Starting /dee2/code/volunteer_pipeline.sh SRR5030853
    current disk space = 160656343040
    free memory = 56717664 
SRR5030853 SRAfilesize
244ef7dc21192d25776fa2cc3049c8b3  SRR5030853.sra
SRR5030853.sra file validated
SRR5030853 is single end
SRR5030853 is conventional basespace
SRR5030853 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030853_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.2565	33.0	31.0	34.0	31.0	34.0
2	32.63825	34.0	31.0	34.0	31.0	34.0
3	32.659	34.0	31.0	34.0	31.0	34.0
4	36.14925	37.0	35.0	37.0	35.0	37.0
5	36.13975	37.0	35.0	37.0	35.0	37.0
6	35.97775	37.0	35.0	37.0	35.0	37.0
7	36.068	37.0	35.0	37.0	35.0	37.0
8	36.112	37.0	35.0	37.0	35.0	37.0
9	37.8515	39.0	38.0	39.0	35.0	39.0
10	37.91075	39.0	38.0	39.0	35.0	39.0
11	37.77475	39.0	38.0	39.0	35.0	39.0
12	37.8485	39.0	38.0	39.0	35.0	39.0
13	37.75525	39.0	38.0	39.0	35.0	39.0
14	39.145	41.0	38.0	41.0	36.0	41.0
15	39.0815	40.0	38.0	41.0	36.0	41.0
16	38.991	40.0	38.0	41.0	36.0	41.0
17	39.17975	40.0	39.0	41.0	36.0	41.0
18	39.13175	41.0	39.0	41.0	36.0	41.0
19	39.00425	40.0	39.0	41.0	35.0	41.0
20	38.99925	40.0	39.0	41.0	35.0	41.0
21	39.08025	40.0	39.0	41.0	35.0	41.0
22	39.173	41.0	39.0	41.0	36.0	41.0
23	39.061	40.0	39.0	41.0	36.0	41.0
24	38.24075	40.0	38.0	41.0	33.0	41.0
25	38.52725	40.0	38.0	41.0	34.0	41.0
26	38.48675	40.0	38.0	41.0	34.0	41.0
27	38.39525	40.0	38.0	41.0	34.0	41.0
28	38.45475	40.0	38.0	41.0	34.0	41.0
29	38.4015	40.0	38.0	41.0	34.0	41.0
30	38.01575	40.0	38.0	41.0	33.0	41.0
31	38.494	40.0	38.0	41.0	34.0	41.0
32	38.571	40.0	38.0	41.0	34.0	41.0
33	36.9515	40.0	37.0	41.0	30.0	41.0
34	35.99625	40.0	36.0	41.0	26.0	41.0
35	32.77875	38.0	31.0	40.0	14.0	41.0
36	29.74775	37.0	21.0	40.0	8.0	41.0
37	29.89825	36.0	24.0	39.0	6.0	41.0
38	32.15625	37.0	30.0	39.0	12.0	41.0
39	31.6555	37.0	30.0	39.0	8.0	41.0
40	32.1705	37.0	31.0	40.0	2.0	41.0
41	29.98575	36.0	26.0	40.0	2.0	41.0
42	31.42225	37.0	30.0	40.0	2.0	41.0
43	29.89975	36.0	26.0	40.0	2.0	41.0
44	30.81675	37.0	30.0	40.0	2.0	41.0
45	29.322	36.0	26.0	40.0	2.0	41.0
46	27.25	34.0	15.0	39.0	2.0	41.0
47	27.1175	34.0	15.0	39.0	2.0	41.0
48	27.50575	35.0	2.0	39.0	2.0	41.0
49	25.675	34.0	2.0	39.0	2.0	41.0
50	22.48675	30.0	2.0	38.0	2.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
10	1.0
11	0.0
12	1.0
13	0.0
14	0.0
15	1.0
16	2.0
17	2.0
18	8.0
19	11.0
20	16.0
21	16.0
22	27.0
23	40.0
24	49.0
25	71.0
26	100.0
27	126.0
28	81.0
29	111.0
30	156.0
31	136.0
32	156.0
33	179.0
34	219.0
35	275.0
36	334.0
37	476.0
38	654.0
39	752.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.645379413974455	25.018782870022537	47.78362133734034	15.552216378662658
2	26.0	25.025	18.6	30.375000000000004
3	23.25	20.724999999999998	25.674999999999997	30.349999999999998
4	32.5	27.500000000000004	16.475	23.525
5	22.900000000000002	39.4	25.124999999999996	12.575
6	30.45	17.525	36.85	15.174999999999999
7	18.275	20.25	24.075	37.4
8	25.95	27.775	15.7	30.575000000000003
9	21.05	32.800000000000004	30.25	15.9
10	22.375	20.9	29.325000000000003	27.400000000000002
11	33.1	12.725	15.825	38.35
12	18.25	19.825	30.4	31.525
13	31.55	18.075	30.975	19.400000000000002
14	29.775000000000002	30.225	22.6	17.4
15	34.9	22.900000000000002	25.8	16.400000000000002
16	19.825	18.975	23.0	38.2
17	23.3	22.725	37.6	16.375
18	24.275	17.625	31.3	26.8
19	34.0	15.525	32.15	18.325
20	39.675	17.8	25.874999999999996	16.650000000000002
21	22.725	22.075	28.000000000000004	27.200000000000003
22	30.425	14.35	42.75	12.475
23	27.525	14.475	41.475	16.525000000000002
24	47.199999999999996	14.875	26.650000000000002	11.275
25	47.775	23.25	16.425	12.55
26	29.175	40.725	15.875	14.224999999999998
27	17.724999999999998	43.65	23.400000000000002	15.225
28	14.85	24.4	43.375	17.375
29	13.0	15.7	53.05	18.25
30	11.375	9.049999999999999	35.55	44.025
31	16.55	7.7	42.55	33.2
32	28.9	7.5	23.525	40.075
33	49.45	9.575	15.5	25.474999999999998
34	56.55	7.6499999999999995	16.75	19.05
35	57.550000000000004	8.475000000000001	19.7	14.274999999999999
36	59.599999999999994	9.35	16.55	14.499999999999998
37	39.375	12.049999999999999	21.425	27.150000000000002
38	27.650000000000002	16.275000000000002	13.925	42.15
39	19.075	25.55	11.825	43.55
40	19.125	43.175000000000004	13.025	24.675
41	27.825	42.175000000000004	12.775	17.224999999999998
42	45.925	29.599999999999998	12.675	11.799999999999999
43	43.7	33.900000000000006	10.549999999999999	11.85
44	30.9	44.05	9.175	15.875
45	20.225	45.175	12.7	21.9
46	15.024999999999999	28.825	23.275000000000002	32.875
47	12.25	17.7	32.625	37.425000000000004
48	13.25	13.950000000000001	22.25	50.55
49	16.125	22.6	15.325	45.95
50	29.475	24.0	11.85	34.675
>>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	0.5
12	1.0
13	0.5
14	0.0
15	0.5
16	1.0
17	1.0
18	1.0
19	0.5
20	0.0
21	1.0
22	2.0
23	1.0
24	0.0
25	0.5
26	1.0
27	0.5
28	0.0
29	2.0
30	4.0
31	9.0
32	14.0
33	21.5
34	29.0
35	39.0
36	49.0
37	64.0
38	79.0
39	67.5
40	56.0
41	56.5
42	57.0
43	91.5
44	126.0
45	177.0
46	228.0
47	263.5
48	299.0
49	363.5
50	428.0
51	608.0
52	788.0
53	645.5
54	503.0
55	458.5
56	414.0
57	379.0
58	344.0
59	247.5
60	151.0
61	125.0
62	99.0
63	110.5
64	122.0
65	75.5
66	29.0
67	25.5
68	22.0
69	34.5
70	47.0
71	66.0
72	85.0
73	46.0
74	7.0
75	6.5
76	6.0
77	3.0
78	0.0
79	1.0
80	2.0
81	2.5
82	3.0
83	2.0
84	1.0
85	1.0
86	1.0
87	1.0
88	1.0
89	0.5
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	0.17500000000000002
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	51.65
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.00968054211036	41.325
2	8.615682478218782	8.9
3	3.581800580832527	5.55
4	1.6456921587608906	3.4000000000000004
5	1.4036786060019362	3.6249999999999996
6	0.9196515004840271	2.85
7	0.6776379477250726	2.45
8	0.3872216844143272	1.6
9	0.1936108422071636	0.8999999999999999
>10	2.420135527589545	23.325000000000003
>50	0.0968054211035818	3.175
>100	0.0484027105517909	2.9000000000000004
