Starting /dee2/code/volunteer_pipeline.sh SRR5030976
    current disk space = 160588513280
    free memory = 73915004 
SRR5030976 SRAfilesize
c95158f7d61da7f628beee0c745eefec  SRR5030976.sra
SRR5030976.sra file validated
SRR5030976 is single end
SRR5030976 is conventional basespace
SRR5030976 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030976_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.55025	34.0	31.0	34.0	31.0	34.0
2	32.87725	34.0	31.0	34.0	31.0	34.0
3	32.777	34.0	31.0	34.0	31.0	34.0
4	36.3335	37.0	37.0	37.0	35.0	37.0
5	36.226	37.0	37.0	37.0	35.0	37.0
6	35.99575	37.0	35.0	37.0	35.0	37.0
7	36.155	37.0	35.0	37.0	35.0	37.0
8	36.2235	37.0	36.0	37.0	35.0	37.0
9	37.85275	39.0	38.0	39.0	35.0	39.0
10	37.96825	39.0	38.0	39.0	35.0	39.0
11	37.74875	39.0	38.0	39.0	35.0	39.0
12	37.82025	39.0	38.0	39.0	35.0	39.0
13	37.78575	39.0	38.0	39.0	35.0	39.0
14	39.099	41.0	39.0	41.0	36.0	41.0
15	39.29475	41.0	39.0	41.0	36.0	41.0
16	39.37025	41.0	39.0	41.0	36.0	41.0
17	39.4165	41.0	39.0	41.0	36.0	41.0
18	39.3285	41.0	39.0	41.0	36.0	41.0
19	39.09525	40.0	39.0	41.0	36.0	41.0
20	39.10275	40.0	39.0	41.0	36.0	41.0
21	39.04375	40.0	39.0	41.0	36.0	41.0
22	39.1265	40.0	39.0	41.0	36.0	41.0
23	38.951	40.0	38.0	41.0	36.0	41.0
24	39.15075	40.0	39.0	41.0	36.0	41.0
25	39.07	41.0	39.0	41.0	36.0	41.0
26	38.72175	40.0	38.0	41.0	34.0	41.0
27	38.81525	40.0	38.0	41.0	35.0	41.0
28	38.58175	40.0	38.0	41.0	34.0	41.0
29	38.1575	40.0	38.0	41.0	33.0	41.0
30	38.436	40.0	38.0	41.0	34.0	41.0
31	38.641	40.0	38.0	41.0	34.0	41.0
32	38.2995	40.0	38.0	41.0	34.0	41.0
33	38.13275	40.0	38.0	41.0	34.0	41.0
34	37.97775	39.0	38.0	40.0	34.0	41.0
35	37.824	39.0	38.0	40.0	33.0	41.0
36	37.58575	39.0	37.0	41.0	32.0	41.0
37	37.572	40.0	37.0	41.0	32.0	41.0
38	37.73075	40.0	37.0	41.0	32.0	41.0
39	37.93775	40.0	38.0	41.0	33.0	41.0
40	38.04425	40.0	38.0	41.0	33.0	41.0
41	38.088	40.0	38.0	41.0	33.0	41.0
42	38.21875	40.0	38.0	41.0	34.0	41.0
43	38.39175	40.0	38.0	41.0	34.0	41.0
44	38.32175	40.0	38.0	41.0	34.0	41.0
45	38.07975	40.0	38.0	41.0	33.0	41.0
46	37.45425	40.0	37.0	41.0	32.0	41.0
47	37.129	40.0	37.0	41.0	31.0	41.0
48	36.64575	39.0	36.0	41.0	30.0	41.0
49	36.75525	39.0	37.0	41.0	31.0	41.0
50	36.33325	39.0	36.0	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	1.0
17	1.0
18	2.0
19	2.0
20	3.0
21	2.0
22	3.0
23	5.0
24	5.0
25	9.0
26	16.0
27	16.0
28	28.0
29	35.0
30	32.0
31	55.0
32	76.0
33	110.0
34	122.0
35	164.0
36	277.0
37	393.0
38	811.0
39	1831.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.678339169584792	21.635817908954476	59.754877438719355	11.930965482741371
2	24.575	25.874999999999996	23.275000000000002	26.275
3	16.950000000000003	19.375	20.65	43.025000000000006
4	25.924999999999997	39.225	12.25	22.6
5	21.25	40.275	27.775	10.7
6	36.925000000000004	16.950000000000003	35.175	10.95
7	11.450000000000001	24.9	25.6	38.05
8	24.5	41.925000000000004	13.625000000000002	19.950000000000003
9	18.099999999999998	39.574999999999996	30.175	12.15
10	19.075	19.825	27.325	33.775
11	29.675	9.5	14.499999999999998	46.325
12	13.450000000000001	14.825	27.450000000000003	44.275
13	22.0	22.05	36.875	19.075
14	41.65	22.175	23.3	12.875
15	38.95	21.025	28.625	11.4
16	12.575	26.025	21.099999999999998	40.300000000000004
17	25.95	20.925	41.699999999999996	11.425
18	30.349999999999998	19.75	25.900000000000002	24.0
19	40.075	13.65	30.225	16.05
20	50.55	17.150000000000002	22.175	10.125
21	20.8	25.650000000000002	26.275	27.275
22	32.4	11.25	49.5	6.8500000000000005
23	24.375	11.725	52.1	11.799999999999999
24	52.949999999999996	12.9	29.575000000000003	4.575
25	57.99999999999999	22.525000000000002	13.875000000000002	5.6000000000000005
26	30.225	50.224999999999994	12.25	7.3
27	13.275	55.400000000000006	23.5	7.825
28	8.05	27.0	52.349999999999994	12.6
29	8.3	11.25	63.449999999999996	17.0
30	7.6499999999999995	4.7	39.625	48.025
31	12.6	3.025	48.449999999999996	35.925000000000004
32	25.05	3.75	23.724999999999998	47.475
33	58.825	5.075	11.924999999999999	24.175
34	70.825	6.0249999999999995	11.525	11.625
35	71.85000000000001	5.575	16.125	6.45
36	42.775	5.65	40.150000000000006	11.425
37	47.65	7.75	21.825	22.775000000000002
38	24.2	13.15	10.8	51.849999999999994
39	12.675	22.900000000000002	6.5	57.925000000000004
40	12.5	51.575	6.7	29.225
41	22.85	57.325	6.15	13.675
42	52.1	33.85	5.8999999999999995	8.15
43	59.050000000000004	29.15	4.45	7.35
44	31.374999999999996	52.25	5.35	11.025
45	14.05	57.199999999999996	10.775	17.974999999999998
46	7.8	28.675	16.2	47.325
47	5.4	13.350000000000001	40.75	40.5
48	5.7250000000000005	11.85	22.2	60.224999999999994
49	10.075000000000001	18.3	12.45	59.175
50	16.275000000000002	41.275	10.674999999999999	31.775
>>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	0.5
10	1.0
11	0.5
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	0.5
28	1.0
29	1.0
30	1.0
31	1.5
32	2.0
33	2.0
34	2.0
35	7.0
36	12.0
37	15.0
38	18.0
39	18.0
40	18.0
41	25.5
42	33.0
43	86.0
44	139.0
45	168.5
46	198.0
47	448.5
48	699.0
49	688.0
50	677.0
51	857.5
52	1038.0
53	709.5
54	381.0
55	356.5
56	332.0
57	290.5
58	249.0
59	148.0
60	47.0
61	39.0
62	31.0
63	40.0
64	49.0
65	35.5
66	22.0
67	16.0
68	10.0
69	8.5
70	7.0
71	17.0
72	27.0
73	13.5
74	0.0
75	0.5
76	1.0
77	0.5
78	0.0
79	1.0
