Starting /dee2/code/volunteer_pipeline.sh SRR5031098
    current disk space = 160475430912
    free memory = 73931828 
SRR5031098 SRAfilesize
300e7240f1fe6f3c13fd9d5d498e9fa7  SRR5031098.sra
SRR5031098.sra file validated
SRR5031098 is single end
SRR5031098 is conventional basespace
SRR5031098 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031098_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	52
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.16425	33.0	31.0	34.0	30.0	34.0
2	32.50525	34.0	31.0	34.0	31.0	34.0
3	32.49475	34.0	31.0	34.0	31.0	34.0
4	36.2115	37.0	35.0	37.0	35.0	37.0
5	36.178	37.0	35.0	37.0	35.0	37.0
6	36.048	37.0	35.0	37.0	35.0	37.0
7	35.92325	37.0	35.0	37.0	35.0	37.0
8	35.77475	37.0	35.0	37.0	35.0	37.0
9	37.1425	39.0	37.0	39.0	34.0	39.0
10	36.9435	39.0	37.0	39.0	33.0	39.0
11	37.53675	39.0	37.0	39.0	35.0	39.0
12	37.76625	39.0	37.0	39.0	35.0	39.0
13	37.47475	39.0	37.0	39.0	35.0	39.0
14	38.583	40.0	38.0	41.0	34.0	41.0
15	37.18775	40.0	37.0	41.0	31.0	41.0
16	36.48575	39.0	36.0	40.0	30.0	41.0
17	36.73925	39.0	36.0	41.0	30.0	41.0
18	38.1895	40.0	37.0	41.0	34.0	41.0
19	38.756	40.0	38.0	41.0	36.0	41.0
20	38.369	40.0	38.0	41.0	34.0	41.0
21	38.70875	40.0	38.0	41.0	35.0	41.0
22	37.6815	39.0	37.0	40.0	32.0	41.0
23	38.1915	39.0	38.0	40.0	34.0	41.0
24	37.686	39.0	37.0	41.0	32.0	41.0
25	38.55875	40.0	38.0	41.0	34.0	41.0
26	38.433	40.0	38.0	41.0	34.0	41.0
27	38.5225	40.0	38.0	41.0	34.0	41.0
28	38.66575	40.0	38.0	41.0	34.0	41.0
29	38.712	40.0	38.0	41.0	35.0	41.0
30	38.93825	40.0	38.0	41.0	35.0	41.0
31	38.90825	40.0	38.0	41.0	35.0	41.0
32	38.9385	40.0	38.0	41.0	35.0	41.0
33	38.969	40.0	39.0	41.0	35.0	41.0
34	38.5575	40.0	38.0	41.0	34.0	41.0
35	37.8735	40.0	37.0	41.0	31.0	41.0
36	33.30975	35.0	30.0	40.0	23.0	41.0
37	34.85275	37.0	33.0	39.0	30.0	40.0
38	36.51325	38.0	35.0	39.0	31.0	40.0
39	36.94025	38.0	37.0	40.0	33.0	40.0
40	37.32875	39.0	37.0	40.0	33.0	41.0
41	37.9475	40.0	38.0	40.0	33.0	41.0
42	37.7615	40.0	38.0	41.0	33.0	41.0
43	37.884	40.0	38.0	41.0	33.0	41.0
44	36.969	39.0	36.0	40.0	31.0	41.0
45	37.1195	39.0	37.0	40.0	32.0	41.0
46	37.0435	40.0	37.0	41.0	31.0	41.0
47	35.904	38.0	35.0	40.0	28.0	41.0
48	36.939	39.0	37.0	40.0	31.0	41.0
49	37.0625	40.0	37.0	41.0	32.0	41.0
50	34.9935	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
16	1.0
17	0.0
18	2.0
19	0.0
20	5.0
21	6.0
22	6.0
23	8.0
24	6.0
25	4.0
26	9.0
27	11.0
28	24.0
29	42.0
30	43.0
31	54.0
32	87.0
33	113.0
34	189.0
35	267.0
36	429.0
37	668.0
38	1218.0
39	808.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	5.4513628407101775	24.781195298824706	57.664416104026	12.10302575643911
2	22.33350025037556	29.819729594391585	19.954932398597897	27.891837756634953
3	17.675	17.25	17.875	47.199999999999996
4	25.900000000000002	39.25	10.875	23.974999999999998
5	20.45	37.05	31.3	11.200000000000001
6	35.475	14.124999999999998	39.45	10.95
7	10.25	26.375	22.5	40.875
8	23.325000000000003	43.025000000000006	12.3	21.349999999999998
9	20.175	41.725	28.175	9.925
10	17.299999999999997	17.65	26.775	38.275
11	32.45	9.875	12.975	44.7
12	13.850000000000001	13.15	25.124999999999996	47.875
13	18.75	18.55	40.175	22.525000000000002
14	41.275	23.1	24.85	10.775
15	37.974999999999994	19.1	29.575000000000003	13.350000000000001
16	11.924999999999999	25.775	18.925	43.375
17	27.075	20.275000000000002	37.8	14.85
18	31.025000000000002	17.150000000000002	27.250000000000004	24.575
19	39.375	12.0	30.25	18.375
20	54.425000000000004	14.75	22.25	8.575000000000001
21	21.75	28.125	21.55	28.575
22	34.150000000000006	9.5	49.525000000000006	6.825
23	23.25	11.25	55.074999999999996	10.424999999999999
24	54.925000000000004	9.475	29.349999999999998	6.25
25	61.85000000000001	20.575	12.625	4.95
26	30.25	52.75	10.299999999999999	6.7
27	11.899999999999999	60.575	21.275	6.25
28	6.7250000000000005	28.325	54.449999999999996	10.5
29	7.049999999999999	8.325000000000001	67.375	17.25
30	6.15	3.5999999999999996	40.625	49.625
31	10.725	2.825	50.24999999999999	36.199999999999996
32	23.075000000000003	3.1	24.425	49.4
33	59.775	4.875	10.4	24.95
34	74.7	3.9	10.424999999999999	10.975
35	74.825	4.825	15.275	5.075
36	45.625	4.6	40.45	9.325
37	50.64999999999999	6.675000000000001	22.650000000000002	20.025000000000002
38	25.25	11.3	9.325	54.125
39	11.375	20.849999999999998	5.475	62.3
40	10.549999999999999	54.025	5.975	29.45
41	20.8	61.775000000000006	4.875	12.55
42	54.50000000000001	33.625	5.875	6.0
43	62.625	26.674999999999997	4.3	6.4
44	32.05	54.074999999999996	3.6999999999999997	10.174999999999999
45	13.525	61.35	9.125	16.0
46	6.825	29.5	15.4	48.275
47	5.125	11.700000000000001	42.925000000000004	40.25
48	6.2	9.325	23.225	61.25000000000001
49	9.225	16.05	10.05	64.67500000000001
50	15.875	42.75	8.9	32.475
>>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	0.5
12	1.0
13	0.5
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	0.5
30	1.0
31	2.5
32	4.0
33	3.0
34	2.0
35	6.0
36	10.0
37	11.0
38	12.0
39	15.0
40	18.0
41	21.0
42	24.0
43	47.5
44	71.0
