Starting /dee2/code/volunteer_pipeline.sh SRR5031008
    current disk space = 160546226176
    free memory = 73926560 
SRR5031008 SRAfilesize
91757802cf85f05cefd0f9d89fba5b78  SRR5031008.sra
SRR5031008.sra file validated
SRR5031008 is single end
SRR5031008 is conventional basespace
SRR5031008 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031008_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	32.29525	33.0	31.0	34.0	31.0	34.0
2	32.55325	34.0	31.0	34.0	31.0	34.0
3	32.5645	34.0	31.0	34.0	31.0	34.0
4	36.15875	37.0	35.0	37.0	35.0	37.0
5	36.05575	37.0	35.0	37.0	35.0	37.0
6	35.781	37.0	35.0	37.0	33.0	37.0
7	35.84725	37.0	35.0	37.0	35.0	37.0
8	35.97	37.0	35.0	37.0	35.0	37.0
9	37.594	39.0	37.0	39.0	35.0	39.0
10	37.56525	39.0	37.0	39.0	35.0	39.0
11	37.16075	39.0	37.0	39.0	33.0	39.0
12	37.61475	39.0	37.0	39.0	35.0	39.0
13	37.553	39.0	37.0	39.0	35.0	39.0
14	38.949	40.0	38.0	41.0	35.0	41.0
15	38.89275	40.0	38.0	41.0	35.0	41.0
16	38.808	40.0	38.0	41.0	35.0	41.0
17	39.04075	40.0	38.0	41.0	35.0	41.0
18	38.97675	41.0	38.0	41.0	35.0	41.0
19	38.85525	40.0	38.0	41.0	35.0	41.0
20	38.81075	40.0	38.0	41.0	35.0	41.0
21	38.89925	40.0	38.0	41.0	35.0	41.0
22	38.89325	40.0	38.0	41.0	35.0	41.0
23	38.574	40.0	38.0	41.0	34.0	41.0
24	38.86375	40.0	38.0	41.0	35.0	41.0
25	38.989	40.0	39.0	41.0	35.0	41.0
26	38.87175	40.0	38.0	41.0	35.0	41.0
27	38.96425	40.0	38.0	41.0	35.0	41.0
28	38.6965	40.0	38.0	41.0	35.0	41.0
29	38.44175	40.0	38.0	41.0	34.0	41.0
30	38.198	40.0	38.0	41.0	33.0	41.0
31	38.42125	40.0	38.0	41.0	34.0	41.0
32	38.482	40.0	38.0	41.0	34.0	41.0
33	38.156	40.0	38.0	41.0	33.0	41.0
34	38.239	40.0	38.0	41.0	34.0	41.0
35	37.98475	40.0	38.0	41.0	33.0	41.0
36	37.7705	40.0	37.0	41.0	33.0	41.0
37	37.2795	40.0	37.0	41.0	31.0	41.0
38	37.2125	39.0	36.0	41.0	31.0	41.0
39	37.74175	40.0	37.0	41.0	33.0	41.0
40	37.81225	40.0	37.0	41.0	33.0	41.0
41	38.0135	40.0	37.0	41.0	33.0	41.0
42	37.78575	40.0	37.0	41.0	33.0	41.0
43	37.7075	40.0	37.0	41.0	33.0	41.0
44	37.79675	40.0	37.0	41.0	33.0	41.0
45	37.735	40.0	37.0	41.0	33.0	41.0
46	37.5455	40.0	37.0	41.0	33.0	41.0
47	37.219	40.0	36.0	41.0	31.0	41.0
48	36.9735	40.0	36.0	41.0	31.0	41.0
49	37.11825	40.0	36.0	41.0	32.0	41.0
50	36.49675	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
12	1.0
13	0.0
14	0.0
15	0.0
16	2.0
17	0.0
18	4.0
19	0.0
20	0.0
21	2.0
22	6.0
23	6.0
24	14.0
25	12.0
26	15.0
27	13.0
28	21.0
29	30.0
30	45.0
31	69.0
32	83.0
33	108.0
34	153.0
35	209.0
36	271.0
37	448.0
38	762.0
39	1726.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.875	24.125	49.225	16.775000000000002
2	22.731829573934835	25.71428571428571	20.50125313283208	31.05263157894737
3	24.075	20.05	22.55	33.324999999999996
4	33.825	27.375	15.4	23.400000000000002
5	22.0	37.974999999999994	27.400000000000002	12.625
6	32.95	14.625	36.675000000000004	15.75
7	17.45	22.325	22.175	38.05
8	24.75	27.925	16.2	31.125000000000004
9	24.099999999999998	30.9	29.275000000000002	15.725
10	23.400000000000002	21.075	28.175	27.35
11	29.7	11.774999999999999	18.875	39.65
12	17.075000000000003	17.025000000000002	31.574999999999996	34.325
13	30.9	18.5	31.825	18.775
14	29.299999999999997	32.675	19.975	18.05
15	37.425000000000004	22.3	25.924999999999997	14.35
16	18.625	19.7	24.575	37.1
17	25.85	21.075	38.725	14.35
18	25.174999999999997	17.349999999999998	32.275	25.2
19	38.550000000000004	13.925	29.975	17.549999999999997
20	44.425	16.775000000000002	25.95	12.85
21	24.15	20.200000000000003	27.500000000000004	28.15
22	29.125	13.950000000000001	46.375	10.549999999999999
23	25.85	14.224999999999998	43.875	16.05
24	50.1	14.649999999999999	26.375	8.875
25	48.85	23.150000000000002	17.175	10.825
26	28.475	44.324999999999996	14.249999999999998	12.950000000000001
27	16.55	45.875	23.3	14.274999999999999
28	12.725	23.974999999999998	47.025	16.275000000000002
29	13.65	12.575	55.125	18.65
30	11.675	7.074999999999999	35.449999999999996	45.800000000000004
31	16.625	5.325	45.75	32.300000000000004
32	26.85	6.9	21.7	44.55
33	51.625	8.875	15.2	24.3
34	59.075	8.5	15.6	16.825000000000003
35	62.224999999999994	8.05	18.45	11.275
36	40.125	8.425	36.275	15.174999999999999
37	45.324999999999996	11.799999999999999	19.900000000000002	22.975
38	24.325	16.925	12.675	46.075
39	18.0	24.125	9.700000000000001	48.175000000000004
40	16.0	46.775	12.0	25.224999999999998
41	24.0	48.0	10.95	17.05
42	46.625	28.875	13.05	11.450000000000001
43	50.0	28.675	10.4	10.925
44	30.825000000000003	47.3	7.775	14.099999999999998
45	20.175	49.3	12.45	18.075
46	14.249999999999998	27.025	17.825	40.9
47	10.375	17.05	38.224999999999994	34.35
48	11.475	13.750000000000002	21.05	53.725
49	13.4	19.125	15.1	52.37500000000001
50	17.625	37.9	13.0	31.474999999999998
>>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	1.0
26	2.0
27	2.5
28	3.0
29	4.5
30	6.0
31	9.0
32	12.0
33	15.5
34	19.0
35	25.0
36	31.0
37	36.0
38	41.0
39	43.5
40	46.0
41	46.0
42	46.0
43	82.5
44	119.0
45	145.5
46	172.0
47	310.0
48	448.0
49	535.5
50	623.0
51	710.0
52	797.0
53	615.5
54	434.0
55	505.0
56	576.0
57	410.0
58	244.0
59	161.5
60	79.0
61	65.0
62	51.0
63	75.5
64	100.0
65	65.5
66	31.0
67	26.5
68	22.0
69	20.0
70	18.0
71	38.0
72	58.0
73	34.0
74	10.0
75	6.0
76	2.0
77	2.0
78	2.0
79	3.5
80	5.0
81	4.0
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	0.25
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	37.824999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.35558493060145	28.125
2	10.310641110376736	7.8
3	4.626569729015202	5.25
