Starting /dee2/code/volunteer_pipeline.sh SRR5031034
    current disk space = 160529514496
    free memory = 73954508 
SRR5031034 SRAfilesize
71fb0f1ebd5272dfe4ce62a6d20e2425  SRR5031034.sra
SRR5031034.sra file validated
SRR5031034 is single end
SRR5031034 is conventional basespace
SRR5031034 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031034_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.334	33.0	31.0	34.0	31.0	34.0
2	32.5955	34.0	31.0	34.0	31.0	34.0
3	32.657	34.0	31.0	34.0	31.0	34.0
4	36.2055	37.0	35.0	37.0	35.0	37.0
5	35.886	37.0	35.0	37.0	35.0	37.0
6	35.866	37.0	35.0	37.0	35.0	37.0
7	35.96725	37.0	35.0	37.0	35.0	37.0
8	35.82975	37.0	35.0	37.0	35.0	37.0
9	37.58675	39.0	37.0	39.0	35.0	39.0
10	37.8445	39.0	37.0	39.0	35.0	39.0
11	37.6445	39.0	37.0	39.0	35.0	39.0
12	37.582	39.0	37.0	39.0	35.0	39.0
13	37.5705	39.0	37.0	39.0	35.0	39.0
14	39.029	40.0	38.0	41.0	35.0	41.0
15	39.06475	40.0	38.0	41.0	35.0	41.0
16	38.963	40.0	38.0	41.0	35.0	41.0
17	38.9175	40.0	38.0	41.0	35.0	41.0
18	39.011	40.0	38.0	41.0	35.0	41.0
19	38.5535	40.0	38.0	41.0	34.0	41.0
20	38.67325	40.0	38.0	41.0	34.0	41.0
21	38.723	40.0	38.0	41.0	35.0	41.0
22	38.93875	40.0	38.0	41.0	35.0	41.0
23	38.58525	40.0	38.0	41.0	34.0	41.0
24	38.666	40.0	38.0	41.0	34.0	41.0
25	38.9215	40.0	38.0	41.0	35.0	41.0
26	38.54825	40.0	38.0	41.0	34.0	41.0
27	38.56975	40.0	38.0	41.0	34.0	41.0
28	38.565	40.0	38.0	41.0	34.0	41.0
29	38.10725	40.0	38.0	41.0	33.0	41.0
30	37.83775	40.0	38.0	41.0	32.0	41.0
31	38.21625	40.0	38.0	41.0	33.0	41.0
32	38.27025	40.0	38.0	41.0	33.0	41.0
33	38.19	40.0	38.0	41.0	33.0	41.0
34	38.349	40.0	38.0	41.0	33.0	41.0
35	38.23675	40.0	38.0	41.0	34.0	41.0
36	37.9135	40.0	37.0	41.0	33.0	41.0
37	37.4695	40.0	37.0	41.0	31.0	41.0
38	36.86225	39.0	36.0	41.0	30.0	41.0
39	37.16025	39.0	37.0	41.0	31.0	41.0
40	37.39275	39.0	37.0	41.0	32.0	41.0
41	37.57175	40.0	37.0	41.0	32.0	41.0
42	37.924	40.0	37.0	41.0	33.0	41.0
43	38.15125	40.0	38.0	41.0	34.0	41.0
44	37.9485	40.0	37.0	41.0	33.0	41.0
45	37.891	40.0	37.0	41.0	33.0	41.0
46	37.712	40.0	37.0	41.0	33.0	41.0
47	36.87625	40.0	35.0	41.0	31.0	41.0
48	36.26125	39.0	35.0	41.0	29.0	41.0
49	36.50975	39.0	35.0	41.0	30.0	41.0
50	36.1625	39.0	35.0	41.0	30.0	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
15	1.0
16	2.0
17	3.0
18	2.0
19	0.0
20	1.0
21	3.0
22	4.0
23	5.0
24	10.0
25	7.0
26	14.0
27	19.0
28	31.0
29	40.0
30	48.0
31	88.0
32	87.0
33	106.0
34	147.0
35	216.0
36	291.0
37	420.0
38	730.0
39	1725.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.625	24.75	44.15	19.475
2	23.60450563204005	27.284105131414265	18.74843554443054	30.36295369211515
3	25.7	15.9	20.95	37.45
4	36.6	26.25	15.25	21.9
5	21.099999999999998	37.15	27.800000000000004	13.950000000000001
6	29.225	13.975000000000001	38.800000000000004	18.0
7	18.875	19.775000000000002	18.975	42.375
8	21.575	27.200000000000003	19.825	31.4
9	26.75	29.475	24.425	19.35
10	23.375	20.349999999999998	29.5	26.775
11	34.35	13.25	16.8	35.6
12	15.775	20.849999999999998	31.55	31.825
13	29.325000000000003	15.525	35.225	19.925
14	28.1	31.15	18.925	21.825
15	35.15	23.125	26.775	14.95
16	21.65	18.25	23.7	36.4
17	29.325000000000003	23.3	32.95	14.424999999999999
18	25.900000000000002	15.925	32.45	25.724999999999998
19	37.574999999999996	15.125	30.599999999999998	16.7
20	43.375	16.625	25.35	14.649999999999999
21	27.375	21.6	21.825	29.2
22	31.6	14.174999999999999	43.1	11.125
23	25.45	14.35	41.025	19.175
24	49.3	14.774999999999999	25.95	9.975000000000001
25	46.800000000000004	24.425	16.45	12.325
26	28.675	40.8	14.799999999999999	15.725
27	17.625	42.975	22.2	17.2
28	14.124999999999998	22.925	43.1	19.85
29	16.125	13.925	51.65	18.3
30	11.924999999999999	8.4	32.925	46.75
31	14.95	6.25	46.175	32.625
32	28.1	6.375	23.3	42.225
33	49.35	13.325000000000001	14.374999999999998	22.95
34	55.2	8.9	19.35	16.55
35	63.449999999999996	7.675	17.349999999999998	11.525
36	43.5	9.049999999999999	34.425	13.025
37	42.825	15.6	20.175	21.4
38	24.375	20.474999999999998	13.175	41.975
39	16.825000000000003	22.025	14.549999999999999	46.6
40	16.650000000000002	43.0	16.1	24.25
41	22.925	44.3	10.075000000000001	22.7
42	43.25	27.425	16.325	13.0
43	48.225	27.650000000000002	9.65	14.475
44	34.4	42.85	8.55	14.2
45	22.8	45.625	14.799999999999999	16.775000000000002
46	18.8	24.575	17.0	39.625
47	11.475	15.625	39.475	33.425
48	15.825	12.325	20.075000000000003	51.775000000000006
49	14.899999999999999	17.625	15.075	52.400000000000006
50	17.875	33.925	13.475000000000001	34.725
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.5
2	1.0
3	0.5
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	0.5
18	1.0
19	1.0
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	3.5
28	7.0
29	3.5
30	0.0
31	4.0
32	8.0
33	10.5
34	13.0
35	19.0
36	25.0
37	30.0
38	35.0
39	39.0
40	43.0
41	49.5
42	56.0
43	73.0
44	90.0
45	122.5
46	155.0
47	237.0
48	319.0
49	416.5
50	514.0
51	662.5
52	811.0
53	623.5
54	436.0
55	517.0
56	598.0
57	471.0
58	344.0
59	224.0
60	104.0
61	77.0
62	50.0
63	138.0
64	226.0
65	126.0
66	26.0
67	22.5
68	19.0
69	22.0
70	25.0
71	54.5
72	84.0
73	43.5
74	3.0
75	2.0
76	1.0
77	1.0
78	1.0
79	2.5
80	4.0
81	2.0
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	0.0
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	39.475
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.31412286257124	30.125
2	9.943001899936668	7.85
3	3.6732108929702343	4.35
4	2.4699176694110196	3.9