45	120.5
46	170.0
47	349.0
48	528.0
49	569.5
50	611.0
51	857.0
52	1103.0
53	777.0
54	451.0
55	426.5
56	402.0
57	385.0
58	368.0
59	227.0
60	86.0
61	60.0
62	34.0
63	42.5
64	51.0
65	34.5
66	18.0
67	11.5
68	5.0
69	6.0
70	7.0
71	12.0
72	17.0
73	10.0
74	3.0
75	3.0
76	3.0
77	1.5
78	0.0
79	0.0
80	0.0
81	0.0
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.025
2	0.15
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	37.55
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.63382157123834	28.025
2	11.18508655126498	8.4
3	3.861517976031957	4.35
4	2.463382157123835	3.6999999999999997
5	1.3315579227696404	2.5
6	1.3981358189081226	3.15
7	0.3994673768308922	1.05
8	0.7989347536617843	2.4
9	0.5992010652463382	2.025
>10	2.929427430093209	21.875
>50	0.13315579227696406	3.075
>100	0.2663115845539281	19.45
>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	229	5.7250000000000005	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	226	5.65	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	191	4.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	66	1.6500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	57	1.425	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	39	0.975	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	32	0.8	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	17	0.42500000000000004	RNA PCR Primer, Index 2 (100% over 35bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCCGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGC	9	0.22499999999999998	RNA PCR Primer, Index 22 (100% over 50bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTCACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCCGGCTAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGACTTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (96% over 26bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	6	0.15	RNA PCR Primer, Index 2 (100% over 34bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTC	6	0.15	RNA PCR Primer, Index 22 (100% over 44bp)
TTTGAACCATCACTCGCCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATCGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTACCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGATTGTCTAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTCACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGCCCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTCGCTCTGAAGGCCTGTTTCCTAGGCTTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.3	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.325	0.0	0.0	0.0
4	0.0	0.35	0.0	0.0	0.0
5	0.0	0.4	0.0	0.0	0.0
6	0.0	0.5	0.0	0.0	0.0
7	0.0	0.8	0.0	0.0	0.0
8	0.0	0.975	0.0	0.0	0.0
9	0.0	1.1	0.0	0.0	0.0
10	0.0	1.175	0.0	0.0	0.0
11	0.0	1.375	0.0	0.0	0.0
12	0.0	1.425	0.0	0.0	0.0
13	0.0	1.575	0.0	0.0	0.0
14	0.0	1.825	0.0	0.0	0.0
15	0.0	2.05	0.0	0.0	0.0
16	0.0	2.775	0.0	0.0	0.0
17	0.0	3.45	0.0	0.0	0.0
18	0.0	4.025	0.0	0.0	0.0
19	0.0	4.475	0.0	0.0	0.0
20	0.0	5.275	0.0	0.0	0.0
21	0.0	9.675	0.0	0.0	0.0
22	0.0	21.175	0.0	0.0	0.0
23	0.0	59.775	0.0	0.0	0.0
24	0.0	79.025	0.0	0.0	0.0
25	0.0	84.375	0.0	0.0	0.0
26	0.0	85.325	0.0	0.0	0.0
27	0.0	85.7	0.0	0.0	0.0
28	0.0	86.0	0.0	0.0	0.0
29	0.0	86.375	0.0	0.0	0.0
30	0.0	86.7	0.0	0.0	0.0
31	0.0	87.225	0.0	0.0	0.0
32	0.0	88.05	0.0	0.0	0.0
33	0.0	88.625	0.0	0.0	0.0
34	0.0	90.25	0.0	0.0	0.0
35	0.0	90.875	0.0	0.0	0.0
36	0.0	91.45	0.0	0.0	0.0
37	0.0	91.975	0.0	0.0	0.0
38	0.0	92.15	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AACGCTG	40	5.315087E-9	44.000004	8
CTGAGCT	40	5.315087E-9	44.000004	11
CTTTAAC	20	6.952051E-4	44.000004	12
ATGATGG	20	6.952051E-4	44.000004	20
TTCAACG	40	5.315087E-9	44.000004	5
GAGCTTG	40	5.315087E-9	44.000004	13
GGATCCG	40	5.315087E-9	44.000004	3
CCGTCTG	40	5.315087E-9	44.000004	7
TATGATG	20	6.952051E-4	44.000004	19
TCGGATC	40	5.315087E-9	44.000004	1
TCAACGC	40	5.315087E-9	44.000004	6
CGGATCC	40	5.315087E-9	44.000004	2
CTTGGCT	20	6.952051E-4	44.000004	16
TAACCTG	20	6.952051E-4	44.000004	15
GATCCGT	40	5.315087E-9	44.000004	4
CCTTTAA	20	6.952051E-4	44.000004	11
GGTAGTA	20	6.952051E-4	44.000004	4
TCCGTCT	40	5.315087E-9	44.000004	6
AGGTAGT	20	6.952051E-4	44.000004	3
ATCCGTC	40	5.315087E-9	44.000004	5
>>END_MODULE
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
Read 224193 spots for SRR5031098.sra
Written 224193 spots for SRR5031098.sra
Read 224189 spots for SRR5031098.sra
Written 224189 spots for SRR5031098.sra
SRR ids: ['SRR5031098.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_ib_kuwxo
SRR5031098.sra spots: 2690272
blocks: [[1, 224189], [224190, 448378], [448379, 672567], [672568, 896756], [896757, 1120945], [1120946, 1345134], [1345135, 1569323], [1569324, 1793512], [1793513, 2017701], [2017702, 2241890], [2241891, 2466079], [2466080, 2690272]]
SRR5031098 file size 465220
SRR5031098 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031098 SRR5031098_1.fastq
Input file:	SRR5031098_1.fastq
trimmed:	SRR5031098-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 07:23:49 2020 >> started

