other |	0.42%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	327314	327314	327314
N_multimapping	1130207	1130207	1130207
N_noFeature	69137	85199	1403715
N_ambiguous	1160944	610970	20282
UnstrandedReadsAssigned:803835 PositiveStrandReadsAssigned:1337747 NegativeStrandReadsAssigned:609919
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030855 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: SRR5030855-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,491,437 reads, 988,028 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,154 rounds

 109283 SRR5030855.ke.tsv
  52636 SRR5030855.se.tsv
 161919 total
==> SRR5030855.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

==> SRR5030855.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	2
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030855 completed mapping pipeline successfully