>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	116	2.9000000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	64	1.6	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	63	1.575	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	33	0.8250000000000001	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	28	0.7000000000000001	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	27	0.675	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	23	0.575	RNA PCR Primer, Index 7 (100% over 35bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGC	21	0.525	RNA PCR Primer, Index 34 (100% over 50bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	19	0.475	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	18	0.44999999999999996	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	16	0.4	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	15	0.375	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	15	0.375	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	15	0.375	RNA PCR Primer, Index 1 (96% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	13	0.325	RNA PCR Primer, Index 1 (96% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	13	0.325	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	13	0.325	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	11	0.27499999999999997	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	11	0.27499999999999997	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	10	0.25	No Hit
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	10	0.25	RNA PCR Primer, Index 1 (100% over 32bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	10	0.25	No Hit
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	9	0.22499999999999998	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	9	0.22499999999999998	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	9	0.22499999999999998	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	8	0.2	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	8	0.2	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	8	0.2	RNA PCR Primer, Index 1 (95% over 23bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	8	0.2	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	7	0.17500000000000002	RNA PCR Primer, Index 2 (100% over 34bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	7	0.17500000000000002	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	7	0.17500000000000002	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGC	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	6	0.15	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	6	0.15	No Hit
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TAAGGCACGCGGTGAATGCCATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	6	0.15	No Hit
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	6	0.15	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	6	0.15	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	6	0.15	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTC	6	0.15	RNA PCR Primer, Index 34 (100% over 44bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGGC	5	0.125	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGATGATGAGAGCTTTGTTCTGAGCTGGAATTCTCGGGTGCCAAGGAA	5	0.125	RNA PCR Primer, Index 1 (100% over 23bp)
GCATTTGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	5	0.125	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	5	0.125	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTC	5	0.125	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	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	0.575	0.0	0.0	0.0
2	0.0	0.575	0.0	0.0	0.0
3	0.0	0.65	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	0.775	0.0	0.0	0.0
7	0.0	1.025	0.0	0.0	0.0
8	0.0	1.125	0.0	0.0	0.0
9	0.0	1.175	0.0	0.0	0.0
10	0.0	1.275	0.0	0.0	0.0
11	0.0	1.375	0.0	0.0	0.0
12	0.0	1.625	0.0	0.0	0.0
13	0.0	1.8	0.0	0.0	0.0
14	0.0	2.025	0.0	0.0	0.0
15	0.0	2.35	0.0	0.0	0.0
16	0.0	3.375	0.0	0.0	0.0
17	0.0	3.975	0.0	0.0	0.0
18	0.0	4.825	0.0	0.0	0.0
19	0.0	5.425	0.0	0.0	0.0
20	0.0	6.25	0.0	0.0	0.0
21	0.0	11.525	0.0	0.0	0.0
22	0.0	21.0	0.0	0.0	0.0
23	0.0	45.075	0.0	0.0	0.0
24	0.0	57.025	0.0	0.0	0.0
25	0.0	62.725	0.0	0.0	0.0
26	0.0	64.55	0.0	0.0	0.0
27	0.0	65.35	0.0	0.0	0.0
28	0.0	65.975	0.0	0.0	0.0
29	0.0	66.3	0.0	0.0	0.0
30	0.0	66.95	0.0	0.0	0.0
31	0.0	67.575	0.0	0.0	0.0
32	0.0	68.475	0.0	0.0	0.0
33	0.0	69.325	0.0	0.0	0.0
34	0.0	72.175	0.0	0.0	0.0
35	0.0	73.15	0.0	0.0	0.0
36	0.0	74.125	0.0	0.0	0.0
37	0.0	74.925	0.0	0.0	0.0
38	0.0	75.125	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
ACGCTGT	20	6.952051E-4	44.000004	9
TCTAGCT	20	6.952051E-4	44.000004	11
TTGTATA	20	6.952051E-4	44.000004	13
AGTAGGT	20	6.952051E-4	44.000004	7
TTCAACG	20	6.952051E-4	44.000004	5
TTATCTA	20	6.952051E-4	44.000004	8
TCGGTGA	20	6.952051E-4	44.000004	15
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
ACATTCA	20	6.952051E-4	44.000004	2
GTATAGT	20	6.952051E-4	44.000004	15
ATAGTTT	20	6.952051E-4	44.000004	17
TAGTAGG	20	6.952051E-4	44.000004	6
GCTGTCG	20	6.952051E-4	44.000004	11
GCTGTAT	20	6.952051E-4	44.000004	15
TATCTAG	20	6.952051E-4	44.000004	9
CTAGCTG	20	6.952051E-4	44.000004	12
TTTGGTT	20	6.952051E-4	44.000004	3
TTGGCTT	20	6.952051E-4	44.000004	17
>>END_MODULE
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321593 spots for SRR5030853.sra
Written 321593 spots for SRR5030853.sra
Read 321596 spots for SRR5030853.sra
Written 321596 spots for SRR5030853.sra
SRR ids: ['SRR5030853.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6gief8hq
SRR5030853.sra spots: 3859119
blocks: [[1, 321593], [321594, 643186], [643187, 964779], [964780, 1286372], [1286373, 1607965], [1607966, 1929558], [1929559, 2251151], [2251152, 2572744], [2572745, 2894337], [2894338, 3215930], [3215931, 3537523], [3537524, 3859119]]
SRR5030853 file size 667794
SRR5030853 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030853 SRR5030853_1.fastq
Input file:	SRR5030853_1.fastq
trimmed:	SRR5030853-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 06:28:49 2020 >> started

