Starting /dee2/code/volunteer_pipeline.sh SRR5030885
    current disk space = 160643203072
    free memory = 73952948 
SRR5030885 SRAfilesize
7e58f36030d3311be198ab2a308b6202  SRR5030885.sra
SRR5030885.sra file validated
SRR5030885 is single end
SRR5030885 is conventional basespace
SRR5030885 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030885_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	32.3005	33.0	31.0	34.0	31.0	34.0
2	32.66975	34.0	31.0	34.0	31.0	34.0
3	32.639	34.0	31.0	34.0	31.0	34.0
4	36.2085	37.0	37.0	37.0	35.0	37.0
5	36.2315	37.0	37.0	37.0	35.0	37.0
6	36.08325	37.0	35.0	37.0	35.0	37.0
7	36.073	37.0	35.0	37.0	35.0	37.0
8	36.1705	37.0	36.0	37.0	35.0	37.0
9	37.90475	39.0	38.0	39.0	35.0	39.0
10	37.83925	39.0	38.0	39.0	35.0	39.0
11	37.879	39.0	38.0	39.0	35.0	39.0
12	37.6135	39.0	38.0	39.0	35.0	39.0
13	37.689	39.0	38.0	39.0	35.0	39.0
14	39.0995	40.0	39.0	41.0	36.0	41.0
15	39.20825	41.0	39.0	41.0	36.0	41.0
16	39.136	40.0	39.0	41.0	36.0	41.0
17	39.2125	40.0	39.0	41.0	36.0	41.0
18	39.324	41.0	39.0	41.0	36.0	41.0
19	39.2485	41.0	39.0	41.0	36.0	41.0
20	39.049	41.0	39.0	41.0	36.0	41.0
21	39.08325	40.0	39.0	41.0	36.0	41.0
22	39.24175	41.0	39.0	41.0	36.0	41.0
23	39.245	41.0	39.0	41.0	36.0	41.0
24	38.39675	40.0	38.0	41.0	33.0	41.0
25	38.6145	40.0	38.0	41.0	34.0	41.0
26	38.7895	40.0	38.0	41.0	34.0	41.0
27	38.86225	41.0	38.0	41.0	35.0	41.0
28	38.62625	40.0	38.0	41.0	34.0	41.0
29	38.2335	40.0	38.0	41.0	33.0	41.0
30	38.40125	40.0	38.0	41.0	33.0	41.0
31	38.842	40.0	38.0	41.0	35.0	41.0
32	38.7685	40.0	38.0	41.0	35.0	41.0
33	37.4605	40.0	37.0	41.0	31.0	41.0
34	37.39575	40.0	37.0	41.0	31.0	41.0
35	37.37475	39.0	37.0	41.0	31.0	41.0
36	32.61625	37.0	30.0	40.0	15.0	41.0
37	35.26375	38.0	33.0	40.0	27.0	41.0
38	36.80525	39.0	36.0	40.0	31.0	41.0
39	37.08125	39.0	37.0	40.0	31.0	41.0
40	36.91325	39.0	37.0	40.0	31.0	41.0
41	36.8335	39.0	36.0	40.0	31.0	41.0
42	36.7265	39.0	36.0	40.0	31.0	41.0
43	36.74725	39.0	36.0	40.0	30.0	41.0
44	36.9345	39.0	37.0	41.0	31.0	41.0
45	36.49725	39.0	36.0	40.0	31.0	41.0
46	33.967	38.0	33.0	40.0	23.0	41.0
47	35.06475	38.0	34.0	40.0	27.0	41.0
48	35.07425	38.0	34.0	40.0	28.0	41.0
49	34.07625	38.0	34.0	40.0	24.0	41.0
50	30.0605	34.0	27.0	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
14	1.0
15	1.0
16	0.0
17	1.0
18	3.0
19	3.0
20	6.0
21	7.0
22	8.0
23	19.0
24	13.0
25	14.0
26	20.0
27	24.0
28	30.0
29	43.0
30	60.0
31	77.0
32	101.0
33	137.0
34	176.0
35	223.0
36	319.0
37	506.0
38	1011.0
39	1197.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.283421118635566	22.623526460998246	50.8653122648608	16.227740155505394
2	22.7	23.849999999999998	20.825	32.625
3	26.163081540770385	19.884942471235618	20.060030015007506	33.89194597298649
4	31.474999999999998	28.499999999999996	13.0	27.025
5	18.625	44.074999999999996	23.849999999999998	13.450000000000001
6	34.225	16.7	34.425	14.649999999999999
7	18.375	19.45	24.775	37.4
8	25.1	30.675	15.825	28.4
9	23.175	33.525	27.875	15.425
10	23.150000000000002	20.625	31.65	24.575
11	28.849999999999998	12.575	17.275	41.3
12	15.1	22.05	30.575000000000003	32.275
13	29.849999999999998	21.3	29.099999999999998	19.75
14	27.375	33.225	21.725	17.675
15	36.0	25.6	24.925	13.475000000000001
16	18.925	21.825	22.675	36.575
17	20.625	22.95	41.425	15.0
18	22.025	19.775000000000002	33.475	24.725
19	39.900000000000006	14.924999999999999	28.349999999999998	16.825000000000003
20	42.975	16.55	28.050000000000004	12.425
21	24.05	18.125	27.85	29.975
22	30.175	12.35	46.550000000000004	10.925
23	28.849999999999998	12.075	42.675000000000004	16.400000000000002
24	52.6	14.799999999999999	24.05	8.55
25	45.925	27.150000000000002	14.975	11.95
26	24.7	46.35	15.475	13.475000000000001
27	16.8	44.3	25.45	13.450000000000001
28	12.525	21.425	48.25	17.8
29	12.4	13.25	53.525	20.825
30	10.424999999999999	8.35	33.525	47.699999999999996
31	16.7	6.65	45.925	30.725
32	31.3	7.925	18.275	42.5
33	54.7	11.924999999999999	12.825000000000001	20.549999999999997
34	57.425000000000004	9.225	17.424999999999997	15.925
35	60.224999999999994	7.475	20.674999999999997	11.625
36	43.675000000000004	9.2	32.300000000000004	14.825
37	43.85	11.625	18.375	26.150000000000002
38	20.325	17.424999999999997	13.425	48.825
39	16.375	26.575	11.0	46.050000000000004
40	16.3	48.85	13.875000000000002	20.974999999999998
41	26.724999999999998	45.050000000000004	11.975	16.25
42	50.375	26.775	12.35	10.5
43	46.800000000000004	31.775	10.45	10.975
44	27.150000000000002	49.725	8.05	15.075
45	18.575	49.025	13.275	19.125
46	14.05	24.9	20.75	40.300000000000004
47	10.5	15.6	40.0	33.900000000000006
48	13.003250812703177	13.778444611152787	18.154538634658664	55.06376594148538
49	15.1	21.675	14.674999999999999	48.55
50	20.225	36.1	15.275	28.4
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.5
20	1.0
21	0.5
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	2.0
28	3.0
29	5.0
30	7.0
31	10.0
32	13.0
33	22.0
34	31.0
35	34.5
36	38.0
37	51.5
38	65.0
39	60.5
40	56.0
41	62.0
42	68.0
43	96.5
44	125.0
45	190.5
46	256.0
47	342.0
48	428.0
49	512.0
50	596.0
51	682.5
52	769.0
53	597.0
54	425.0
55	449.0
56	473.0
57	373.0
58	273.0
59	171.0
60	69.0
61	57.5
62	46.0
63	88.0
64	130.0
65	85.5
66	41.0
67	27.5
68	14.0
69	14.5
70	15.0
71	26.0
72	37.0
73	20.5
74	4.0
75	3.0
76	2.0
77	3.5
78	5.0
79	6.5
80	8.0
81	4.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.325
2	0.0
3	0.05
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	0.025
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	40.1
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.81296758104739	30.0
2	10.41147132169576	8.35
3	4.675810473815462	5.625
