Starting /dee2/code/volunteer_pipeline.sh SRR5031088
    current disk space = 160484999168
    free memory = 73930824 
SRR5031088 SRAfilesize
11afee6877d025741ca3ee73e2bc4cd8  SRR5031088.sra
SRR5031088.sra file validated
SRR5031088 is single end
SRR5031088 is conventional basespace
SRR5031088 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031088_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	31.96225	31.0	31.0	34.0	30.0	34.0
2	32.424	33.0	31.0	34.0	31.0	34.0
3	32.4125	33.0	31.0	34.0	31.0	34.0
4	36.1525	37.0	35.0	37.0	35.0	37.0
5	36.08725	37.0	35.0	37.0	35.0	37.0
6	36.05475	37.0	35.0	37.0	35.0	37.0
7	35.78975	37.0	35.0	37.0	35.0	37.0
8	35.64475	37.0	35.0	37.0	33.0	37.0
9	36.979	39.0	37.0	39.0	33.0	39.0
10	36.722	39.0	37.0	39.0	32.0	39.0
11	37.41075	39.0	37.0	39.0	34.0	39.0
12	37.7235	39.0	37.0	39.0	35.0	39.0
13	37.48075	39.0	37.0	39.0	35.0	39.0
14	38.33175	40.0	38.0	41.0	33.0	41.0
15	37.194	40.0	37.0	41.0	31.0	41.0
16	36.7575	39.0	36.0	40.0	31.0	41.0
17	36.97175	39.0	36.0	40.0	31.0	41.0
18	38.1235	40.0	37.0	41.0	34.0	41.0
19	38.68025	40.0	38.0	41.0	35.0	41.0
20	38.2255	40.0	38.0	41.0	34.0	41.0
21	38.54775	40.0	38.0	41.0	34.0	41.0
22	37.3735	39.0	37.0	40.0	32.0	41.0
23	37.98125	39.0	37.0	40.0	34.0	41.0
24	37.017	39.0	36.0	40.0	31.0	41.0
25	37.95475	40.0	37.0	41.0	33.0	41.0
26	38.016	40.0	38.0	41.0	34.0	41.0
27	38.1725	40.0	38.0	41.0	34.0	41.0
28	38.3585	40.0	38.0	41.0	34.0	41.0
29	38.24975	40.0	38.0	41.0	34.0	41.0
30	38.615	40.0	38.0	41.0	34.0	41.0
31	38.68275	40.0	38.0	41.0	35.0	41.0
32	38.69325	40.0	38.0	41.0	35.0	41.0
33	38.8005	40.0	38.0	41.0	35.0	41.0
34	38.057	40.0	38.0	41.0	33.0	41.0
35	37.51475	40.0	37.0	41.0	31.0	41.0
36	33.65275	36.0	30.0	40.0	23.0	41.0
37	35.503	37.0	34.0	39.0	30.0	40.0
38	36.4955	38.0	35.0	40.0	30.0	40.0
39	36.9625	39.0	37.0	40.0	32.0	41.0
40	37.1785	39.0	37.0	40.0	33.0	41.0
41	37.42475	39.0	37.0	40.0	33.0	41.0
42	37.27325	40.0	37.0	40.0	32.0	41.0
43	37.43225	40.0	37.0	41.0	32.0	41.0
44	36.51075	38.0	35.0	40.0	30.0	41.0
45	36.605	39.0	36.0	40.0	30.0	41.0
46	36.66925	39.0	36.0	40.0	30.0	41.0
47	35.729	38.0	34.0	40.0	28.0	41.0
48	36.91575	39.0	36.0	40.0	31.0	41.0
49	37.2915	40.0	37.0	41.0	32.0	41.0
50	35.586	38.0	34.0	40.0	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
12	1.0
13	1.0
14	0.0
15	2.0
16	2.0
17	1.0
18	2.0
19	2.0
20	1.0
21	7.0
22	8.0
23	2.0
24	8.0
25	10.0
26	12.0
27	16.0
28	23.0
29	28.0
30	49.0
31	63.0
32	100.0
33	133.0
34	179.0
35	300.0
36	460.0
37	736.0
38	1132.0
39	722.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.527381845461365	27.25681420355089	49.287321830457614	13.928482120530134
2	25.025025025025027	28.37837837837838	18.66866866866867	27.927927927927925
3	25.35	18.45	23.175	33.025
4	34.0	32.925	12.7	20.375
5	19.85	36.75	30.375000000000004	13.025
6	27.1	16.425	42.5	13.975000000000001
7	16.425	20.599999999999998	21.675	41.3
8	21.85	32.1	16.075	29.975
9	24.099999999999998	32.05	26.724999999999998	17.125
10	23.825	16.725	28.299999999999997	31.15
11	31.924999999999997	11.0	18.95	38.125
12	16.525000000000002	17.375	34.025	32.074999999999996
13	31.75	14.875	33.275	20.1
14	33.0	28.499999999999996	20.1	18.4
15	38.675	16.275000000000002	29.599999999999998	15.45
16	17.8	15.775	24.474999999999998	41.949999999999996
17	32.125	17.025000000000002	36.375	14.475
18	32.525	16.075	30.5	20.9
19	37.125	16.775000000000002	31.1	15.0
20	47.225	17.125	22.275	13.375
21	21.575	24.75	27.450000000000003	26.224999999999998
22	30.975	11.625	45.2	12.2
23	26.0	11.825	46.150000000000006	16.025
24	47.975	12.9	27.650000000000002	11.475
25	50.075	22.925	16.900000000000002	10.100000000000001
26	29.7	44.800000000000004	15.049999999999999	10.45
27	18.65	45.85	24.224999999999998	11.275
28	13.850000000000001	24.0	47.4	14.75
29	12.675	11.450000000000001	55.725	20.150000000000002
30	11.924999999999999	6.625	35.85	45.6
31	15.024999999999999	4.75	45.1	35.125
32	26.8	7.225	21.325	44.65
33	54.15	9.075	12.55	24.224999999999998
34	61.35	9.4	14.000000000000002	15.25
35	65.0	8.075000000000001	18.325	8.6
36	43.1	8.450000000000001	35.949999999999996	12.5
37	46.1	10.975	18.55	24.375
38	22.35	17.675	12.975	47.0
39	14.249999999999998	26.025	8.425	51.300000000000004
40	14.075	48.4	11.025	26.5
41	24.15	47.699999999999996	9.125	19.025
42	47.175	30.025000000000002	10.45	12.35
43	50.575	30.5	7.75	11.175
44	29.099999999999998	46.9	8.225	15.775
45	16.5	49.725	14.249999999999998	19.525000000000002
46	11.700000000000001	25.1	18.375	44.824999999999996
47	7.775	15.950000000000001	38.175	38.1
48	8.7	12.35	20.5	58.45
49	13.100000000000001	19.025	14.75	53.125
50	17.549999999999997	35.699999999999996	15.425	31.324999999999996
>>END_MODULE
>>Per sequence GC content	warn
#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	0.0
26	0.0
27	0.5
28	1.0
29	1.5
30	2.0
31	2.0
32	2.0
33	5.0
34	8.0
35	8.0
36	8.0
37	15.0
38	22.0
39	20.0
40	18.0
41	30.0
42	42.0
43	74.0
44	106.0
45	135.5
46	165.0
47	273.0
48	381.0
49	487.5
50	594.0
51	783.0
52	972.0
53	700.5
54	429.0
55	508.5
56	588.0
57	468.5
58	349.0
59	231.0
60	113.0
61	80.5
62	48.0
63	50.5
64	53.0
65	38.5
66	24.0
67	18.5
68	13.0
69	13.0
70	13.0
71	26.5
72	40.0
73	22.0
74	4.0
75	2.0
76	0.0
77	0.0
78	0.0
79	2.5
80	5.0
81	2.5
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	0.025
2	0.1
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	41.925000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	77.22122838401908	32.375
2	9.898628503279665	8.3
3	3.9952295766249257	5.025
4	1.9677996422182469	3.3000000000000003
5	1.3714967203339297	2.875
6	0.7751937984496124	1.95
7	1.073345259391771	3.15
8	0.4770423375074538	1.6
9	0.2385211687537269	0.8999999999999999
>10	2.5044722719141324	19.925