4	2.6437541308658297	4.0
5	1.255783212161269	2.375
6	0.9253139458030404	2.1
7	0.9253139458030404	2.45
8	0.5948446794448117	1.7999999999999998
9	0.7931262392597489	2.7
>10	3.1064111037673494	24.725
>50	0.2643754130865829	8.425
>100	0.19828155981493722	10.25
>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	148	3.6999999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	137	3.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	125	3.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	95	2.375	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	81	2.025	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	64	1.6	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	49	1.225	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	47	1.175	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	45	1.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	35	0.8750000000000001	RNA PCR Primer, Index 7 (100% over 35bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	32	0.8	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	28	0.7000000000000001	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	27	0.675	RNA PCR Primer, Index 1 (100% over 33bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	19	0.475	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGC	19	0.475	RNA PCR Primer, Index 28 (100% over 50bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTC	15	0.375	RNA PCR Primer, Index 28 (100% over 44bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 31bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	14	0.35000000000000003	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	12	0.3	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	12	0.3	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	10	0.25	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	9	0.22499999999999998	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	9	0.22499999999999998	No Hit
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	9	0.22499999999999998	RNA PCR Primer, Index 2 (100% over 34bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	9	0.22499999999999998	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	9	0.22499999999999998	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 24bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTGGAATTC	7	0.17500000000000002	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	7	0.17500000000000002	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	6	0.15	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	6	0.15	No Hit
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCTC	5	0.125	No Hit
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CAGGAGGATCACGAGTTCGAGGCCAGCCTGGGCTACACATTTTTGGAATT	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAA	5	0.125	RNA PCR Primer, Index 2 (97% over 36bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	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	0.525	0.0	0.0	0.0
2	0.0	0.525	0.0	0.0	0.0
3	0.0	0.65	0.0	0.0	0.0
4	0.0	0.7	0.0	0.0	0.0
5	0.0	0.75	0.0	0.0	0.0
6	0.0	0.8	0.0	0.0	0.0
7	0.0	1.325	0.0	0.0	0.0
8	0.0	1.5	0.0	0.0	0.0
9	0.0	1.575	0.0	0.0	0.0
10	0.0	1.75	0.0	0.0	0.0
11	0.0	1.95	0.0	0.0	0.0
12	0.0	2.35	0.0	0.0	0.0
13	0.0	2.6	0.0	0.0	0.0
14	0.0	2.825	0.0	0.0	0.0
15	0.0	3.15	0.0	0.0	0.0
16	0.0	4.475	0.0	0.0	0.0
17	0.0	5.3	0.0	0.0	0.0
18	0.0	6.65	0.0	0.0	0.0
19	0.0	7.225	0.0	0.0	0.0
20	0.0	8.25	0.0	0.0	0.0
21	0.0	13.275	0.0	0.0	0.0
22	0.0	23.725	0.0	0.0	0.0
23	0.0	52.325	0.0	0.0	0.0
24	0.0	64.725	0.0	0.0	0.0
25	0.0	70.7	0.0	0.0	0.0
26	0.0	72.1	0.0	0.0	0.0
27	0.0	72.95	0.0	0.0	0.0
28	0.0	73.625	0.0	0.0	0.0
29	0.0	74.35	0.0	0.0	0.0
30	0.0	74.825	0.0	0.0	0.0
31	0.0	75.625	0.0	0.0	0.0
32	0.0	76.475	0.0	0.0	0.0
33	0.0	77.65	0.0	0.0	0.0
34	0.0	80.375	0.0	0.0	0.0
35	0.0	81.8	0.0	0.0	0.0
36	0.0	82.9	0.0	0.0	0.0
37	0.0	83.975	0.0	0.0	0.0
38	0.0	84.625	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AATCCAG	20	6.952051E-4	44.000004	8
ATCCAGG	20	6.952051E-4	44.000004	9
TCCAGGA	20	6.952051E-4	44.000004	10
CTTGGTG	20	6.952051E-4	44.000004	16
ACATTCA	40	5.315087E-9	44.000004	2
GCTGTCG	40	5.315087E-9	44.000004	11
AGTAATC	20	6.952051E-4	44.000004	5
TAATCCA	20	6.952051E-4	44.000004	7
GCTTGGT	20	6.952051E-4	44.000004	15
TTGGTGG	20	6.952051E-4	44.000004	17
CTGTCGG	40	5.315087E-9	44.000004	12
GTAATCC	20	6.952051E-4	44.000004	6
GTCGGTG	40	5.315087E-9	44.000004	14
AACATTC	40	5.315087E-9	44.000004	1
CCAGGAT	20	6.952051E-4	44.000004	11
TGTCGGT	40	5.315087E-9	44.000004	13
AACGCTG	35	1.02281774E-7	44.0	8
GGTGAGT	30	1.9515464E-6	44.0	17
AAGTAAT	25	3.6958358E-5	44.0	4
TCAAGTA	25	3.6958358E-5	44.0	2
>>END_MODULE
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210289 spots for SRR5031008.sra
Written 210289 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
Read 210279 spots for SRR5031008.sra
Written 210279 spots for SRR5031008.sra
SRR ids: ['SRR5031008.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_wbc65nf5
SRR5031008.sra spots: 2523358
blocks: [[1, 210279], [210280, 420558], [420559, 630837], [630838, 841116], [841117, 1051395], [1051396, 1261674], [1261675, 1471953], [1471954, 1682232], [1682233, 1892511], [1892512, 2102790], [2102791, 2313069], [2313070, 2523358]]
SRR5031008 file size 436284
SRR5031008 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031008 SRR5031008_1.fastq
Input file:	SRR5031008_1.fastq
trimmed:	SRR5031008-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 07:04:59 2020 >> started

