Starting /dee2/code/volunteer_pipeline.sh SRR5031079
    current disk space = 448119398400
    free memory = 1181743200 
SRR5031079 SRAfilesize
c8d807ea8c153977138240bc96924326  SRR5031079.sra
SRR5031079.sra file validated
SRR5031079 is single end
SRR5031079 is conventional basespace
SRR5031079 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031079_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	31.89275	31.0	31.0	34.0	30.0	34.0
2	32.43825	33.0	31.0	34.0	31.0	34.0
3	32.457	34.0	31.0	34.0	31.0	34.0
4	36.19725	37.0	35.0	37.0	35.0	37.0
5	36.13425	37.0	35.0	37.0	35.0	37.0
6	36.011	37.0	35.0	37.0	35.0	37.0
7	35.87825	37.0	35.0	37.0	35.0	37.0
8	35.6245	37.0	35.0	37.0	33.0	37.0
9	36.99025	39.0	37.0	39.0	33.0	39.0
10	36.6085	39.0	37.0	39.0	32.0	39.0
11	37.43725	39.0	37.0	39.0	34.0	39.0
12	37.71525	39.0	37.0	39.0	35.0	39.0
13	37.3945	39.0	37.0	39.0	35.0	39.0
14	38.223	40.0	38.0	41.0	33.0	41.0
15	37.01325	39.0	36.0	41.0	30.0	41.0
16	36.637	39.0	36.0	40.0	31.0	41.0
17	36.8605	39.0	36.0	41.0	31.0	41.0
18	38.19275	40.0	37.0	41.0	34.0	41.0
19	38.825	40.0	38.0	41.0	36.0	41.0
20	38.414	40.0	38.0	41.0	34.0	41.0
21	38.6025	40.0	38.0	41.0	34.0	41.0
22	37.48275	39.0	37.0	40.0	32.0	41.0
23	37.95675	39.0	37.0	40.0	34.0	41.0
24	37.18875	39.0	37.0	40.0	31.0	41.0
25	38.088	40.0	37.0	41.0	33.0	41.0
26	38.077	40.0	38.0	41.0	33.0	41.0
27	38.24575	40.0	38.0	41.0	34.0	41.0
28	38.451	40.0	38.0	41.0	34.0	41.0
29	38.50175	40.0	38.0	41.0	34.0	41.0
30	38.809	40.0	38.0	41.0	35.0	41.0
31	38.83825	40.0	38.0	41.0	35.0	41.0
32	38.71675	40.0	38.0	41.0	35.0	41.0
33	38.6465	40.0	38.0	41.0	35.0	41.0
34	38.13875	40.0	38.0	41.0	33.0	41.0
35	37.47125	40.0	37.0	41.0	30.0	41.0
36	33.3945	35.0	30.0	39.0	23.0	41.0
37	35.22775	37.0	33.0	39.0	30.0	40.0
38	36.6595	38.0	36.0	40.0	31.0	40.0
39	36.78975	38.0	36.0	40.0	32.0	40.0
40	37.13625	39.0	37.0	40.0	32.0	41.0
41	37.538	40.0	37.0	40.0	33.0	41.0
42	37.43225	40.0	37.0	41.0	32.0	41.0
43	37.71325	40.0	37.0	41.0	33.0	41.0
44	36.93725	39.0	36.0	40.0	31.0	41.0
45	36.91875	39.0	36.0	40.0	31.0	41.0
46	36.74975	39.0	36.0	40.0	31.0	41.0
47	35.6875	38.0	34.0	40.0	28.0	41.0
48	36.914	39.0	36.0	40.0	31.0	41.0
49	37.19125	40.0	37.0	41.0	32.0	41.0
50	35.23675	38.0	34.0	40.0	28.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
17	3.0
18	1.0
19	4.0
20	5.0
21	6.0
22	11.0
23	10.0
24	4.0
25	9.0
26	11.0
27	15.0
28	22.0
29	39.0
30	27.0
31	73.0
32	99.0
33	133.0
34	171.0
35	242.0
36	454.0
37	783.0
38	1157.0
39	721.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.476619154788697	26.331582895723933	52.41310327581895	14.778694673668417
2	22.2972972972973	27.75275275275275	17.417417417417415	32.532532532532535
3	28.15	17.95	19.25	34.65
4	35.025	27.775	12.1	25.1
5	21.15	41.025	28.199999999999996	9.625
6	33.6	14.649999999999999	37.425000000000004	14.325
7	13.575000000000001	23.724999999999998	20.275000000000002	42.425000000000004
8	24.15	29.825000000000003	13.275	32.75
9	25.025	34.1	26.200000000000003	14.674999999999999
10	19.400000000000002	18.975	30.175	31.45
11	30.025000000000002	9.475	16.175	44.324999999999996
12	14.149999999999999	15.25	33.725	36.875
13	32.85	16.2	32.7	18.25
14	29.675	33.825	20.45	16.05
15	37.125	20.65	25.5	16.725
16	18.675	17.575	21.0	42.75
17	24.9	18.825	40.6	15.675
18	25.75	16.625	32.275	25.35
19	40.25	13.700000000000001	27.3	18.75
20	49.2	12.0	26.85	11.95
21	23.150000000000002	20.825	25.674999999999997	30.349999999999998
22	28.799999999999997	10.925	49.575	10.7
23	26.724999999999998	12.2	48.375	12.7
24	52.949999999999996	11.325000000000001	26.150000000000002	9.575
25	53.474999999999994	24.4	14.6	7.5249999999999995
26	28.799999999999997	49.275000000000006	13.100000000000001	8.825
27	16.275000000000002	51.349999999999994	23.125	9.25
28	10.0	26.0	50.975	13.025
29	10.225	10.8	60.050000000000004	18.925
30	8.6	5.7	38.875	46.825
31	13.375	3.325	48.699999999999996	34.599999999999994
32	26.674999999999997	4.825	22.225	46.275
33	57.275	7.249999999999999	11.975	23.5
34	66.77499999999999	5.800000000000001	14.649999999999999	12.775
35	68.89999999999999	5.8500000000000005	16.825000000000003	8.425
36	45.925	6.175	35.949999999999996	11.95
37	48.3	8.725	19.650000000000002	23.325000000000003
38	24.099999999999998	14.725	11.0	50.175000000000004
39	14.7	23.175	8.725	53.400000000000006
40	14.2	50.175000000000004	9.025	26.6
41	24.05	52.25	6.9750000000000005	16.725
42	50.6	32.275	8.075000000000001	9.049999999999999
43	54.37499999999999	31.125000000000004	5.575	8.924999999999999
44	31.2	51.324999999999996	5.45	12.025
45	17.4	52.949999999999996	11.450000000000001	18.2
46	10.424999999999999	27.450000000000003	17.349999999999998	44.775
47	5.925	15.375	40.125	38.574999999999996
48	7.75	12.65	20.375	59.22500000000001
49	11.075	18.425	13.700000000000001	56.8
50	16.825000000000003	38.125	13.825000000000001	31.225
>>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	0.5
16	1.0
17	0.5
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	2.0
30	4.0
31	4.0
32	4.0
33	4.0
34	4.0
35	10.5
36	17.0
37	18.0
38	19.0
39	19.5
40	20.0
41	20.0
42	20.0
43	46.0
44	72.0
45	102.5
46	133.0
47	270.0
48	407.0
49	494.5
50	582.0
51	744.5
52	907.0
53	726.5
54	546.0
55	566.5
56	587.0
57	458.5
58	330.0
59	208.0
60	86.0
61	67.0
62	48.0
63	76.5
64	105.0
65	73.0
66	41.0
67	31.0
68	21.0
69	16.5
70	12.0
71	18.5
72	25.0
73	14.5
74	4.0
75	3.0
76	2.0
77	1.0
78	0.0
79	1.0
80	2.0
81	1.0
82	0.0
83	0.0
84	0.0
85	0.5
86	1.0
87	0.5
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	39.7
#Duplication Level	Percentage of deduplicated	Percentage of total
1	77.51889168765743	30.775000000000002