Wed Mar  4 07:23:50 2020 >> done (1.694s)
2690272 reads processed; of these:
    158 ( 0.01%) short reads filtered out after trimming by size control
      2 ( 0.00%) empty reads filtered out after trimming by size control
2690112 (99.99%) reads available; of these:
 235079 ( 8.74%) trimmed reads available after processing
2455033 (91.26%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     66	  0.00%
 19	     93	  0.00%
 20	    145	  0.01%
 21	    236	  0.01%
 22	    426	  0.02%
 23	    504	  0.02%
 24	    520	  0.02%
 25	    680	  0.03%
 26	    495	  0.02%
 27	    619	  0.02%
 28	    725	  0.03%
 29	   1510	  0.06%
 30	    719	  0.03%
 31	    767	  0.03%
 32	    957	  0.04%
 33	   2081	  0.08%
 34	   2780	  0.10%
 35	   8657	  0.32%
 36	   4612	  0.17%
 37	   3887	  0.14%
 38	   3379	  0.13%
 39	   3947	  0.15%
 40	   4850	  0.18%
 41	   5738	  0.21%
 42	   6961	  0.26%
 43	  11387	  0.42%
 44	  11823	  0.44%
 45	  17265	  0.64%
 46	  20073	  0.75%
 47	  18273	  0.68%
 48	  52576	  1.95%
 49	  48328	  1.80%
 50	2455033	 91.26%
2690112 reads passed initial QC