>50	0.2981514609421586	9.85
>100	0.17889087656529518	10.75
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	159	3.975	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	140	3.5000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	131	3.2750000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	93	2.325	RNA PCR Primer, Index 1 (100% over 30bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	76	1.9	RNA PCR Primer, Index 1 (97% over 35bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	72	1.7999999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	46	1.15	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	45	1.125	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	40	1.0	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTC	30	0.75	RNA PCR Primer, Index 12 (100% over 44bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGC	29	0.7250000000000001	RNA PCR Primer, Index 12 (100% over 50bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	24	0.6	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTT	22	0.5499999999999999	RNA PCR Primer, Index 12 (100% over 36bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	22	0.5499999999999999	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (96% over 30bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	15	0.375	RNA PCR Primer, Index 1 (97% over 35bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	12	0.3	RNA PCR Primer, Index 1 (100% over 31bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTG	11	0.27499999999999997	RNA PCR Primer, Index 12 (100% over 37bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	11	0.27499999999999997	RNA PCR Primer, Index 2 (100% over 34bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTAT	10	0.25	RNA PCR Primer, Index 12 (100% over 48bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	10	0.25	RNA PCR Primer, Index 2 (100% over 34bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	8	0.2	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	7	0.17500000000000002	RNA PCR Primer, Index 2 (100% over 34bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAACAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACCTTGTAATCTC	6	0.15	RNA PCR Primer, Index 12 (97% over 44bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AGAATTGTGGCTGGACATCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGACTTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (96% over 33bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
TGGAATTCTCGGGTGCCAAGGCACTCCAGTCACCTTGTAATCTCGTATGC	6	0.15	RNA PCR Primer, Index 12 (98% over 50bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
ACCACAGGGTAGAACCACGGACTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATACCCGTCGCCGCGCTCTCCCTCTCCCCCCGTCCGCCTCCCGGGCGGGC	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGGCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
CTGGGCTACACATTTTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTT	5	0.125	RNA PCR Primer, Index 12 (100% over 36bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GACACAAGGGTTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTT	5	0.125	RNA PCR Primer, Index 12 (100% over 36bp)
TTCAAGTAATCCAGGCTAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	5	0.125	No Hit
AATTCCACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	1.125	0.0	0.0	0.0
2	0.0	1.25	0.0	0.0	0.0
3	0.0	1.6	0.0	0.0	0.0
4	0.0	1.65	0.0	0.0	0.0
5	0.0	1.9	0.0	0.0	0.0
6	0.0	2.0	0.0	0.0	0.0
7	0.0	3.175	0.0	0.0	0.0
8	0.0	3.4	0.0	0.0	0.0
9	0.0	3.55	0.0	0.0	0.0
10	0.0	3.675	0.0	0.0	0.0
11	0.0	3.875	0.0	0.0	0.0
12	0.0	4.225	0.0	0.0	0.0
13	0.0	4.575	0.0	0.0	0.0
14	0.0	5.05	0.0	0.0	0.0
15	0.0	6.225	0.0	0.0	0.0
16	0.0	9.15	0.0	0.0	0.0
17	0.0	10.375	0.0	0.0	0.0
18	0.0	12.225	0.0	0.0	0.0
19	0.0	12.75	0.0	0.0	0.0
20	0.0	13.925	0.0	0.0	0.0
21	0.0	19.075	0.0	0.0	0.0
22	0.0	30.475	0.0	0.0	0.0
23	0.0	59.6	0.0	0.0	0.0
24	0.0	72.3	0.0	0.0	0.0
25	0.0	77.525	0.0	0.0	0.0
26	0.0	78.825	0.0	0.0	0.0
27	0.0	79.7	0.0	0.0	0.0
28	0.0	80.425	0.0	0.0	0.0
29	0.0	81.175	0.0	0.0	0.0
30	0.0	81.675	0.0	0.0	0.0
31	0.0	82.275	0.0	0.0	0.0
32	0.0	83.575	0.0	0.0	0.0
33	0.0	84.4	0.0	0.0	0.0
34	0.0	86.325	0.0	0.0	0.0
35	0.0	87.375	0.0	0.0	0.0
36	0.0	88.225	0.0	0.0	0.0
37	0.0	88.95	0.0	0.0	0.0
38	0.0	89.35	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
TTCAACG	40	5.315087E-9	44.000004	5
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	45	2.728484E-10	44.000004	3
TCAACGC	40	5.315087E-9	44.000004	6
CGGATCC	45	2.728484E-10	44.000004	2
GCTGTCG	45	2.728484E-10	44.000004	11
GATCCGT	45	2.728484E-10	44.000004	4
GCTTGGT	20	6.952051E-4	44.000004	15
TTGGCTT	20	6.952051E-4	44.000004	17
TTGGTGG	20	6.952051E-4	44.000004	17
TCCGTCT	45	2.728484E-10	44.000004	6
ATCCGTC	45	2.728484E-10	44.000004	5
TGAGCTT	45	2.728484E-10	44.000004	12
ATTCAAC	45	2.728484E-10	44.000004	4
>>END_MODULE
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208539 spots for SRR5031088.sra
Written 208539 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
Read 208531 spots for SRR5031088.sra
Written 208531 spots for SRR5031088.sra
SRR ids: ['SRR5031088.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_a41wt64j
SRR5031088.sra spots: 2502380
blocks: [[1, 208531], [208532, 417062], [417063, 625593], [625594, 834124], [834125, 1042655], [1042656, 1251186], [1251187, 1459717], [1459718, 1668248], [1668249, 1876779], [1876780, 2085310], [2085311, 2293841], [2293842, 2502380]]
SRR5031088 file size 432654
SRR5031088 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031088 SRR5031088_1.fastq
Input file:	SRR5031088_1.fastq
trimmed:	SRR5031088-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 07:21:49 2020 >> started

