Starting /dee2/code/volunteer_pipeline.sh SRR5031075
    current disk space = 160487997440
    free memory = 73946348 
SRR5031075 SRAfilesize
316485a7edacc080aacafbd7a9331459  SRR5031075.sra
SRR5031075.sra file validated
SRR5031075 is single end
SRR5031075 is conventional basespace
SRR5031075 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031075_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	32.332	33.0	31.0	34.0	31.0	34.0
2	32.6005	34.0	31.0	34.0	31.0	34.0
3	32.618	34.0	31.0	34.0	31.0	34.0
4	36.173	37.0	35.0	37.0	35.0	37.0
5	35.917	37.0	35.0	37.0	35.0	37.0
6	35.7865	37.0	35.0	37.0	33.0	37.0
7	35.9725	37.0	35.0	37.0	35.0	37.0
8	35.8115	37.0	35.0	37.0	35.0	37.0
9	37.585	39.0	37.0	39.0	35.0	39.0
10	37.76875	39.0	37.0	39.0	35.0	39.0
11	37.6335	39.0	37.0	39.0	35.0	39.0
12	37.629	39.0	37.0	39.0	35.0	39.0
13	37.65675	39.0	37.0	39.0	35.0	39.0
14	39.1185	41.0	38.0	41.0	36.0	41.0
15	38.898	40.0	38.0	41.0	35.0	41.0
16	38.95	40.0	38.0	41.0	35.0	41.0
17	38.86075	40.0	38.0	41.0	35.0	41.0
18	39.0315	40.0	38.0	41.0	35.0	41.0
19	38.76675	40.0	38.0	41.0	35.0	41.0
20	38.90025	40.0	38.0	41.0	35.0	41.0
21	38.8025	40.0	38.0	41.0	34.0	41.0
22	38.9705	40.0	38.0	41.0	35.0	41.0
23	38.76775	40.0	38.0	41.0	35.0	41.0
24	38.798	40.0	38.0	41.0	34.0	41.0
25	39.083	41.0	39.0	41.0	35.0	41.0
26	38.84425	40.0	38.0	41.0	35.0	41.0
27	38.77925	40.0	38.0	41.0	34.0	41.0
28	38.72225	40.0	38.0	41.0	35.0	41.0
29	38.2565	40.0	38.0	41.0	33.0	41.0
30	38.26625	40.0	38.0	41.0	33.0	41.0
31	38.5235	40.0	38.0	41.0	34.0	41.0
32	38.38	40.0	38.0	41.0	34.0	41.0
33	38.4075	40.0	38.0	41.0	34.0	41.0
34	38.54925	40.0	38.0	41.0	34.0	41.0
35	38.22425	40.0	38.0	41.0	34.0	41.0
36	37.97525	40.0	37.0	41.0	33.0	41.0
37	37.38375	39.0	37.0	41.0	31.0	41.0
38	36.6785	39.0	35.0	41.0	30.0	41.0
39	37.09575	39.0	36.0	41.0	31.0	41.0
40	37.462	40.0	37.0	41.0	31.0	41.0
41	37.5335	40.0	37.0	41.0	32.0	41.0
42	37.7765	40.0	37.0	41.0	33.0	41.0
43	37.96175	40.0	37.0	41.0	33.0	41.0
44	37.64275	40.0	37.0	41.0	33.0	41.0
45	37.60475	40.0	37.0	41.0	33.0	41.0
46	37.6115	40.0	37.0	41.0	33.0	41.0
47	37.26225	40.0	36.0	41.0	31.0	41.0
48	36.85775	40.0	36.0	41.0	31.0	41.0
49	37.1495	40.0	36.0	41.0	32.0	41.0
50	36.553	39.0	35.0	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
14	1.0
15	3.0
16	1.0
17	0.0
18	0.0
19	2.0
20	3.0
21	3.0
22	2.0
23	8.0
24	6.0
25	12.0
26	10.0
27	11.0
28	25.0
29	40.0
30	51.0
31	75.0
32	74.0
33	111.0
34	152.0
35	214.0
36	285.0
37	454.0
38	685.0
39	1772.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.95	25.650000000000002	49.325	16.075
2	24.380475594493117	26.758448060075096	18.823529411764707	30.037546933667088
3	24.125	20.7	22.625	32.550000000000004
4	34.525	27.375	14.625	23.474999999999998
5	22.1	40.1	26.5	11.3
6	34.425	15.8	34.55	15.225
7	17.075000000000003	21.075	22.0	39.85
8	24.575	28.000000000000004	15.975	31.45
9	22.900000000000002	32.525	27.450000000000003	17.125
10	21.6	22.075	28.349999999999998	27.975
11	31.55	10.125	17.224999999999998	41.099999999999994
12	15.950000000000001	17.599999999999998	32.5	33.95
13	32.975	16.675	32.2	18.15
14	32.574999999999996	31.3	19.75	16.375
15	36.35	24.525	25.8	13.325000000000001
16	18.875	18.65	24.224999999999998	38.25
17	25.224999999999998	22.3	37.7	14.774999999999999
18	25.75	16.975	29.775000000000002	27.500000000000004
19	36.925000000000004	13.975000000000001	31.45	17.65
20	44.0	15.15	26.775	14.075
21	23.674999999999997	20.599999999999998	26.424999999999997	29.299999999999997
22	29.825000000000003	12.25	46.0	11.924999999999999
23	27.275	13.3	43.35	16.075
24	50.8	14.524999999999999	26.424999999999997	8.25
25	50.425	24.45	15.8	9.325
26	29.525000000000002	44.224999999999994	14.475	11.774999999999999
27	15.625	46.475	23.7	14.2
28	11.275	24.525	47.975	16.225
29	12.35	13.55	56.175	17.925
30	10.025	6.800000000000001	37.075	46.1
31	15.525	5.25	45.574999999999996	33.650000000000006
32	29.5	5.25	22.1	43.15
33	52.225	8.799999999999999	14.149999999999999	24.825
34	60.650000000000006	6.7250000000000005	17.7	14.924999999999999
35	65.14999999999999	6.625	18.525	9.700000000000001
36	43.85	6.75	35.925000000000004	13.475000000000001
37	43.275000000000006	11.325000000000001	21.099999999999998	24.3
38	24.375	16.675	13.275	45.675
39	16.55	23.45	10.725	49.275000000000006
40	16.5	46.400000000000006	11.450000000000001	25.650000000000002
41	25.575	48.675000000000004	7.9750000000000005	17.775
42	47.699999999999996	30.775000000000002	11.4	10.125
43	51.275000000000006	29.225	7.85	11.65
44	32.4	46.2	8.0	13.4
45	19.15	48.4	13.55	18.9
46	14.149999999999999	26.174999999999997	17.625	42.05
47	9.425	15.225	37.65	37.7
48	11.924999999999999	12.575	21.325	54.175
49	12.65	18.725	15.85	52.775000000000006
50	18.9	34.625	13.825000000000001	32.65
>>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	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	1.5
26	3.0
27	1.5
28	0.0
29	0.5
30	1.0
31	6.0
32	11.0
33	13.5
34	16.0
35	17.5
36	19.0
37	21.5
38	24.0
39	32.0
40	40.0
41	53.5
42	67.0
43	85.0
44	103.0
45	142.0
46	181.0
47	309.0
48	437.0
49	535.5
50	634.0
51	752.0
52	870.0
53	635.0
54	400.0
55	454.0
56	508.0
57	363.0
58	218.0
59	146.0
60	74.0
