Starting /dee2/code/volunteer_pipeline.sh SRR5030913
    current disk space = 160640270336
    free memory = 73935836 
SRR5030913 SRAfilesize
d5c9de27eed91ea32c7a0879fbb241c9  SRR5030913.sra
SRR5030913.sra file validated
SRR5030913 is single end
SRR5030913 is conventional basespace
SRR5030913 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030913_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.23375	33.0	31.0	34.0	31.0	34.0
2	32.69175	34.0	31.0	34.0	31.0	34.0
3	32.6475	34.0	31.0	34.0	31.0	34.0
4	36.15275	37.0	35.0	37.0	35.0	37.0
5	36.25525	37.0	37.0	37.0	35.0	37.0
6	35.9395	37.0	35.0	37.0	35.0	37.0
7	36.092	37.0	35.0	37.0	35.0	37.0
8	36.129	37.0	35.0	37.0	35.0	37.0
9	37.9075	39.0	38.0	39.0	35.0	39.0
10	37.9075	39.0	38.0	39.0	35.0	39.0
11	37.827	39.0	38.0	39.0	35.0	39.0
12	37.878	39.0	38.0	39.0	35.0	39.0
13	37.9065	39.0	38.0	39.0	35.0	39.0
14	39.3225	41.0	39.0	41.0	36.0	41.0
15	39.36625	41.0	39.0	41.0	36.0	41.0
16	39.2045	40.0	39.0	41.0	36.0	41.0
17	39.2765	41.0	39.0	41.0	36.0	41.0
18	39.32275	41.0	39.0	41.0	36.0	41.0
19	39.0315	40.0	39.0	41.0	36.0	41.0
20	39.3025	41.0	39.0	41.0	36.0	41.0
21	39.18275	41.0	39.0	41.0	36.0	41.0
22	39.354	41.0	39.0	41.0	36.0	41.0
23	39.115	40.0	39.0	41.0	36.0	41.0
24	38.28775	40.0	38.0	41.0	33.0	41.0
25	38.65875	40.0	38.0	41.0	34.0	41.0
26	38.527	40.0	38.0	41.0	34.0	41.0
27	38.56275	40.0	38.0	41.0	34.0	41.0
28	38.818	40.0	38.0	41.0	35.0	41.0
29	38.859	40.0	38.0	41.0	35.0	41.0
30	38.6665	40.0	38.0	41.0	34.0	41.0
31	39.02325	41.0	39.0	41.0	35.0	41.0
32	39.03125	41.0	39.0	41.0	35.0	41.0
33	37.4345	40.0	38.0	41.0	31.0	41.0
34	36.89025	40.0	37.0	41.0	30.0	41.0
35	32.30025	38.0	30.0	40.0	9.0	41.0
36	28.531	36.0	15.0	40.0	8.0	41.0
37	28.90525	35.0	22.0	39.0	6.0	40.0
38	31.86225	37.0	30.0	39.0	9.0	41.0
39	31.0275	37.0	28.0	40.0	6.0	41.0
40	32.191	37.0	31.0	40.0	2.0	41.0
41	29.7675	36.0	25.0	40.0	2.0	41.0
42	31.62375	37.0	30.0	40.0	2.0	41.0
43	29.5445	36.0	24.0	40.0	2.0	41.0
44	30.91525	37.0	30.0	40.0	2.0	41.0
45	28.173	36.0	18.0	40.0	2.0	41.0
46	26.025	34.0	7.0	39.0	2.0	41.0
47	26.30425	34.0	2.0	39.0	2.0	41.0
48	27.38875	35.0	2.0	40.0	2.0	41.0
49	25.26625	34.0	2.0	40.0	2.0	41.0
50	21.85725	28.0	2.0	38.0	2.0	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
14	1.0
15	0.0
16	4.0
17	2.0
18	6.0
19	6.0
20	13.0
21	20.0
22	24.0
23	28.0
24	40.0
25	62.0
26	104.0
27	156.0
28	82.0
29	106.0
30	177.0
31	176.0
32	176.0
33	179.0
34	244.0
35	262.0
36	315.0
37	395.0
38	579.0
39	843.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.74467551991982	23.72838887496868	54.72312703583062	12.80380856928088
2	24.75	27.0	22.35	25.900000000000002
3	17.375	19.625	21.175	41.825
4	24.825	36.6	14.45	24.125
5	22.0	38.125	28.625	11.25
6	33.5	17.5	37.625	11.375
7	15.575	23.525	25.35	35.55
8	24.875	41.625	14.075	19.425
9	16.900000000000002	39.25	32.225	11.625
10	21.0	20.525	26.900000000000002	31.574999999999996
11	33.025	13.100000000000001	14.649999999999999	39.225
12	15.45	18.025	24.5	42.025
13	19.725	22.5	37.6	20.175
14	37.0	22.875	26.950000000000003	13.175
15	36.8	21.375	27.925	13.900000000000002
16	14.099999999999998	25.724999999999998	21.425	38.75
17	24.725	24.125	37.125	14.025000000000002
18	28.799999999999997	20.05	28.225	22.925
19	36.15	14.725	31.25	17.875
20	47.4	18.75	22.475	11.375
21	22.075	27.025	24.325	26.575
22	31.55	11.75	48.699999999999996	8.0
23	23.599999999999998	13.725000000000001	49.25	13.425
24	51.349999999999994	12.9	28.249999999999996	7.5
25	54.125	21.325	15.75	8.799999999999999
26	29.349999999999998	48.949999999999996	11.35	10.35
27	14.2	52.849999999999994	22.975	9.975000000000001
28	9.2	27.425	51.175000000000004	12.2