Wed Mar  4 06:28:51 2020 >> done (2.259s)
3859119 reads processed; of these:
    215 ( 0.01%) short reads filtered out after trimming by size control
      8 ( 0.00%) empty reads filtered out after trimming by size control
3858896 (99.99%) reads available; of these:
 470086 (12.18%) trimmed reads available after processing
3388810 (87.82%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     61	  0.00%
 19	    106	  0.00%
 20	    176	  0.00%
 21	    246	  0.01%
 22	    440	  0.01%
 23	    570	  0.01%
 24	    564	  0.01%
 25	    780	  0.02%
 26	    695	  0.02%
 27	    955	  0.02%
 28	   1180	  0.03%
 29	   1822	  0.05%
 30	   1503	  0.04%
 31	   1820	  0.05%
 32	   4861	  0.13%
 33	  14848	  0.38%
 34	  27199	  0.70%
 35	   7563	  0.20%
 36	   8353	  0.22%
 37	   4686	  0.12%
 38	   9133	  0.24%
 39	   9570	  0.25%
 40	  17613	  0.46%
 41	   9478	  0.25%
 42	  25605	  0.66%
 43	  10392	  0.27%
 44	  39945	  1.04%
 45	  29386	  0.76%
 46	  27313	  0.71%
 47	  31026	  0.80%
 48	  81457	  2.11%
 49	 100740	  2.61%
 50	3388810	 87.82%
3858896 reads passed initial QC