5	1.3932868904369855	2.75
6	1.3932868904369855	3.3000000000000003
7	0.5699810006333123	1.575
8	0.5699810006333123	1.7999999999999998
9	0.37998733375554145	1.35
>10	2.7232425585813806	19.625
>50	0.31665611146295125	9.475
>100	0.253324889170361	13.900000000000002
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	173	4.324999999999999	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	162	4.05	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	116	2.9000000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	105	2.625	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	95	2.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	91	2.275	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	74	1.8499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	67	1.675	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGC	52	1.3	RNA PCR Primer, Index 5 (97% over 35bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	45	1.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	35	0.8750000000000001	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	31	0.775	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	21	0.525	RNA PCR Primer, Index 1 (100% over 33bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	17	0.42500000000000004	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	17	0.42500000000000004	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	15	0.375	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTC	15	0.375	RNA PCR Primer, Index 6 (100% over 44bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	12	0.3	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	12	0.3	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 25bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	11	0.27499999999999997	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGC	10	0.25	RNA PCR Primer, Index 6 (100% over 50bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
CACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCT	9	0.22499999999999998	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	9	0.22499999999999998	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	8	0.2	No Hit
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TTCCAATTAGTAGATTCTGAATAAACCCAGAAGAGAGTACCATGGAATTC	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGTGGAATTCTCGGGTGC	6	0.15	No Hit
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	6	0.15	RNA PCR Primer, Index 6 (100% over 34bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CCGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGC	6	0.15	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGGGCTAGGGCTAACAGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGC	5	0.125	RNA PCR Primer, Index 5 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGTACCGTGAGTAATAATGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCTGGGTCGGGGTTTCGTACGTAGCAGAGCAGCTCTGGAATTCTCGGGTG	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	5	0.125	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTGC	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.25	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.4	0.0	0.0	0.0
4	0.0	0.425	0.0	0.0	0.0
5	0.0	0.525	0.0	0.0	0.0
6	0.0	0.575	0.0	0.0	0.0
7	0.0	1.1	0.0	0.0	0.0
8	0.0	1.325	0.0	0.0	0.0
9	0.0	1.375	0.0	0.0	0.0
10	0.0	1.575	0.0	0.0	0.0
11	0.0	1.75	0.0	0.0	0.0
12	0.0	2.0	0.0	0.0	0.0
13	0.0	2.225	0.0	0.0	0.0
14	0.0	2.55	0.0	0.0	0.0
15	0.0	2.85	0.0	0.0	0.0
16	0.0	4.8	0.0	0.0	0.0
17	0.0	5.4	0.0	0.0	0.0
18	0.0	6.55	0.0	0.0	0.0
19	0.0	7.175	0.0	0.0	0.0
20	0.0	7.975	0.0	0.0	0.0
21	0.0	12.575	0.0	0.0	0.0
22	0.0	21.75	0.0	0.0	0.0
23	0.0	47.675	0.0	0.0	0.0
24	0.0	59.425	0.0	0.0	0.0
25	0.0	65.175	0.0	0.0	0.0
26	0.0	66.775	0.0	0.0	0.0
27	0.0	67.625	0.0	0.0	0.0
28	0.0	68.15	0.0	0.0	0.0
29	0.0	68.775	0.0	0.0	0.0
30	0.0	69.25	0.0	0.0	0.0
31	0.0	70.2	0.0	0.0	0.0
32	0.0	71.575	0.0	0.0	0.0
33	0.0	72.75	0.0	0.0	0.0
34	0.0	79.275	0.0	0.0	0.0
35	0.0	80.85	0.0	0.0	0.0
36	0.0	82.05	0.0	0.0	0.0
37	0.0	83.5	0.0	0.0	0.0
38	0.0	84.15	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
ACGCTGT	40	5.315087E-9	44.000004	9
CTGAGCT	45	2.728484E-10	44.000004	11
TTGTATA	20	6.952051E-4	44.000004	13
TTCAACG	40	5.315087E-9	44.000004	5
TCGGTGA	40	5.315087E-9	44.000004	15
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
CATTCAA	40	5.315087E-9	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
CGGATCC	45	2.728484E-10	44.000004	2
GTGAGTT	20	6.952051E-4	44.000004	18
ACATTCA	40	5.315087E-9	44.000004	2
GTATAGT	20	6.952051E-4	44.000004	15
CTTGGCT	45	2.728484E-10	44.000004	16
GCTGTCG	40	5.315087E-9	44.000004	11
GATCCGT	45	2.728484E-10	44.000004	4
GCTTGGC	45	2.728484E-10	44.000004	15
>>END_MODULE
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
Read 287007 spots for SRR5031034.sra
Written 287007 spots for SRR5031034.sra
SRR ids: ['SRR5031034.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_yx_oh5_i
SRR5031034.sra spots: 3444084
blocks: [[1, 287007], [287008, 574014], [574015, 861021], [861022, 1148028], [1148029, 1435035], [1435036, 1722042], [1722043, 2009049], [2009050, 2296056], [2296057, 2583063], [2583064, 2870070], [2870071, 3157077], [3157078, 3444084]]
SRR5031034 file size 595873
SRR5031034 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031034 SRR5031034_1.fastq
Input file:	SRR5031034_1.fastq
trimmed:	SRR5031034-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 07:10:52 2020 >> started