Wed Mar  4 07:21:50 2020 >> done (1.537s)
2502380 reads processed; of these:
    213 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
2502158 (99.99%) reads available; of these:
 193569 ( 7.74%) trimmed reads available after processing
2308589 (92.26%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     59	  0.00%
 19	    105	  0.00%
 20	    183	  0.01%
 21	    207	  0.01%
 22	    378	  0.02%
 23	    452	  0.02%
 24	    492	  0.02%
 25	    658	  0.03%
 26	    439	  0.02%
 27	    556	  0.02%
 28	    715	  0.03%
 29	   1165	  0.05%
 30	    679	  0.03%
 31	    806	  0.03%
 32	   1042	  0.04%
 33	   2121	  0.08%
 34	   2750	  0.11%
 35	   7249	  0.29%
 36	   3830	  0.15%
 37	   3841	  0.15%
 38	   3514	  0.14%
 39	   4055	  0.16%
 40	   4470	  0.18%
 41	   4828	  0.19%
 42	   5562	  0.22%
 43	   9365	  0.37%
 44	   9417	  0.38%
 45	  12229	  0.49%
 46	  15039	  0.60%
 47	  15543	  0.62%
 48	  40291	  1.61%
 49	  41529	  1.66%
 50	2308589	 92.26%
2502158 reads passed initial QC