29	8.575000000000001	12.125	60.6	18.7
30	9.950000000000001	5.45	39.725	44.875
31	12.475	4.675	47.599999999999994	35.25
32	24.325	5.8999999999999995	23.425	46.35
33	54.625	6.875000000000001	15.125	23.375
34	67.35	6.575	11.450000000000001	14.625
35	62.525	6.175	21.4	9.9
36	67.125	7.1499999999999995	15.2	10.525
37	39.85	10.65	22.275	27.224999999999998
38	25.4	12.075	12.525	50.0
39	16.725	25.275	7.925	50.075
40	13.975000000000001	50.125	8.774999999999999	27.125
41	26.8	49.925000000000004	8.924999999999999	14.35
42	52.225	31.45	8.200000000000001	8.125
43	50.275000000000006	34.1	7.925	7.7
44	31.324999999999996	50.4	6.5	11.774999999999999
45	16.35	50.224999999999994	9.1	24.325
46	9.325	30.95	26.474999999999998	33.25
47	8.825	15.174999999999999	34.050000000000004	41.949999999999996
48	10.025	10.25	22.8	56.925000000000004
49	11.700000000000001	24.7	12.2	51.4
50	33.1	26.525	8.525	31.85
>>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	0.5
16	1.0
17	1.0
18	1.0
19	1.0
20	1.0
21	0.5
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	0.5
28	0.0
29	0.5
30	1.0
31	6.0
32	11.0
33	16.0
34	21.0
35	32.5
36	44.0
37	54.0
38	64.0
39	59.5
40	55.0
41	59.0
42	63.0
43	85.5
44	108.0
45	180.0
46	252.0
47	307.5
48	363.0
49	502.5
50	642.0
51	795.0
52	948.0
53	725.0
54	502.0
55	403.0
56	304.0
57	297.5
58	291.0
59	204.0
60	117.0
61	91.5
62	66.0
63	69.0
64	72.0
65	49.5
66	27.0
67	15.5
68	4.0
69	5.5
70	7.0
71	14.0
72	21.0
73	14.0
74	7.0
75	4.0
76	1.0
77	1.5
78	2.0
79	1.5
80	1.0
81	1.0
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	0.22499999999999998
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	warn
#Total Deduplicated Percentage	51.975
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.18278018278018	41.675000000000004
2	8.080808080808081	8.4
3	3.896103896103896	6.075
4	2.1645021645021645	4.5
5	1.0101010101010102	2.625
6	0.9620009620009621	3.0
7	0.6253006253006254	2.275
8	0.5291005291005291	2.1999999999999997
9	0.2886002886002886	1.35
>10	2.1645021645021645	21.4
>50	0.0481000481000481	2.175
>100	0.0481000481000481	4.324999999999999
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	173	4.324999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	87	2.175	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	49	1.225	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	29	0.7250000000000001	RNA PCR Primer, Index 1 (96% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	22	0.5499999999999999	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	16	0.4	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	13	0.325	RNA PCR Primer, Index 1 (100% over 35bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 33bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 32bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGC	10	0.25	RNA PCR Primer, Index 26 (100% over 50bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	10	0.25	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	10	0.25	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (95% over 23bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	8	0.2	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	8	0.2	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	8	0.2	No Hit
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	7	0.17500000000000002	No Hit
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	6	0.15	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACCCCA	6	0.15	RNA PCR Primer, Index 1 (95% over 24bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
TGAGGTAGTAGTTTGTGCTGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTC	6	0.15	RNA PCR Primer, Index 26 (100% over 44bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	5	0.125	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAATTCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	5	0.125	No Hit
CAGTGCAATAGTATTGTCAAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATCCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.25	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.25	0.0	0.0	0.0
4	0.0	0.275	0.0	0.0	0.0
5	0.0	0.325	0.0	0.0	0.0
6	0.0	0.375	0.0	0.0	0.0
7	0.0	0.575	0.0	0.0	0.0
8	0.0	0.675	0.0	0.0	0.0
9	0.0	0.7	0.0	0.0	0.0
10	0.0	0.775	0.0	0.0	0.0
11	0.0	0.85	0.0	0.0	0.0
12	0.0	0.975	0.0	0.0	0.0
13	0.0	1.125	0.0	0.0	0.0
14	0.0	1.275	0.0	0.0	0.0
15	0.0	1.6	0.0	0.0	0.0
16	0.0	2.325	0.0	0.0	0.0
17	0.0	2.775	0.0	0.0	0.0
18	0.0	3.325	0.0	0.0	0.0
19	0.0	4.1	0.0	0.0	0.0
20	0.0	5.175	0.0	0.0	0.0
21	0.0	8.95	0.0	0.0	0.0
22	0.0	20.075	0.0	0.0	0.0
23	0.0	52.225	0.0	0.0	0.0
24	0.0	67.525	0.0	0.0	0.0
25	0.0	74.05	0.0	0.0	0.0
26	0.0	75.05	0.0	0.0	0.0
27	0.0	75.4	0.0	0.0	0.0
28	0.0	76.075	0.0	0.0	0.0
29	0.0	76.4	0.0	0.0	0.0
30	0.0	76.9	0.0	0.0	0.0
31	0.0	77.6	0.0	0.0	0.0
32	0.0	78.225	0.0	0.0	0.0
33	0.0	79.1	0.0	0.0	0.0
34	0.0	80.775	0.0	0.0	0.0
35	0.0	81.575	0.0	0.0	0.0
36	0.0	82.05	0.0	0.0	0.0
37	0.0	82.525	0.0	0.0	0.0
38	0.0	83.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AAGTAAT	40	5.315087E-9	44.000004	4
TCAAGTA	40	5.315087E-9	44.000004	2
AATCCAG	40	5.315087E-9	44.000004	8
CTGAGCT	20	6.952051E-4	44.000004	11
ATCCAGG	40	5.315087E-9	44.000004	9
TTCAAGT	40	5.315087E-9	44.000004	1
CGGGGCC	20	6.952051E-4	44.000004	32
AGGATAG	40	5.315087E-9	44.000004	13
ATAGGCT	40	5.315087E-9	44.000004	16
GAGCTTG	20	6.952051E-4	44.000004	13
GGATCCG	20	6.952051E-4	44.000004	3
CCGTCTG	20	6.952051E-4	44.000004	7
TCGGATC	20	6.952051E-4	44.000004	1
CGGATCC	20	6.952051E-4	44.000004	2
TCCAGGA	40	5.315087E-9	44.000004	10
ACATCCT	20	6.952051E-4	44.000004	6
ACATTCA	40	5.315087E-9	44.000004	2
GAGTTGG	20	6.952051E-4	44.000004	20
GGATAGG	40	5.315087E-9	44.000004	14
CTTGGCT	20	6.952051E-4	44.000004	16
>>END_MODULE
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393243 spots for SRR5030913.sra
Written 393243 spots for SRR5030913.sra
Read 393244 spots for SRR5030913.sra
Written 393244 spots for SRR5030913.sra
SRR ids: ['SRR5030913.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_yeva0x8_
SRR5030913.sra spots: 4718917
blocks: [[1, 393243], [393244, 786486], [786487, 1179729], [1179730, 1572972], [1572973, 1966215], [1966216, 2359458], [2359459, 2752701], [2752702, 3145944], [3145945, 3539187], [3539188, 3932430], [3932431, 4325673], [4325674, 4718917]]
SRR5030913 file size 816815
SRR5030913 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030913 SRR5030913_1.fastq
Input file:	SRR5030913_1.fastq
trimmed:	SRR5030913-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 06:43:17 2020 >> started

Wed Mar  4 06:43:20 2020 >> done (2.800s)
4718917 reads processed; of these:
    188 ( 0.00%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
4718724 (100.00%) reads available; of these:
 576047 (12.21%) trimmed reads available after processing
4142677 (87.79%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     55	  0.00%
 19	     74	  0.00%
 20	    183	  0.00%
 21	    278	  0.01%
 22	    501	  0.01%
 23	    658	  0.01%
 24	    530	  0.01%
 25	    715	  0.02%
 26	    627	  0.01%
 27	    901	  0.02%
 28	   1101	  0.02%
 29	   2218	  0.05%
 30	   1390	  0.03%
 31	   1827	  0.04%
 32	   5165	  0.11%
 33	  14310	  0.30%
 34	  44515	  0.94%
 35	   9599	  0.20%
 36	  11512	  0.24%
 37	   5078	  0.11%
 38	  11573	  0.25%
 39	   8986	  0.19%
 40	  20054	  0.42%
