Starting /dee2/code/volunteer_pipeline.sh SRR5031076
    current disk space = 160488701952
    free memory = 1052809612 
SRR5031076 SRAfilesize
d8f810c6ff348838d725afc248ac990c  SRR5031076.sra
SRR5031076.sra file validated
SRR5031076 is single end
SRR5031076 is conventional basespace
SRR5031076 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031076_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	32.28775	33.0	31.0	34.0	31.0	34.0
2	32.529	34.0	31.0	34.0	31.0	34.0
3	32.60925	34.0	31.0	34.0	31.0	34.0
4	36.17475	37.0	35.0	37.0	35.0	37.0
5	35.8725	37.0	35.0	37.0	35.0	37.0
6	35.79925	37.0	35.0	37.0	33.0	37.0
7	35.87525	37.0	35.0	37.0	35.0	37.0
8	35.72875	37.0	35.0	37.0	33.0	37.0
9	37.50075	39.0	37.0	39.0	35.0	39.0
10	37.72125	39.0	37.0	39.0	35.0	39.0
11	37.573	39.0	37.0	39.0	35.0	39.0
12	37.60525	39.0	37.0	39.0	35.0	39.0
13	37.64275	39.0	37.0	39.0	35.0	39.0
14	38.9315	40.0	38.0	41.0	35.0	41.0
15	38.829	40.0	38.0	41.0	35.0	41.0
16	38.86225	40.0	38.0	41.0	35.0	41.0
17	38.819	40.0	38.0	41.0	35.0	41.0
18	38.981	40.0	38.0	41.0	35.0	41.0
19	38.79	40.0	38.0	41.0	34.0	41.0
20	38.8265	40.0	38.0	41.0	34.0	41.0
21	38.80225	40.0	38.0	41.0	34.0	41.0
22	38.986	40.0	39.0	41.0	35.0	41.0
23	38.84525	40.0	38.0	41.0	35.0	41.0
24	38.836	40.0	38.0	41.0	35.0	41.0
25	39.03475	40.0	39.0	41.0	35.0	41.0
26	38.68175	40.0	38.0	41.0	34.0	41.0
27	38.77	40.0	38.0	41.0	35.0	41.0
28	38.811	40.0	38.0	41.0	35.0	41.0
29	38.504	40.0	38.0	41.0	34.0	41.0
30	38.34225	40.0	38.0	41.0	34.0	41.0
31	38.571	40.0	38.0	41.0	34.0	41.0
32	38.33425	40.0	38.0	41.0	34.0	41.0
33	38.14325	40.0	38.0	41.0	33.0	41.0
34	38.294	40.0	38.0	41.0	34.0	41.0
35	38.101	40.0	38.0	41.0	33.0	41.0
36	37.801	40.0	37.0	41.0	33.0	41.0
37	37.5285	40.0	37.0	41.0	31.0	41.0
38	36.78925	39.0	36.0	41.0	30.0	41.0
39	37.199	39.0	37.0	41.0	31.0	41.0
40	37.5265	40.0	37.0	41.0	32.0	41.0
41	37.60025	40.0	37.0	41.0	33.0	41.0
42	37.98275	40.0	38.0	41.0	33.0	41.0
43	38.27925	40.0	38.0	41.0	34.0	41.0
44	38.09125	40.0	38.0	41.0	33.0	41.0
45	38.0615	40.0	38.0	41.0	33.0	41.0
46	37.73825	40.0	37.0	41.0	33.0	41.0
47	37.3795	40.0	37.0	41.0	32.0	41.0
48	36.78575	40.0	36.0	41.0	30.0	41.0
49	37.11025	40.0	36.0	41.0	31.0	41.0
50	36.52725	39.0	36.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
10	1.0
11	0.0
12	0.0
13	0.0
14	0.0
15	1.0
16	3.0
17	3.0
18	1.0
19	3.0
20	1.0
21	2.0
22	3.0
23	3.0
24	6.0
25	10.0
26	7.0
27	20.0
28	32.0
29	35.0
30	51.0
31	59.0
32	87.0
33	96.0
34	165.0
35	205.0
36	299.0
37	412.0
38	742.0
39	1753.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.35	25.75	51.55	14.35
2	23.74749498997996	27.55511022044088	18.562124248496996	30.135270541082164
3	23.45	21.8	21.325	33.425
4	31.45	27.575	15.275	25.7
5	22.7	39.324999999999996	27.675	10.299999999999999
6	36.025	15.325	33.725	14.924999999999999
7	14.875	22.125	23.7	39.300000000000004
8	26.974999999999998	28.499999999999996	15.15	29.375
9	20.925	34.975	28.775000000000002	15.325
10	20.474999999999998	24.65	27.224999999999998	27.650000000000002
11	31.2	9.125	18.475	41.199999999999996
12	14.75	19.075	30.599999999999998	35.575
13	31.874999999999996	18.175	31.65	18.3
14	31.75	32.300000000000004	20.349999999999998	15.6
15	34.75	24.349999999999998	28.025	12.875
16	19.625	19.5	22.675	38.2
17	23.799999999999997	22.625	38.9	14.674999999999999
18	24.875	18.224999999999998	28.999999999999996	27.900000000000002
19	36.125	13.675	32.25	17.95
20	42.5	14.825	29.65	13.025
21	22.45	19.825	29.725	28.000000000000004
22	29.299999999999997	11.774999999999999	49.1	9.825000000000001
23	27.625	12.85	45.5	14.025000000000002
24	52.800000000000004	13.325000000000001	27.125	6.75
25	52.075	25.25	14.325	8.35
26	28.525	48.225	12.775	10.475
27	15.325	48.825	25.35	10.5
28	9.875	24.8	50.4	14.924999999999999
29	10.575	12.174999999999999	57.675	19.575
30	8.95	5.825	38.9	46.325
31	13.4	4.65	46.325	35.625
32	28.575	5.325	22.125	43.974999999999994
33	55.55	7.8	13.175	23.474999999999998
34	64.875	6.5	15.275	13.350000000000001
35	65.325	6.325	20.0	8.35
36	44.6	6.8500000000000005	36.475	12.075
37	44.975	9.4	20.95	24.675
38	24.075	14.95	11.25	49.725
39	14.899999999999999	24.825	9.575	50.7
40	14.399999999999999	49.0	9.875	26.724999999999998
41	25.025	49.675000000000004	8.375	16.925
42	51.075	29.925	10.225	8.774999999999999
43	53.349999999999994	29.75	7.049999999999999	9.85
44	31.45	49.65	6.225	12.675
45	17.925	51.324999999999996	11.375	19.375
46	11.85	27.05	19.225	41.875
47	8.325000000000001	13.850000000000001	39.074999999999996	38.75
48	9.8	11.4	21.2	57.599999999999994
49	11.525	19.8	13.675	55.00000000000001
50	19.475	36.199999999999996	12.2	32.125
>>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	0.5
14	1.0
15	0.5
16	0.0
17	0.5
18	1.0
19	1.0
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	0.5
28	0.0
29	1.5
30	3.0
31	5.5
32	8.0
33	12.0
34	16.0
35	16.0
36	16.0
37	22.0
38	28.0
39	31.0
40	34.0
41	39.0
42	44.0
43	85.0
44	126.0
45	161.5
46	197.0
47	318.5
48	440.0
49	573.5
50	707.0
51	824.5
52	942.0
53	665.5
54	389.0
55	432.0
56	475.0
57	355.0
58	235.0
59	149.5
60	64.0
61	53.5
62	43.0
63	71.5
64	100.0
65	63.0
66	26.0
67	18.5
68	11.0
69	17.5
70	24.0
71	39.5
72	55.0
73	29.0
74	3.0
75	2.0
76	1.0
77	2.5
78	4.0
79	2.5
80	1.0
81	2.5
82	4.0
83	2.0
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	0.2