criterion=sequence-density
sequence-density=74.84
sequence-density-rank=1
fanout-score=21.74
fanout-score-rank=2
prefix-density=77.38
prefix-fanout=21.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCC


criterion=fanout-score
sequence-density=4.11
sequence-density-rank=3
fanout-score=56.80
fanout-score-rank=1
prefix-density=77.16
prefix-fanout=3.0
sequence=GAATTCTCGGGGGCCAAGGAACT
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCC -o SRR5030853 -
Input file:	STDIN
trimmed:	SRR5030853-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCATGGCATCTCGTATGCC
-- 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 06:29:08 2020 >> started

Wed Mar  4 06:29:14 2020 >> done (6.120s)
3755992 reads processed; of these:
 171261 ( 4.56%) short reads filtered out after trimming by size control
  22481 ( 0.60%) empty reads filtered out after trimming by size control
3562250 (94.84%) reads available; of these:
2973879 (83.48%) trimmed reads available after processing
 588371 (16.52%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  26933	  0.76%
 19	  35273	  0.99%
 20	 185265	  5.20%
 21	 378003	 10.61%
 22	 924451	 25.95%
 23	 463352	 13.01%
 24	 226061	  6.35%
 25	  60474	  1.70%
 26	  31064	  0.87%
 27	  24118	  0.68%
 28	  25519	  0.72%
 29	  21252	  0.60%
 30	  27368	  0.77%
 31	  33821	  0.95%
 32	  36856	  1.03%
 33	  92925	  2.61%
 34	  40725	  1.14%
 35	  30850	  0.87%
 36	  43082	  1.21%
 37	  18286	  0.51%
 38	  21851	  0.61%
 39	  21221	  0.60%
 40	  31729	  0.89%
 41	  38526	  1.08%
 42	  49411	  1.39%
 43	  33233	  0.93%
 44	  30937	  0.87%
 45	  41317	  1.16%
 46	  32404	  0.91%
 47	  23381	  0.66%
 48	   8783	  0.25%
 49	  16369	  0.46%
 50	 487410	 13.68%


criterion=sequence-density
sequence-density=6.60
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=20
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=41
fanout-score=380.41
fanout-score-rank=1
prefix-density=1.99
prefix-fanout=1.9
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:29:36
                             Started mapping on |	Mar 04 06:29:36
                                    Finished on |	Mar 04 06:30:01
       Mapping speed, Million of reads per hour |	527.78

                          Number of input reads |	3665154
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1962918
                        Uniquely mapped reads % |	53.56%
                          Average mapped length |	28.01
                       Number of splices: Total |	2468
            Number of splices: Annotated (sjdb) |	321
                       Number of splices: GT/AG |	2302
                       Number of splices: GC/AG |	36
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	129
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.38
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1123685
             % of reads mapped to multiple loci |	30.66%
        Number of reads mapped to too many loci |	77848
             % of reads mapped to too many loci |	2.12%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.11%
                     % of reads unmapped: other |	0.55%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	578551	578551	578551
N_multimapping	1123685	1123685	1123685
N_noFeature	93379	115412	1386108
N_ambiguous	1100376	593145	20841
UnstrandedReadsAssigned:769163 PositiveStrandReadsAssigned:1254361 NegativeStrandReadsAssigned:555969
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030853 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: SRR5030853-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,665,154 reads, 900,809 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,163 rounds

 109283 SRR5030853.ke.tsv
  52636 SRR5030853.se.tsv
 161919 total
==> SRR5030853.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

==> SRR5030853.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030853 completed mapping pipeline successfully