80	2.0
81	1.5
82	1.0
83	0.5
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	0.05
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	0.0
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	34.55
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.1808972503618	25.974999999999998
2	9.623733719247468	6.65
3	3.61794500723589	3.75
4	3.256150506512301	4.5
5	1.447178002894356	2.5
6	0.9406657018813315	1.95
7	0.723589001447178	1.7500000000000002
8	0.5065123010130246	1.4000000000000001
9	0.361794500723589	1.125
>10	3.762662807525326	26.224999999999998
>50	0.2894356005788712	6.2
>100	0.2894356005788712	17.974999999999998
>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	282	7.049999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	186	4.65	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	140	3.5000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	111	2.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	67	1.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	57	1.425	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	45	1.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	45	1.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	40	1.0	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	39	0.975	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	32	0.8	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	32	0.8	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTC	21	0.525	RNA PCR Primer, Index 43 (100% over 44bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	20	0.5	RNA PCR Primer, Index 7 (97% over 35bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	19	0.475	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 33bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	12	0.3	No Hit
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGC	12	0.3	RNA PCR Primer, Index 43 (100% over 50bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTAC	8	0.2	RNA PCR Primer, Index 30 (97% over 36bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	7	0.17500000000000002	No Hit
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTAT	6	0.15	RNA PCR Primer, Index 43 (100% over 48bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CAGCAGCACACTGTGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	6	0.15	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTCTACGGAGACTGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	5	0.125	RNA PCR Primer, Index 3 (100% over 34bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTATCAGAATCTCCAGGGGTACTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTACAGTACTGTGATAACTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TTAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.3	0.0	0.0	0.0
2	0.0	0.375	0.0	0.0	0.0
3	0.0	0.525	0.0	0.0	0.0
4	0.0	0.525	0.0	0.0	0.0
5	0.0	0.6	0.0	0.0	0.0
6	0.0	0.625	0.0	0.0	0.0
7	0.0	1.175	0.0	0.0	0.0
8	0.0	1.375	0.0	0.0	0.0
9	0.0	1.425	0.0	0.0	0.0
10	0.0	1.5	0.0	0.0	0.0
11	0.0	1.675	0.0	0.0	0.0
12	0.0	2.05	0.0	0.0	0.0
13	0.0	2.275	0.0	0.0	0.0
14	0.0	2.475	0.0	0.0	0.0
15	0.0	3.1	0.0	0.0	0.0
16	0.0	4.325	0.0	0.0	0.0
17	0.0	4.95	0.0	0.0	0.0
18	0.0	5.975	0.0	0.0	0.0
19	0.0	6.425	0.0	0.0	0.0
20	0.0	7.675	0.0	0.0	0.0
21	0.0	13.525	0.0	0.0	0.0
22	0.0	25.5	0.0	0.0	0.0
23	0.0	60.525	0.0	0.0	0.0
24	0.0	77.975	0.0	0.0	0.0
25	0.0	84.4	0.0	0.0	0.0
26	0.0	85.5	0.0	0.0	0.0
27	0.0	86.225	0.0	0.0	0.0
28	0.0	86.65	0.0	0.0	0.0
29	0.0	87.05	0.0	0.0	0.0
30	0.0	87.45	0.0	0.0	0.0
31	0.0	88.4	0.0	0.0	0.0
32	0.0	89.2	0.0	0.0	0.0
33	0.0	90.2	0.0	0.0	0.0
34	0.0	91.4	0.0	0.0	0.0
35	0.0	91.925	0.0	0.0	0.0
36	0.0	92.475	0.0	0.0	0.0
37	0.0	92.825	0.0	0.0	0.0
38	0.0	93.175	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	20	6.952051E-4	44.000004	8
GAGGTAG	20	6.952051E-4	44.000004	2
AAGTAAT	40	5.315087E-9	44.000004	4
TCAAGTA	40	5.315087E-9	44.000004	2
TTGCACT	20	6.952051E-4	44.000004	3
ACGCTGT	20	6.952051E-4	44.000004	9
AATCCAG	40	5.315087E-9	44.000004	8
ATCCAGG	40	5.315087E-9	44.000004	9
AGTAGGT	20	6.952051E-4	44.000004	7
TTCAAGT	40	5.315087E-9	44.000004	1
TTCAACG	20	6.952051E-4	44.000004	5
AGGATAG	40	5.315087E-9	44.000004	13
CCCGGCC	20	6.952051E-4	44.000004	13
TCGGTGA	20	6.952051E-4	44.000004	15
ATAGGCT	40	5.315087E-9	44.000004	16
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
TATTGCA	20	6.952051E-4	44.000004	1
TCCAGGA	40	5.315087E-9	44.000004	10
ACATCCT	20	6.952051E-4	44.000004	6
>>END_MODULE
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251417 spots for SRR5030976.sra
Written 251417 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
Read 251415 spots for SRR5030976.sra
Written 251415 spots for SRR5030976.sra
SRR ids: ['SRR5030976.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_0_xauez_
SRR5030976.sra spots: 3016982
blocks: [[1, 251415], [251416, 502830], [502831, 754245], [754246, 1005660], [1005661, 1257075], [1257076, 1508490], [1508491, 1759905], [1759906, 2011320], [2011321, 2262735], [2262736, 2514150], [2514151, 2765565], [2765566, 3016982]]
SRR5030976 file size 521840
SRR5030976 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030976 SRR5030976_1.fastq
Input file:	SRR5030976_1.fastq
trimmed:	SRR5030976-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 06:58:11 2020 >> started