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	35.825
#Duplication Level	Percentage of deduplicated	Percentage of total
1	72.71458478715981	26.05
2	11.65387299371947	8.35
3	4.3963712491277045	4.725
4	3.14026517794836	4.5
5	1.5352407536636425	2.75
6	1.04675505931612	2.25
7	0.9769713886950453	2.45
8	0.2791346824842987	0.8
9	0.48848569434752265	1.575
>10	3.0006978367062107	20.45
>50	0.5582693649685974	15.375
>100	0.20935101186322402	10.725
>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	166	4.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	139	3.4750000000000005	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	124	3.1	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	96	2.4	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	92	2.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	86	2.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	83	2.075	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	69	1.725	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	39	0.975	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	23	0.575	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	21	0.525	RNA PCR Primer, Index 5 (97% over 35bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTC	19	0.475	RNA PCR Primer, Index 48 (100% over 44bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	19	0.475	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	15	0.375	RNA PCR Primer, Index 1 (100% over 33bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	11	0.27499999999999997	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	10	0.25	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	9	0.22499999999999998	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 48 (100% over 50bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCG	7	0.17500000000000002	RNA PCR Primer, Index 10 (97% over 36bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	6	0.15	RNA PCR Primer, Index 3 (100% over 34bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTGGAATT	5	0.125	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTGTGCTTGATCTAACCATGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.25	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.425	0.0	0.0	0.0
4	0.0	0.45	0.0	0.0	0.0
5	0.0	0.475	0.0	0.0	0.0
6	0.0	0.525	0.0	0.0	0.0
7	0.0	1.1	0.0	0.0	0.0
8	0.0	1.2	0.0	0.0	0.0
9	0.0	1.225	0.0	0.0	0.0
10	0.0	1.275	0.0	0.0	0.0
11	0.0	1.4	0.0	0.0	0.0
12	0.0	1.55	0.0	0.0	0.0
13	0.0	1.75	0.0	0.0	0.0
14	0.0	2.025	0.0	0.0	0.0
15	0.0	2.6	0.0	0.0	0.0
16	0.0	3.5	0.0	0.0	0.0
17	0.0	4.225	0.0	0.0	0.0
18	0.0	5.225	0.0	0.0	0.0
19	0.0	5.55	0.0	0.0	0.0
20	0.0	6.325	0.0	0.0	0.0
21	0.0	11.625	0.0	0.0	0.0
22	0.0	24.95	0.0	0.0	0.0
23	0.0	55.175	0.0	0.0	0.0
24	0.0	69.5	0.0	0.0	0.0
25	0.0	75.65	0.0	0.0	0.0
26	0.0	77.15	0.0	0.0	0.0
27	0.0	77.825	0.0	0.0	0.0
28	0.0	78.475	0.0	0.0	0.0
29	0.0	79.1	0.0	0.0	0.0
30	0.0	79.525	0.0	0.0	0.0
31	0.0	80.25	0.0	0.0	0.0
32	0.0	81.05	0.0	0.0	0.0
33	0.0	82.125	0.0	0.0	0.0
34	0.0	85.15	0.0	0.0	0.0
35	0.0	86.05	0.0	0.0	0.0
36	0.0	86.7	0.0	0.0	0.0
37	0.0	87.5	0.0	0.0	0.0
38	0.0	87.85	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	20	6.952051E-4	44.000004	2
CTGAGCT	45	2.728484E-10	44.000004	11
CTTTAAC	20	6.952051E-4	44.000004	12
GAGCTTG	45	2.728484E-10	44.000004	13
GGATCCG	45	2.728484E-10	44.000004	3
CCGTCTG	45	2.728484E-10	44.000004	7
TCGGATC	45	2.728484E-10	44.000004	1
AACCTGT	20	6.952051E-4	44.000004	16
CGGATCC	45	2.728484E-10	44.000004	2
ACATCCT	20	6.952051E-4	44.000004	6
TAACCTG	20	6.952051E-4	44.000004	15
GATCCGT	45	2.728484E-10	44.000004	4
ACCCTTT	20	6.952051E-4	44.000004	9
CCTTTAA	20	6.952051E-4	44.000004	11
GGTAGTA	20	6.952051E-4	44.000004	4
TGAGGTA	20	6.952051E-4	44.000004	1
TCCGTCT	45	2.728484E-10	44.000004	6
GACCCTT	20	6.952051E-4	44.000004	8
ATCCGTC	45	2.728484E-10	44.000004	5
CCCTTTA	20	6.952051E-4	44.000004	10
>>END_MODULE
Read 56628 spots for SRR5031076.sra
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SRR ids: ['SRR5031076.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd__hqtwub4
SRR5031076.sra spots: 2718166
blocks: [[1, 56628], [56629, 113256], [113257, 169884], [169885, 226512], [226513, 283140], [283141, 339768], [339769, 396396], [396397, 453024], [453025, 509652], [509653, 566280], [566281, 622908], [622909, 679536], [679537, 736164], [736165, 792792], [792793, 849420], [849421, 906048], [906049, 962676], [962677, 1019304], [1019305, 1075932], [1075933, 1132560], [1132561, 1189188], [1189189, 1245816], [1245817, 1302444], [1302445, 1359072], [1359073, 1415700], [1415701, 1472328], [1472329, 1528956], [1528957, 1585584], [1585585, 1642212], [1642213, 1698840], [1698841, 1755468], [1755469, 1812096], [1812097, 1868724], [1868725, 1925352], [1925353, 1981980], [1981981, 2038608], [2038609, 2095236], [2095237, 2151864], [2151865, 2208492], [2208493, 2265120], [2265121, 2321748], [2321749, 2378376], [2378377, 2435004], [2435005, 2491632], [2491633, 2548260], [2548261, 2604888], [2604889, 2661516], [2661517, 2718166]]
SRR5031076 file size 470053
SRR5031076 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5031076 SRR5031076_1.fastq
Input file:	SRR5031076_1.fastq
trimmed:	SRR5031076-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):	32
Wed Mar  4 07:19:16 2020 >> started