4	2.680798004987531	4.3
5	1.1221945137157108	2.25
6	0.6857855361596009	1.6500000000000001
7	0.9351620947630923	2.625
8	0.3740648379052369	1.2
9	0.3740648379052369	1.35
>10	3.366583541147132	23.775
>50	0.3740648379052369	10.225
>100	0.18703241895261846	8.649999999999999
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	119	2.9749999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	117	2.9250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	110	2.75	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	86	2.15	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	82	2.0500000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	70	1.7500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	63	1.575	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	57	1.425	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	51	1.275	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	36	0.8999999999999999	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	30	0.75	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	22	0.5499999999999999	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	21	0.525	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	20	0.5	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	20	0.5	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (100% over 30bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	19	0.475	RNA PCR Primer, Index 1 (100% over 35bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	17	0.42500000000000004	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTC	15	0.375	RNA PCR Primer, Index 1 (100% over 44bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	14	0.35000000000000003	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	14	0.35000000000000003	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	13	0.325	No Hit
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	12	0.3	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	12	0.3	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGC	10	0.25	RNA PCR Primer, Index 1 (100% over 50bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	10	0.25	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	9	0.22499999999999998	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	8	0.2	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	7	0.17500000000000002	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	7	0.17500000000000002	No Hit
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	7	0.17500000000000002	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	7	0.17500000000000002	No Hit
TAGCAGCACGTAAATATTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	6	0.15	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TTTCTATGATGAATCAAACTAGCTCACTATGACTGCTAATGAAAACACAG	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CTCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAG	5	0.125	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TATGCAAGGGCAAGCTCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATGGAAT	5	0.125	No Hit
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	5	0.125	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.25	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.325	0.0	0.0	0.0
4	0.0	0.35	0.0	0.0	0.0
5	0.0	0.375	0.0	0.0	0.0
6	0.0	0.4	0.0	0.0	0.0
7	0.0	0.95	0.0	0.0	0.0
8	0.0	1.175	0.0	0.0	0.0
9	0.0	1.3	0.0	0.0	0.0
10	0.0	1.375	0.0	0.0	0.0
11	0.0	1.6	0.0	0.0	0.0
12	0.0	1.825	0.0	0.0	0.0
13	0.0	2.025	0.0	0.0	0.0
14	0.0	2.25	0.0	0.0	0.0
15	0.0	2.5	0.0	0.0	0.0
16	0.0	3.3	0.0	0.0	0.0
17	0.0	3.7	0.0	0.0	0.0
18	0.0	4.75	0.0	0.0	0.0
19	0.0	5.375	0.0	0.0	0.0
20	0.0	6.3	0.0	0.0	0.0
21	0.0	12.225	0.0	0.0	0.0
22	0.0	24.25	0.0	0.0	0.0
23	0.0	52.45	0.0	0.0	0.0
24	0.0	62.05	0.0	0.0	0.0
25	0.0	67.125	0.0	0.0	0.0
26	0.0	68.15	0.0	0.0	0.0
27	0.0	68.675	0.0	0.0	0.0
28	0.0	69.05	0.0	0.0	0.0
29	0.0	69.475	0.0	0.0	0.0
30	0.0	69.75	0.0	0.0	0.0
31	0.0	70.375	0.0	0.0	0.0
32	0.0	71.075	0.0	0.0	0.0
33	0.0	71.9	0.0	0.0	0.0
34	0.0	75.2	0.0	0.0	0.0
35	0.0	76.575	0.0	0.0	0.0
36	0.0	77.3	0.0	0.0	0.0
37	0.0	78.15	0.0	0.0	0.0
38	0.0	78.725	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTTTTGG	20	6.952051E-4	44.000004	18
GAGGTAG	20	6.952051E-4	44.000004	2
CTTGGTG	20	6.952051E-4	44.000004	16
GGTAGTA	20	6.952051E-4	44.000004	4
TTGGCTT	20	6.952051E-4	44.000004	17
TTGGTGG	20	6.952051E-4	44.000004	17
CTGTTGG	20	6.952051E-4	44.000004	19
TCTTTTG	20	6.952051E-4	44.000004	17
GTAGTAG	20	6.952051E-4	44.000004	5
TGTAAAC	20	6.952051E-4	44.000004	1
ACCGGTC	25	3.6958358E-5	44.0	10
AACCGGT	25	3.6958358E-5	44.0	9
GGTCTCT	25	3.6958358E-5	44.0	13
CTCTTTT	25	3.6958358E-5	44.0	16
GAGCTTG	55	0.0	44.0	13
GGATCCG	55	0.0	44.0	3
CCGTCTG	50	1.4551915E-11	44.0	7
TCGGATC	55	0.0	44.0	1
CGGATCC	55	0.0	44.0	2
CTTGGCT	30	1.9515464E-6	44.0	16
>>END_MODULE
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
Read 317704 spots for SRR5030885.sra
Written 317704 spots for SRR5030885.sra
Read 317703 spots for SRR5030885.sra
Written 317703 spots for SRR5030885.sra
SRR ids: ['SRR5030885.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_scc9we1y
SRR5030885.sra spots: 3812437
blocks: [[1, 317703], [317704, 635406], [635407, 953109], [953110, 1270812], [1270813, 1588515], [1588516, 1906218], [1906219, 2223921], [2223922, 2541624], [2541625, 2859327], [2859328, 3177030], [3177031, 3494733], [3494734, 3812437]]
SRR5030885 file size 659701
SRR5030885 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030885 SRR5030885_1.fastq
Input file:	SRR5030885_1.fastq
trimmed:	SRR5030885-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 06:36:41 2020 >> started