Wed Mar  4 07:10:54 2020 >> done (1.952s)
3444084 reads processed; of these:
    305 ( 0.01%) short reads filtered out after trimming by size control
     12 ( 0.00%) empty reads filtered out after trimming by size control
3443767 (99.99%) reads available; of these:
 185445 ( 5.38%) trimmed reads available after processing
3258322 (94.62%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    115	  0.00%
 19	    120	  0.00%
 20	    226	  0.01%
 21	    293	  0.01%
 22	    476	  0.01%
 23	    533	  0.02%
 24	    571	  0.02%
 25	    827	  0.02%
 26	    637	  0.02%
 27	    813	  0.02%
 28	    931	  0.03%
 29	   1584	  0.05%
 30	   1030	  0.03%
 31	   1174	  0.03%
 32	   1379	  0.04%
 33	   1459	  0.04%
 34	   1618	  0.05%
 35	   3320	  0.10%
 36	   3133	  0.09%
 37	   3251	  0.09%
 38	   3284	  0.10%
 39	   3619	  0.11%
 40	   3936	  0.11%
 41	   3994	  0.12%
 42	   5211	  0.15%
 43	   7215	  0.21%
 44	  10672	  0.31%
 45	  13963	  0.41%
 46	  20601	  0.60%
 47	  23819	  0.69%
 48	  32479	  0.94%
 49	  33162	  0.96%
 50	3258322	 94.62%
3443767 reads passed initial QC