2	9.005037783375315	7.1499999999999995
3	4.534005037783375	5.4
4	1.8261964735516372	2.9000000000000004
5	1.2594458438287155	2.5
6	0.9445843828715366	2.25
7	0.6297229219143577	1.7500000000000002
8	0.4408060453400504	1.4000000000000001
9	0.5667506297229219	2.025
>10	2.707808564231738	20.575
>50	0.2518891687657431	6.950000000000001
>100	0.3148614609571789	16.325
>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
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	155	3.875	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	133	3.325	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	128	3.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	105	2.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	85	2.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	73	1.825	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	56	1.4000000000000001	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTT	37	0.9249999999999999	RNA PCR Primer, Index 1 (97% over 35bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	21	0.525	RNA PCR Primer, Index 1 (96% over 30bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGC	17	0.42500000000000004	RNA PCR Primer, Index 3 (100% over 50bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTC	15	0.375	RNA PCR Primer, Index 3 (100% over 44bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	11	0.27499999999999997	No Hit
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	9	0.22499999999999998	RNA PCR Primer, Index 3 (100% over 34bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	9	0.22499999999999998	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 31bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATTGTCTGCTGGGTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	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)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	7	0.17500000000000002	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTAT	6	0.15	RNA PCR Primer, Index 3 (100% over 48bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTA	6	0.15	RNA PCR Primer, Index 3 (100% over 36bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	6	0.15	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGGGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	5	0.125	RNA PCR Primer, Index 3 (100% over 34bp)
CGCGACCTCAGATCAGCCGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	5	0.125	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	5	0.125	No Hit
TATTGCACTCGTCCCGGCCTCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>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	0.55	0.0	0.0	0.0
2	0.0	0.575	0.0	0.0	0.0
3	0.0	0.8	0.0	0.0	0.0
4	0.0	0.8	0.0	0.0	0.0
5	0.0	0.9	0.0	0.0	0.0
6	0.0	1.05	0.0	0.0	0.0
7	0.0	1.675	0.0	0.0	0.0
8	0.0	1.95	0.0	0.0	0.0
9	0.0	2.0	0.0	0.0	0.0
10	0.0	2.225	0.0	0.0	0.0
11	0.0	2.325	0.0	0.0	0.0
12	0.0	2.5	0.0	0.0	0.0
13	0.0	2.625	0.0	0.0	0.0
14	0.0	2.75	0.0	0.0	0.0
15	0.0	3.325	0.0	0.0	0.0
16	0.0	4.625	0.0	0.0	0.0
17	0.0	5.55	0.0	0.0	0.0
18	0.0	6.45	0.0	0.0	0.0
19	0.0	6.9	0.0	0.0	0.0
20	0.0	7.75	0.0	0.0	0.0
21	0.0	12.45	0.0	0.0	0.0
22	0.0	24.7	0.0	0.0	0.0
23	0.0	57.475	0.0	0.0	0.0
24	0.0	72.325	0.0	0.0	0.0
25	0.0	78.55	0.0	0.0	0.0
26	0.0	80.375	0.0	0.0	0.0
27	0.0	81.15	0.0	0.0	0.0
28	0.0	81.725	0.0	0.0	0.0
29	0.0	82.275	0.0	0.0	0.0
30	0.0	82.6	0.0	0.0	0.0
31	0.0	83.225	0.0	0.0	0.0
32	0.0	84.25	0.0	0.0	0.0
33	0.0	84.975	0.0	0.0	0.0
34	0.0	87.475	0.0	0.0	0.0
35	0.0	88.025	0.0	0.0	0.0
36	0.0	88.425	0.0	0.0	0.0
37	0.0	89.0	0.0	0.0	0.0
38	0.0	89.35	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
ATCCAGG	20	6.952051E-4	44.000004	9
TTCAAGT	20	6.952051E-4	44.000004	1
AGGATAG	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
GCTGGAA	20	6.952051E-4	44.000004	20
TCCAGGA	20	6.952051E-4	44.000004	10
GAGTTGG	20	6.952051E-4	44.000004	20
GGATAGG	20	6.952051E-4	44.000004	14
AGTAATC	20	6.952051E-4	44.000004	5
GGCTTGG	40	5.315087E-9	44.000004	19
TAATCCA	20	6.952051E-4	44.000004	7
AGTTGGA	20	6.952051E-4	44.000004	21
TTGGCTT	20	6.952051E-4	44.000004	17
CTGTTGG	20	6.952051E-4	44.000004	19
CAGGATA	20	6.952051E-4	44.000004	12
GTAATCC	20	6.952051E-4	44.000004	6
TGAGTTG	20	6.952051E-4	44.000004	19
GATAGGC	20	6.952051E-4	44.000004	15
>>END_MODULE
Read 43342 spots for SRR5031079.sra
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SRR ids: ['SRR5031079.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_h5xodhmp
SRR5031079.sra spots: 2080416
blocks: [[1, 43342], [43343, 86684], [86685, 130026], [130027, 173368], [173369, 216710], [216711, 260052], [260053, 303394], [303395, 346736], [346737, 390078], [390079, 433420], [433421, 476762], [476763, 520104], [520105, 563446], [563447, 606788], [606789, 650130], [650131, 693472], [693473, 736814], [736815, 780156], [780157, 823498], [823499, 866840], [866841, 910182], [910183, 953524], [953525, 996866], [996867, 1040208], [1040209, 1083550], [1083551, 1126892], [1126893, 1170234], [1170235, 1213576], [1213577, 1256918], [1256919, 1300260], [1300261, 1343602], [1343603, 1386944], [1386945, 1430286], [1430287, 1473628], [1473629, 1516970], [1516971, 1560312], [1560313, 1603654], [1603655, 1646996], [1646997, 1690338], [1690339, 1733680], [1733681, 1777022], [1777023, 1820364], [1820365, 1863706], [1863707, 1907048], [1907049, 1950390], [1950391, 1993732], [1993733, 2037074], [2037075, 2080416]]
SRR5031079 file size 359514
SRR5031079 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5031079 SRR5031079_1.fastq
Input file:	SRR5031079_1.fastq
trimmed:	SRR5031079-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):	32
Sun May  2 20:00:20 2021 >> started