Wed Mar  4 07:19:17 2020 >> done (1.683s)
2718166 reads processed; of these:
    203 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
2717957 (99.99%) reads available; of these:
 136481 ( 5.02%) trimmed reads available after processing
2581476 (94.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     53	  0.00%
 19	     62	  0.00%
 20	    143	  0.01%
 21	    201	  0.01%
 22	    332	  0.01%
 23	    370	  0.01%
 24	    390	  0.01%
 25	    500	  0.02%
 26	    453	  0.02%
 27	    580	  0.02%
 28	    715	  0.03%
 29	   1071	  0.04%
 30	    694	  0.03%
 31	    819	  0.03%
 32	    869	  0.03%
 33	   1157	  0.04%
 34	   1247	  0.05%
 35	   2402	  0.09%
 36	   2139	  0.08%
 37	   2443	  0.09%
 38	   2271	  0.08%
 39	   2471	  0.09%
 40	   2798	  0.10%
 41	   2788	  0.10%
 42	   3700	  0.14%
 43	   5364	  0.20%
 44	   8030	  0.30%
 45	  10022	  0.37%
 46	  13817	  0.51%
 47	  17864	  0.66%
 48	  25323	  0.93%
 49	  25393	  0.93%
 50	2581476	 94.98%
2717957 reads passed initial QC