Wed Mar  4 06:58:14 2020 >> done (2.995s)
3016982 reads processed; of these:
    173 ( 0.01%) short reads filtered out after trimming by size control
      2 ( 0.00%) empty reads filtered out after trimming by size control
3016807 (99.99%) reads available; of these:
 185493 ( 6.15%) trimmed reads available after processing
2831314 (93.85%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     55	  0.00%
 19	     87	  0.00%
 20	    140	  0.00%
 21	    215	  0.01%
 22	    387	  0.01%
 23	    449	  0.01%
 24	    395	  0.01%
 25	    564	  0.02%
 26	    419	  0.01%
 27	    665	  0.02%
 28	    738	  0.02%
 29	   1328	  0.04%
 30	    700	  0.02%
 31	    768	  0.03%
 32	    805	  0.03%
 33	   1081	  0.04%
 34	   1437	  0.05%
 35	   2445	  0.08%
 36	   2156	  0.07%
 37	   2162	  0.07%
 38	   2221	  0.07%
 39	   2568	  0.09%
 40	   3043	  0.10%
 41	   3381	  0.11%
 42	   4942	  0.16%
 43	   6930	  0.23%
 44	  10238	  0.34%
 45	  12893	  0.43%
 46	  16945	  0.56%
 47	  19868	  0.66%
 48	  35249	  1.17%
 49	  50219	  1.66%
 50	2831314	 93.85%
3016807 reads passed initial QC