Sun May  2 20:00:21 2021 >> done (1.252s)
2080416 reads processed; of these:
    196 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
2080215 (99.99%) reads available; of these:
 172143 ( 8.28%) trimmed reads available after processing
1908072 (91.72%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     58	  0.00%
 19	    123	  0.01%
 20	    171	  0.01%
 21	    250	  0.01%
 22	    342	  0.02%
 23	    487	  0.02%
 24	    429	  0.02%
 25	    594	  0.03%
 26	    427	  0.02%
 27	    601	  0.03%
 28	    638	  0.03%
 29	   1293	  0.06%
 30	    704	  0.03%
 31	    763	  0.04%
 32	    945	  0.05%
 33	   1761	  0.08%
 34	   2308	  0.11%
 35	   5561	  0.27%
 36	   3190	  0.15%
 37	   3058	  0.15%
 38	   2928	  0.14%
 39	   3371	  0.16%
 40	   3725	  0.18%
 41	   4253	  0.20%
 42	   4950	  0.24%
 43	   8306	  0.40%
 44	   9607	  0.46%
 45	  13406	  0.64%
 46	  14187	  0.68%
 47	  12700	  0.61%
 48	  33118	  1.59%
 49	  37889	  1.82%
 50	1908072	 91.72%
2080215 reads passed initial QC