61	56.5
62	39.0
63	90.5
64	142.0
65	87.0
66	32.0
67	27.5
68	23.0
69	33.5
70	44.0
71	71.0
72	98.0
73	51.5
74	5.0
75	4.0
76	3.0
77	3.0
78	3.0
79	2.5
80	2.0
81	2.5
82	3.0
83	1.5
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	0.125
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	36.8
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.13586956521739	27.650000000000002
2	10.326086956521738	7.6
3	4.3478260869565215	4.8
4	2.4456521739130435	3.5999999999999996
5	1.2907608695652173	2.375
6	1.2228260869565217	2.7
7	0.6114130434782609	1.575
8	0.5434782608695652	1.6
9	0.6793478260869565	2.25
>10	2.717391304347826	20.674999999999997
>50	0.33967391304347827	9.700000000000001
>100	0.33967391304347827	15.475
>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	148	3.6999999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	134	3.35	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	118	2.9499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	113	2.825	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	106	2.65	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	99	2.475	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	94	2.35	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	75	1.875	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	56	1.4000000000000001	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	47	1.175	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	43	1.075	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	42	1.05	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	31	0.775	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTC	29	0.7250000000000001	RNA PCR Primer, Index 5 (97% over 35bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	26	0.65	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	15	0.375	No Hit
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTC	14	0.35000000000000003	RNA PCR Primer, Index 47 (100% over 44bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 31bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	10	0.25	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	9	0.22499999999999998	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 47 (100% over 50bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	8	0.2	RNA PCR Primer, Index 1 (100% over 24bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	6	0.15	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	6	0.15	RNA PCR Primer, Index 3 (100% over 34bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AAACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
GTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.3	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.4	0.0	0.0	0.0
5	0.0	0.475	0.0	0.0	0.0
6	0.0	0.5	0.0	0.0	0.0
7	0.0	0.95	0.0	0.0	0.0
8	0.0	1.075	0.0	0.0	0.0
9	0.0	1.125	0.0	0.0	0.0
10	0.0	1.375	0.0	0.0	0.0
11	0.0	1.45	0.0	0.0	0.0
12	0.0	1.6	0.0	0.0	0.0
13	0.0	1.8	0.0	0.0	0.0
14	0.0	2.0	0.0	0.0	0.0
15	0.0	2.375	0.0	0.0	0.0
16	0.0	3.55	0.0	0.0	0.0
17	0.0	4.175	0.0	0.0	0.0
18	0.0	5.375	0.0	0.0	0.0
19	0.0	5.675	0.0	0.0	0.0
20	0.0	6.925	0.0	0.0	0.0
21	0.0	12.725	0.0	0.0	0.0
22	0.0	23.725	0.0	0.0	0.0
23	0.0	51.875	0.0	0.0	0.0
24	0.0	65.675	0.0	0.0	0.0
25	0.0	71.775	0.0	0.0	0.0
26	0.0	73.325	0.0	0.0	0.0
27	0.0	74.1	0.0	0.0	0.0
28	0.0	74.8	0.0	0.0	0.0
29	0.0	75.325	0.0	0.0	0.0
30	0.0	76.025	0.0	0.0	0.0
31	0.0	76.825	0.0	0.0	0.0
32	0.0	77.85	0.0	0.0	0.0
33	0.0	78.775	0.0	0.0	0.0
34	0.0	82.4	0.0	0.0	0.0
35	0.0	83.325	0.0	0.0	0.0
36	0.0	84.05	0.0	0.0	0.0
37	0.0	85.05	0.0	0.0	0.0
38	0.0	85.65	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	40	5.315087E-9	44.000004	8
GGTGAGT	40	5.315087E-9	44.000004	17
ACGCTGT	40	5.315087E-9	44.000004	9
CTTTAAC	20	6.952051E-4	44.000004	12
TTCAACG	40	5.315087E-9	44.000004	5
TCGGTGA	40	5.315087E-9	44.000004	15
AACCTGT	20	6.952051E-4	44.000004	16
CATTCAA	40	5.315087E-9	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
CTTGGCT	20	6.952051E-4	44.000004	16
TAACCTG	20	6.952051E-4	44.000004	15
GCTGTCG	45	2.728484E-10	44.000004	11
ACCCTTT	20	6.952051E-4	44.000004	9
CGGTGAG	40	5.315087E-9	44.000004	16
CCTTTAA	20	6.952051E-4	44.000004	11
TTGGCTT	20	6.952051E-4	44.000004	17
GACCCTT	20	6.952051E-4	44.000004	8
CCCTTTA	20	6.952051E-4	44.000004	10
CTGTCGG	45	2.728484E-10	44.000004	12
TTAACCT	20	6.952051E-4	44.000004	14
>>END_MODULE
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219653 spots for SRR5031075.sra
Written 219653 spots for SRR5031075.sra
Read 219657 spots for SRR5031075.sra
Written 219657 spots for SRR5031075.sra
SRR ids: ['SRR5031075.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_9i9ylf8r
SRR5031075.sra spots: 2635840
blocks: [[1, 219653], [219654, 439306], [439307, 658959], [658960, 878612], [878613, 1098265], [1098266, 1317918], [1317919, 1537571], [1537572, 1757224], [1757225, 1976877], [1976878, 2196530], [2196531, 2416183], [2416184, 2635840]]
SRR5031075 file size 455783
SRR5031075 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031075 SRR5031075_1.fastq
Input file:	SRR5031075_1.fastq
trimmed:	SRR5031075-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 07:19:00 2020 >> started