criterion=sequence-density
sequence-density=92.94
sequence-density-rank=1
fanout-score=17.51
fanout-score-rank=2
prefix-density=93.88
prefix-fanout=17.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC


criterion=fanout-score
sequence-density=3.78
sequence-density-rank=4
fanout-score=72.76
fanout-score-rank=1
prefix-density=94.30
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 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC -o SRR5031098 -
Input file:	STDIN
trimmed:	SRR5031098-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC
-- 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 07:24:05 2020 >> started

Wed Mar  4 07:24:09 2020 >> done (4.231s)
2632260 reads processed; of these:
 103593 ( 3.94%) short reads filtered out after trimming by size control
   9400 ( 0.36%) empty reads filtered out after trimming by size control
2519267 (95.71%) reads available; of these:
2466721 (97.91%) trimmed reads available after processing
  52546 ( 2.09%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12798	  0.51%
 19	  29815	  1.18%
 20	 141699	  5.62%
 21	 317604	 12.61%
 22	1003019	 39.81%
 23	 487948	 19.37%
 24	 167814	  6.66%
 25	  28083	  1.11%
 26	  13262	  0.53%
 27	  12489	  0.50%
 28	  13904	  0.55%
 29	  10628	  0.42%
 30	  17503	  0.69%
 31	  22066	  0.88%
 32	  22828	  0.91%
 33	  52089	  2.07%
 34	  18861	  0.75%
 35	  12189	  0.48%
 36	  13599	  0.54%
 37	   6860	  0.27%
 38	   7617	  0.30%
 39	   6465	  0.26%
 40	   8676	  0.34%
 41	  10686	  0.42%
 42	  10843	  0.43%
 43	   7279	  0.29%
 44	   5737	  0.23%
 45	   6684	  0.27%
 46	   4743	  0.19%
 47	   3362	  0.13%
 48	    658	  0.03%
 49	   1279	  0.05%
 50	  40180	  1.59%


criterion=sequence-density
sequence-density=7.33
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.47
sequence-density-rank=29
fanout-score=16.41
fanout-score-rank=1
prefix-density=7.74
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:24:31
                             Started mapping on |	Mar 04 07:24:31
                                    Finished on |	Mar 04 07:24:57
       Mapping speed, Million of reads per hour |	356.83

                          Number of input reads |	2577119
                      Average input read length |	24
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1227359
                        Uniquely mapped reads % |	47.63%
                          Average mapped length |	23.14
                       Number of splices: Total |	6918
            Number of splices: Annotated (sjdb) |	2863
                       Number of splices: GT/AG |	6834
                       Number of splices: GC/AG |	36
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	46
                      Mismatch rate per base, % |	0.29%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.69
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.09
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1148147
             % of reads mapped to multiple loci |	44.55%
        Number of reads mapped to too many loci |	38607
             % of reads mapped to too many loci |	1.50%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	5.91%
                     % of reads unmapped: other |	0.42%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	201613	201613	201613
N_multimapping	1148147	1148147	1148147
N_noFeature	61213	71787	913769
N_ambiguous	679721	409930	5968
UnstrandedReadsAssigned:486425 PositiveStrandReadsAssigned:745642 NegativeStrandReadsAssigned:307622
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031098 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: SRR5031098-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,577,119 reads, 524,431 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,091 rounds

 109283 SRR5031098.ke.tsv
  52636 SRR5031098.se.tsv
 161919 total
==> SRR5031098.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

==> SRR5031098.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031098 completed mapping pipeline successfully