criterion=sequence-density
sequence-density=82.70
sequence-density-rank=1
fanout-score=21.92
fanout-score-rank=1
prefix-density=85.59
prefix-fanout=21.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC


criterion=fanout-score
sequence-density=82.70
sequence-density-rank=1
fanout-score=21.92
fanout-score-rank=1
prefix-density=85.59
prefix-fanout=21.2
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC -o SRR5031034 -
Input file:	STDIN
trimmed:	SRR5031034-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCC
-- 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 07:11:10 2020 >> started

Wed Mar  4 07:11:14 2020 >> done (4.439s)
3360785 reads processed; of these:
 200208 ( 5.96%) short reads filtered out after trimming by size control
  13858 ( 0.41%) empty reads filtered out after trimming by size control
3146719 (93.63%) reads available; of these:
2940334 (93.44%) trimmed reads available after processing
 206385 ( 6.56%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18276	  0.58%
 19	  30557	  0.97%
 20	 157308	  5.00%
 21	 307934	  9.79%
 22	 848554	 26.97%
 23	 409551	 13.02%
 24	 184850	  5.87%
 25	  58708	  1.87%
 26	  30616	  0.97%
 27	  24740	  0.79%
 28	  27471	  0.87%
 29	  24663	  0.78%
 30	  34095	  1.08%
 31	  46297	  1.47%
 32	  48664	  1.55%
 33	 203547	  6.47%
 34	  60859	  1.93%
 35	  44532	  1.42%
 36	  51086	  1.62%
 37	  24581	  0.78%
 38	  30144	  0.96%
 39	  24754	  0.79%
 40	  36163	  1.15%
 41	  42211	  1.34%
 42	  47676	  1.52%
 43	  33642	  1.07%
 44	  26203	  0.83%
 45	  36972	  1.17%
 46	  27373	  0.87%
 47	  21979	  0.70%
 48	   1949	  0.06%
 49	   2999	  0.10%
 50	 177765	  5.65%


criterion=sequence-density
sequence-density=8.23
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.48
sequence-density-rank=32
fanout-score=17.53
fanout-score-rank=1
prefix-density=8.46
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:11:35
                             Started mapping on |	Mar 04 07:11:35
                                    Finished on |	Mar 04 07:11:59
       Mapping speed, Million of reads per hour |	484.46

                          Number of input reads |	3229701
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1637973
                        Uniquely mapped reads % |	50.72%
                          Average mapped length |	25.53
                       Number of splices: Total |	2367
            Number of splices: Annotated (sjdb) |	418
                       Number of splices: GT/AG |	2210
                       Number of splices: GC/AG |	36
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	119
                      Mismatch rate per base, % |	0.24%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	995189
             % of reads mapped to multiple loci |	30.81%
        Number of reads mapped to too many loci |	99836
             % of reads mapped to too many loci |	3.09%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	14.31%
                     % of reads unmapped: other |	1.07%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	596539	596539	596539
N_multimapping	995189	995189	995189
N_noFeature	88343	116741	1085532
N_ambiguous	878296	395328	19208
UnstrandedReadsAssigned:671334 PositiveStrandReadsAssigned:1125904 NegativeStrandReadsAssigned:533233
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031034 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: SRR5031034-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,229,701 reads, 770,731 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,189 rounds

 109283 SRR5031034.ke.tsv
  52636 SRR5031034.se.tsv
 161919 total
==> SRR5031034.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

==> SRR5031034.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031034 completed mapping pipeline successfully