Wed Mar  4 06:36:43 2020 >> done (2.293s)
3812437 reads processed; of these:
    208 ( 0.01%) short reads filtered out after trimming by size control
     10 ( 0.00%) empty reads filtered out after trimming by size control
3812219 (99.99%) reads available; of these:
 310175 ( 8.14%) trimmed reads available after processing
3502044 (91.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     67	  0.00%
 19	     82	  0.00%
 20	    230	  0.01%
 21	    216	  0.01%
 22	    370	  0.01%
 23	    497	  0.01%
 24	    546	  0.01%
 25	    630	  0.02%
 26	    553	  0.01%
 27	    743	  0.02%
 28	    906	  0.02%
 29	   1310	  0.03%
 30	   1021	  0.03%
 31	   1376	  0.04%
 32	   1759	  0.05%
 33	   3256	  0.09%
 34	   9282	  0.24%
 35	   4546	  0.12%
 36	   3497	  0.09%
 37	   3396	  0.09%
 38	   5290	  0.14%
 39	   4663	  0.12%
 40	   8057	  0.21%
 41	   6094	  0.16%
 42	  10171	  0.27%
 43	   8384	  0.22%
 44	  23763	  0.62%
 45	  21076	  0.55%
 46	  20833	  0.55%
 47	  25637	  0.67%
 48	  58620	  1.54%
 49	  83304	  2.19%
 50	3502044	 91.86%
3812219 reads passed initial QC