criterion=sequence-density
sequence-density=93.11
sequence-density-rank=1
fanout-score=18.07
fanout-score-rank=1
prefix-density=94.38
prefix-fanout=17.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=93.11
sequence-density-rank=1
fanout-score=18.07
fanout-score-rank=1
prefix-density=94.38
prefix-fanout=17.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC -o SRR5030976 -
Input file:	STDIN
trimmed:	SRR5030976-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC
-- 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 06:58:34 2020 >> started

Wed Mar  4 06:58:41 2020 >> done (7.361s)
2952620 reads processed; of these:
 171623 ( 5.81%) short reads filtered out after trimming by size control
  12767 ( 0.43%) empty reads filtered out after trimming by size control
2768230 (93.76%) reads available; of these:
2725933 (98.47%) trimmed reads available after processing
  42297 ( 1.53%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17796	  0.64%
 19	  38866	  1.40%
 20	 155765	  5.63%
 21	 371165	 13.41%
 22	1050479	 37.95%
 23	 527198	 19.04%
 24	 182572	  6.60%
 25	  29128	  1.05%
 26	  15290	  0.55%
 27	  14928	  0.54%
 28	  16175	  0.58%
 29	  11768	  0.43%
 30	  20412	  0.74%
 31	  28572	  1.03%
 32	  29793	  1.08%
 33	  44708	  1.62%
 34	  24560	  0.89%
 35	  15777	  0.57%
 36	  16573	  0.60%
 37	   9586	  0.35%
 38	  10130	  0.37%
 39	   9550	  0.34%
 40	  12282	  0.44%
 41	  17046	  0.62%
 42	  18168	  0.66%
 43	  13474	  0.49%
 44	  10203	  0.37%
 45	  10414	  0.38%
 46	   7795	  0.28%
 47	   5434	  0.20%
 48	    518	  0.02%
 49	    949	  0.03%
 50	  31156	  1.13%


criterion=sequence-density
sequence-density=5.47
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.44
sequence-density-rank=31
fanout-score=7.86
fanout-score-rank=1
prefix-density=3.47
prefix-fanout=1.0
sequence=TAGTAGGTTGTGTGGTTTT
                                 Started job on |	Mar 04 06:59:10
                             Started mapping on |	Mar 04 06:59:11
                                    Finished on |	Mar 04 06:59:36
       Mapping speed, Million of reads per hour |	407.87

                          Number of input reads |	2832417
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1341647
                        Uniquely mapped reads % |	47.37%
                          Average mapped length |	23.26
                       Number of splices: Total |	1132
            Number of splices: Annotated (sjdb) |	190
                       Number of splices: GT/AG |	1040
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	75
                      Mismatch rate per base, % |	0.12%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.68
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1272042
             % of reads mapped to multiple loci |	44.91%
        Number of reads mapped to too many loci |	51378
             % of reads mapped to too many loci |	1.81%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.23%
                     % of reads unmapped: other |	0.68%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	218728	218728	218728
N_multimapping	1272042	1272042	1272042
N_noFeature	52558	63442	1023380
N_ambiguous	727516	454986	8009
UnstrandedReadsAssigned:561573 PositiveStrandReadsAssigned:823219 NegativeStrandReadsAssigned:310258
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5030976 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: SRR5030976-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,832,417 reads, 549,827 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,119 rounds

 109283 SRR5030976.ke.tsv
  52636 SRR5030976.se.tsv
 161919 total
==> SRR5030976.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

==> SRR5030976.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030976 completed mapping pipeline successfully