criterion=sequence-density
sequence-density=89.97
sequence-density-rank=1
fanout-score=19.08
fanout-score-rank=2
prefix-density=91.26
prefix-fanout=18.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC


criterion=fanout-score
sequence-density=3.83
sequence-density-rank=3
fanout-score=69.50
fanout-score-rank=1
prefix-density=90.88
prefix-fanout=2.9
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC -o SRR5031079 -
Input file:	STDIN
trimmed:	SRR5031079-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCC
-- 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):	32
Sun May  2 20:00:35 2021 >> started

Sun May  2 20:00:38 2021 >> done (3.172s)
2033988 reads processed; of these:
 123302 ( 6.06%) short reads filtered out after trimming by size control
  11528 ( 0.57%) empty reads filtered out after trimming by size control
1899158 (93.37%) reads available; of these:
1842433 (97.01%) trimmed reads available after processing
  56725 ( 2.99%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11753	  0.62%
 19	  21703	  1.14%
 20	 121971	  6.42%
 21	 245709	 12.94%
 22	 692058	 36.44%
 23	 304020	 16.01%
 24	 131204	  6.91%
 25	  36474	  1.92%
 26	  17394	  0.92%
 27	  13018	  0.69%
 28	  14057	  0.74%
 29	  10639	  0.56%
 30	  14612	  0.77%
 31	  23772	  1.25%
 32	  15799	  0.83%
 33	  52917	  2.79%
 34	  14846	  0.78%
 35	  11545	  0.61%
 36	  12935	  0.68%
 37	   6865	  0.36%
 38	   7046	  0.37%
 39	   6872	  0.36%
 40	  10085	  0.53%
 41	  12078	  0.64%
 42	  12667	  0.67%
 43	   8539	  0.45%
 44	   5735	  0.30%
 45	   7274	  0.38%
 46	   5313	  0.28%
 47	   3782	  0.20%
 48	    688	  0.04%
 49	   1235	  0.07%
 50	  44553	  2.35%


criterion=sequence-density
sequence-density=8.05
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=12
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=0.51
sequence-density-rank=26
fanout-score=28.11
fanout-score-rank=1
prefix-density=14.32
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	May 02 20:01:12
                             Started mapping on |	May 02 20:01:12
                                    Finished on |	May 02 20:01:40
       Mapping speed, Million of reads per hour |	250.12

                          Number of input reads |	1945385
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1067390
                        Uniquely mapped reads % |	54.87%
                          Average mapped length |	23.63
                       Number of splices: Total |	4427
            Number of splices: Annotated (sjdb) |	1386
                       Number of splices: GT/AG |	4357
                       Number of splices: GC/AG |	41
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	28
                      Mismatch rate per base, % |	0.35%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.80
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	688646
             % of reads mapped to multiple loci |	35.40%
        Number of reads mapped to too many loci |	26833
             % of reads mapped to too many loci |	1.38%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.77%
                     % of reads unmapped: other |	0.58%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	189349	189349	189349
N_multimapping	688646	688646	688646
N_noFeature	66693	76170	678000
N_ambiguous	635346	291500	8000
UnstrandedReadsAssigned:365351 PositiveStrandReadsAssigned:699720 NegativeStrandReadsAssigned:381390
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031079 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: SRR5031079-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,945,385 reads, 548,631 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,070 rounds

 109283 SRR5031079.ke.tsv
  52636 SRR5031079.se.tsv
 161919 total
==> SRR5031079.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

==> SRR5031079.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	1
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031079 completed mapping pipeline successfully