criterion=sequence-density
sequence-density=77.60
sequence-density-rank=1
fanout-score=19.52
fanout-score-rank=2
prefix-density=79.90
prefix-fanout=19.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC


criterion=fanout-score
sequence-density=1.97
sequence-density-rank=9
fanout-score=122.48
fanout-score-rank=1
prefix-density=79.53
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC -o SRR5030885 -
Input file:	STDIN
trimmed:	SRR5030885-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 06:37:04 2020 >> started

Wed Mar  4 06:37:09 2020 >> done (4.990s)
3714470 reads processed; of these:
 172003 ( 4.63%) short reads filtered out after trimming by size control
  12204 ( 0.33%) empty reads filtered out after trimming by size control
3530263 (95.04%) reads available; of these:
3059598 (86.67%) trimmed reads available after processing
 470665 (13.33%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17434	  0.49%
 19	  31843	  0.90%
 20	 204892	  5.80%
 21	 411580	 11.66%
 22	1033125	 29.26%
 23	 404076	 11.45%
 24	 184891	  5.24%
 25	  48571	  1.38%
 26	  24132	  0.68%
 27	  20410	  0.58%
 28	  21036	  0.60%
 29	  16284	  0.46%
 30	  24051	  0.68%
 31	  30801	  0.87%
 32	  32596	  0.92%
 33	 130834	  3.71%
 34	  41909	  1.19%
 35	  33553	  0.95%
 36	  38758	  1.10%
 37	  19562	  0.55%
 38	  20627	  0.58%
 39	  22395	  0.63%
 40	  32200	  0.91%
 41	  41468	  1.17%
 42	  48436	  1.37%
 43	  35220	  1.00%
 44	  31157	  0.88%
 45	  36815	  1.04%
 46	  29700	  0.84%
 47	  26890	  0.76%
 48	   5778	  0.16%
 49	  16906	  0.48%
 50	 412333	 11.68%


criterion=sequence-density
sequence-density=4.28
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.63
sequence-density-rank=20
fanout-score=13.45
fanout-score-rank=1
prefix-density=8.41
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 06:37:34
                             Started mapping on |	Mar 04 06:37:35
                                    Finished on |	Mar 04 06:38:04
       Mapping speed, Million of reads per hour |	450.37

                          Number of input reads |	3628012
                      Average input read length |	29
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2083306
                        Uniquely mapped reads % |	57.42%
                          Average mapped length |	28.11
                       Number of splices: Total |	1453
            Number of splices: Annotated (sjdb) |	311
                       Number of splices: GT/AG |	1313
                       Number of splices: GC/AG |	28
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	112
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.40
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1066570
             % of reads mapped to multiple loci |	29.40%
        Number of reads mapped to too many loci |	93749
             % of reads mapped to too many loci |	2.58%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.12%
                     % of reads unmapped: other |	0.48%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	478136	478136	478136
N_multimapping	1066570	1066570	1066570
N_noFeature	94530	119458	1461037
N_ambiguous	1162204	628430	25395
UnstrandedReadsAssigned:826572 PositiveStrandReadsAssigned:1335418 NegativeStrandReadsAssigned:596874
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030885 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: SRR5030885-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,628,012 reads, 990,028 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,163 rounds

 109283 SRR5030885.ke.tsv
  52636 SRR5030885.se.tsv
 161919 total
==> SRR5030885.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

==> SRR5030885.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030885 completed mapping pipeline successfully