Wed Mar  4 07:19:02 2020 >> done (1.360s)
2635840 reads processed; of these:
    203 ( 0.01%) short reads filtered out after trimming by size control
      7 ( 0.00%) empty reads filtered out after trimming by size control
2635630 (99.99%) reads available; of these:
 128803 ( 4.89%) trimmed reads available after processing
2506827 (95.11%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     58	  0.00%
 19	     82	  0.00%
 20	    150	  0.01%
 21	    190	  0.01%
 22	    313	  0.01%
 23	    362	  0.01%
 24	    436	  0.02%
 25	    587	  0.02%
 26	    468	  0.02%
 27	    622	  0.02%
 28	    706	  0.03%
 29	   1014	  0.04%
 30	    657	  0.02%
 31	    811	  0.03%
 32	    852	  0.03%
 33	   1123	  0.04%
 34	   1394	  0.05%
 35	   2798	  0.11%
 36	   2508	  0.10%
 37	   2856	  0.11%
 38	   2556	  0.10%
 39	   2767	  0.10%
 40	   3033	  0.12%
 41	   2982	  0.11%
 42	   3815	  0.14%
 43	   5338	  0.20%
 44	   7083	  0.27%
 45	   8830	  0.34%
 46	  12797	  0.49%
 47	  15551	  0.59%
 48	  22893	  0.87%
 49	  23171	  0.88%
 50	2506827	 95.11%
2635630 reads passed initial QC