criterion=sequence-density
sequence-density=87.67
sequence-density-rank=1
fanout-score=20.26
fanout-score-rank=1
prefix-density=89.70
prefix-fanout=19.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC


criterion=fanout-score
sequence-density=87.67
sequence-density-rank=1
fanout-score=20.26
fanout-score-rank=1
prefix-density=89.70
prefix-fanout=19.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC -o SRR5031076 -
Input file:	STDIN
trimmed:	SRR5031076-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGGCAATCTCGTATGCC
-- 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):	32
Wed Mar  4 07:19:34 2020 >> started

Wed Mar  4 07:19:38 2020 >> done (4.089s)
2656185 reads processed; of these:
 129002 ( 4.86%) short reads filtered out after trimming by size control
   8819 ( 0.33%) empty reads filtered out after trimming by size control
2518364 (94.81%) reads available; of these:
2415357 (95.91%) trimmed reads available after processing
 103007 ( 4.09%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13088	  0.52%
 19	  26320	  1.05%
 20	 143479	  5.70%
 21	 328890	 13.06%
 22	 836285	 33.21%
 23	 373187	 14.82%
 24	 172478	  6.85%
 25	  43322	  1.72%
 26	  22362	  0.89%
 27	  18185	  0.72%
 28	  19506	  0.77%
 29	  14507	  0.58%
 30	  21486	  0.85%
 31	  24229	  0.96%
 32	  30667	  1.22%
 33	  78441	  3.11%
 34	  26287	  1.04%
 35	  18605	  0.74%
 36	  21505	  0.85%
 37	  12028	  0.48%
 38	  13125	  0.52%
 39	  12411	  0.49%
 40	  20633	  0.82%
 41	  26635	  1.06%
 42	  29794	  1.18%
 43	  20682	  0.82%
 44	  15210	  0.60%
 45	  20459	  0.81%
 46	  14663	  0.58%
 47	  11170	  0.44%
 48	   1028	  0.04%
 49	   1366	  0.05%
 50	  86331	  3.43%


criterion=sequence-density
sequence-density=6.73
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=39
fanout-score=92.77
fanout-score-rank=1
prefix-density=1.91
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:20:17
                             Started mapping on |	Mar 04 07:20:17
                                    Finished on |	Mar 04 07:20:46
       Mapping speed, Million of reads per hour |	320.29

                          Number of input reads |	2580136
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1385010
                        Uniquely mapped reads % |	53.68%
                          Average mapped length |	24.26
                       Number of splices: Total |	1510
            Number of splices: Annotated (sjdb) |	269
                       Number of splices: GT/AG |	1411
                       Number of splices: GC/AG |	21
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	78
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.09
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	886004
             % of reads mapped to multiple loci |	34.34%
        Number of reads mapped to too many loci |	44342
             % of reads mapped to too many loci |	1.72%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.73%
                     % of reads unmapped: other |	0.53%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	309122	309122	309122
N_multimapping	886004	886004	886004
N_noFeature	58943	73810	954575
N_ambiguous	793293	422348	11266
UnstrandedReadsAssigned:532774 PositiveStrandReadsAssigned:888852 NegativeStrandReadsAssigned:419169
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031076 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: SRR5031076-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,580,136 reads, 681,202 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,125 rounds

 109283 SRR5031076.ke.tsv
  52636 SRR5031076.se.tsv
 161919 total
==> SRR5031076.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

==> SRR5031076.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031076 completed mapping pipeline successfully