criterion=sequence-density
sequence-density=90.96
sequence-density-rank=1
fanout-score=17.92
fanout-score-rank=2
prefix-density=91.05
prefix-fanout=17.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC


criterion=fanout-score
sequence-density=2.81
sequence-density-rank=5
fanout-score=102.52
fanout-score-rank=1
prefix-density=92.34
prefix-fanout=3.1
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC -o SRR5031088 -
Input file:	STDIN
trimmed:	SRR5031088-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCC
-- 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 07:22:08 2020 >> started

Wed Mar  4 07:22:12 2020 >> done (3.850s)
2447166 reads processed; of these:
 275947 (11.28%) short reads filtered out after trimming by size control
  26601 ( 1.09%) empty reads filtered out after trimming by size control
2144618 (87.64%) reads available; of these:
2083013 (97.13%) trimmed reads available after processing
  61605 ( 2.87%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  15661	  0.73%
 19	  32447	  1.51%
 20	 155433	  7.25%
 21	 275858	 12.86%
 22	 728576	 33.97%
 23	 329793	 15.38%
 24	 159917	  7.46%
 25	  40578	  1.89%
 26	  22489	  1.05%
 27	  17709	  0.83%
 28	  18335	  0.85%
 29	  12386	  0.58%
 30	  17505	  0.82%
 31	  24652	  1.15%
 32	  24472	  1.14%
 33	  46120	  2.15%
 34	  27040	  1.26%
 35	  21786	  1.02%
 36	  23349	  1.09%
 37	   9707	  0.45%
 38	   9548	  0.45%
 39	   8166	  0.38%
 40	   9328	  0.43%
 41	  11916	  0.56%
 42	  12535	  0.58%
 43	   8584	  0.40%
 44	   6398	  0.30%
 45	   9831	  0.46%
 46	   8270	  0.39%
 47	   5265	  0.25%
 48	    770	  0.04%
 49	    922	  0.04%
 50	  49272	  2.30%


criterion=sequence-density
sequence-density=10.38
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=13
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.70
sequence-density-rank=23
fanout-score=12.37
fanout-score-rank=1
prefix-density=8.54
prefix-fanout=1.0
sequence=TGAGCTTGGCTAT
                                 Started job on |	Mar 04 07:22:33
                             Started mapping on |	Mar 04 07:22:33
                                    Finished on |	Mar 04 07:22:59
       Mapping speed, Million of reads per hour |	304.56

                          Number of input reads |	2199610
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1174814
                        Uniquely mapped reads % |	53.41%
                          Average mapped length |	23.52
                       Number of splices: Total |	3068
            Number of splices: Annotated (sjdb) |	440
                       Number of splices: GT/AG |	2987
                       Number of splices: GC/AG |	43
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	38
                      Mismatch rate per base, % |	0.32%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.89
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.28
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	810334
             % of reads mapped to multiple loci |	36.84%
        Number of reads mapped to too many loci |	45864
             % of reads mapped to too many loci |	2.09%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.62%
                     % of reads unmapped: other |	1.04%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	214462	214462	214462
N_multimapping	810334	810334	810334
N_noFeature	64380	75623	767053
N_ambiguous	651589	284449	6363
UnstrandedReadsAssigned:458845 PositiveStrandReadsAssigned:814742 NegativeStrandReadsAssigned:401398
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031088 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: SRR5031088-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,199,610 reads, 551,232 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,136 rounds

 109283 SRR5031088.ke.tsv
  52636 SRR5031088.se.tsv
 161919 total
==> SRR5031088.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

==> SRR5031088.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031088 completed mapping pipeline successfully