criterion=sequence-density
sequence-density=84.69
sequence-density-rank=1
fanout-score=21.15
fanout-score-rank=1
prefix-density=86.74
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC


criterion=fanout-score
sequence-density=84.69
sequence-density-rank=1
fanout-score=21.15
fanout-score-rank=1
prefix-density=86.74
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC -o SRR5031075 -
Input file:	STDIN
trimmed:	SRR5031075-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTCGAAGATCTCGTATGCC
-- 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 07:19:15 2020 >> started

Wed Mar  4 07:19:18 2020 >> done (2.967s)
2573615 reads processed; of these:
 136817 ( 5.32%) short reads filtered out after trimming by size control
  10366 ( 0.40%) empty reads filtered out after trimming by size control
2426432 (94.28%) reads available; of these:
2281376 (94.02%) trimmed reads available after processing
 145056 ( 5.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12703	  0.52%
 19	  26923	  1.11%
 20	 134290	  5.53%
 21	 292354	 12.05%
 22	 733848	 30.24%
 23	 350159	 14.43%
 24	 169360	  6.98%
 25	  44955	  1.85%
 26	  22665	  0.93%
 27	  17695	  0.73%
 28	  19989	  0.82%
 29	  16122	  0.66%
 30	  22295	  0.92%
 31	  26324	  1.08%
 32	  29634	  1.22%
 33	  83064	  3.42%
 34	  26091	  1.08%
 35	  19401	  0.80%
 36	  22561	  0.93%
 37	  13057	  0.54%
 38	  15155	  0.62%
 39	  13671	  0.56%
 40	  21523	  0.89%
 41	  29283	  1.21%
 42	  34244	  1.41%
 43	  23158	  0.95%
 44	  17002	  0.70%
 45	  26618	  1.10%
 46	  19248	  0.79%
 47	  14136	  0.58%
 48	   1300	  0.05%
 49	   1565	  0.06%
 50	 126039	  5.19%


criterion=sequence-density
sequence-density=7.19
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=37
fanout-score=107.78
fanout-score-rank=1
prefix-density=1.79
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:19:38
                             Started mapping on |	Mar 04 07:19:38
                                    Finished on |	Mar 04 07:20:03
       Mapping speed, Million of reads per hour |	358.34

                          Number of input reads |	2488447
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1282410
                        Uniquely mapped reads % |	51.53%
                          Average mapped length |	24.62
                       Number of splices: Total |	1956
            Number of splices: Annotated (sjdb) |	252
                       Number of splices: GT/AG |	1868
                       Number of splices: GC/AG |	23
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	65
                      Mismatch rate per base, % |	0.22%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.85
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	830134
             % of reads mapped to multiple loci |	33.36%
        Number of reads mapped to too many loci |	46279
             % of reads mapped to too many loci |	1.86%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	12.62%
                     % of reads unmapped: other |	0.63%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	375903	375903	375903
N_multimapping	830134	830134	830134
N_noFeature	62782	78104	889091
N_ambiguous	714679	374589	12268
UnstrandedReadsAssigned:504949 PositiveStrandReadsAssigned:829717 NegativeStrandReadsAssigned:381051
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031075 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: SRR5031075-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,488,447 reads, 609,878 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,108 rounds

 109283 SRR5031075.ke.tsv
  52636 SRR5031075.se.tsv
 161919 total
==> SRR5031075.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

==> SRR5031075.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031075 completed mapping pipeline successfully