Wed Mar  4 07:05:00 2020 >> done (1.490s)
2523358 reads processed; of these:
    178 ( 0.01%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
2523176 (99.99%) reads available; of these:
 140377 ( 5.56%) trimmed reads available after processing
2382799 (94.44%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     68	  0.00%
 19	     69	  0.00%
 20	    189	  0.01%
 21	    202	  0.01%
 22	    355	  0.01%
 23	    398	  0.02%
 24	    414	  0.02%
 25	    524	  0.02%
 26	    456	  0.02%
 27	    559	  0.02%
 28	    732	  0.03%
 29	   1133	  0.04%
 30	    725	  0.03%
 31	    758	  0.03%
 32	    852	  0.03%
 33	   1091	  0.04%
 34	   1242	  0.05%
 35	   2374	  0.09%
 36	   2074	  0.08%
 37	   2392	  0.09%
 38	   2413	  0.10%
 39	   2685	  0.11%
 40	   2946	  0.12%
 41	   3103	  0.12%
 42	   3932	  0.16%
 43	   5441	  0.22%
 44	   7721	  0.31%
 45	   9349	  0.37%
 46	  13707	  0.54%
 47	  16508	  0.65%
 48	  24035	  0.95%
 49	  31930	  1.27%
 50	2382799	 94.44%
2523176 reads passed initial QC


criterion=sequence-density
sequence-density=83.70
sequence-density-rank=1
fanout-score=21.25
fanout-score-rank=1
prefix-density=85.79
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC


criterion=fanout-score
sequence-density=83.70
sequence-density-rank=1
fanout-score=21.25
fanout-score-rank=1
prefix-density=85.79
prefix-fanout=20.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC -o SRR5031008 -
Input file:	STDIN
trimmed:	SRR5031008-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGCC
-- 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 07:05:14 2020 >> started

Wed Mar  4 07:05:18 2020 >> done (3.757s)
2463101 reads processed; of these:
 158117 ( 6.42%) short reads filtered out after trimming by size control
  18171 ( 0.74%) empty reads filtered out after trimming by size control
2286813 (92.84%) reads available; of these:
2153632 (94.18%) trimmed reads available after processing
 133181 ( 5.82%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12074	  0.53%
 19	  25184	  1.10%
 20	 122857	  5.37%
 21	 257243	 11.25%
 22	 679573	 29.72%
 23	 315528	 13.80%
 24	 142384	  6.23%
 25	  40412	  1.77%
 26	  21745	  0.95%
 27	  16930	  0.74%
 28	  19857	  0.87%
 29	  14070	  0.62%
 30	  20760	  0.91%
 31	  25819	  1.13%
 32	  29952	  1.31%
 33	  74170	  3.24%
 34	  34579	  1.51%
 35	  29986	  1.31%
 36	  36430	  1.59%
 37	  15929	  0.70%
 38	  16087	  0.70%
 39	  15889	  0.69%
 40	  24096	  1.05%
 41	  33517	  1.47%
 42	  39408	  1.72%
 43	  28041	  1.23%
 44	  19933	  0.87%
 45	  24676	  1.08%
 46	  18441	  0.81%
 47	  13507	  0.59%
 48	   1503	  0.07%
 49	   2946	  0.13%
 50	 113287	  4.95%


criterion=sequence-density
sequence-density=6.50
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.38
sequence-density-rank=31
fanout-score=27.36
fanout-score-rank=1
prefix-density=10.43
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 07:05:39
                             Started mapping on |	Mar 04 07:05:40
                                    Finished on |	Mar 04 07:06:04
       Mapping speed, Million of reads per hour |	352.03

                          Number of input reads |	2346888
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1223534
                        Uniquely mapped reads % |	52.13%
                          Average mapped length |	25.47
                       Number of splices: Total |	1251
            Number of splices: Annotated (sjdb) |	200
                       Number of splices: GT/AG |	1186
                       Number of splices: GC/AG |	12
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	53
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.81
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	795714
             % of reads mapped to multiple loci |	33.91%
        Number of reads mapped to too many loci |	60334
             % of reads mapped to too many loci |	2.57%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.66%
                     % of reads unmapped: other |	0.73%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	327640	327640	327640
N_multimapping	795714	795714	795714
N_noFeature	62483	78884	836914
N_ambiguous	691423	360730	12038
UnstrandedReadsAssigned:469628 PositiveStrandReadsAssigned:783920 NegativeStrandReadsAssigned:374582
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031008 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: SRR5031008-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,346,888 reads, 593,852 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,148 rounds

 109283 SRR5031008.ke.tsv
  52636 SRR5031008.se.tsv
 161919 total
==> SRR5031008.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

==> SRR5031008.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031008 completed mapping pipeline successfully