 41	  10699	  0.23%
 42	  31671	  0.67%
 43	  11445	  0.24%
 44	  61646	  1.31%
 45	  33728	  0.71%
 46	  26462	  0.56%
 47	  30821	  0.65%
 48	 106933	  2.27%
 49	 120792	  2.56%
 50	4142677	 87.79%
4718724 reads passed initial QC


criterion=sequence-density
sequence-density=81.45
sequence-density-rank=1
fanout-score=18.44
fanout-score-rank=3
prefix-density=84.23
prefix-fanout=17.8
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=1.69
sequence-density-rank=8
fanout-score=441.38
fanout-score-rank=1
prefix-density=83.41
prefix-fanout=8.9
sequence=GGAATTCTCGGTGCCAAGGA
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC -o SRR5030913 -
Input file:	STDIN
trimmed:	SRR5030913-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCC
-- 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 06:43:39 2020 >> started

Wed Mar  4 06:43:46 2020 >> done (6.939s)
4603633 reads processed; of these:
 152732 ( 3.32%) short reads filtered out after trimming by size control
  17504 ( 0.38%) empty reads filtered out after trimming by size control
4433397 (96.30%) reads available; of these:
3917192 (88.36%) trimmed reads available after processing
 516205 (11.64%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  28043	  0.63%
 19	  45481	  1.03%
 20	 187685	  4.23%
 21	 493094	 11.12%
 22	1457919	 32.88%
 23	 762305	 17.19%
 24	 270509	  6.10%
 25	  45392	  1.02%
 26	  23001	  0.52%
 27	  22892	  0.52%
 28	  25517	  0.58%
 29	  21266	  0.48%
 30	  33769	  0.76%
 31	  39938	  0.90%
 32	  43405	  0.98%
 33	  78062	  1.76%
 34	  41869	  0.94%
 35	  28456	  0.64%
 36	  41459	  0.94%
 37	  18585	  0.42%
 38	  22027	  0.50%
 39	  20872	  0.47%
 40	  29473	  0.66%
 41	  34267	  0.77%
 42	  42122	  0.95%
 43	  28491	  0.64%
 44	  33199	  0.75%
 45	  29585	  0.67%
 46	  24746	  0.56%
 47	  19707	  0.44%
 48	   9509	  0.21%
 49	  16253	  0.37%
 50	 414499	  9.35%


criterion=sequence-density
sequence-density=5.06
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=20
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.46
sequence-density-rank=32
fanout-score=11.40
fanout-score-rank=1
prefix-density=0.93
prefix-fanout=5.7
sequence=GGAATTCTCGGGGCCCAGGAA
                                 Started job on |	Mar 04 06:44:08
                             Started mapping on |	Mar 04 06:44:09
                                    Finished on |	Mar 04 06:44:52
       Mapping speed, Million of reads per hour |	380.80

                          Number of input reads |	4548488
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2218572
                        Uniquely mapped reads % |	48.78%
                          Average mapped length |	27.05
                       Number of splices: Total |	2163
            Number of splices: Annotated (sjdb) |	279
                       Number of splices: GT/AG |	1974
                       Number of splices: GC/AG |	22
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	164
                      Mismatch rate per base, % |	0.19%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.25
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.16
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1843547
             % of reads mapped to multiple loci |	40.53%
        Number of reads mapped to too many loci |	87456
             % of reads mapped to too many loci |	1.92%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.25%
                     % of reads unmapped: other |	0.52%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	486369	486369	486369
N_multimapping	1843547	1843547	1843547
N_noFeature	97660	116859	1748017
N_ambiguous	1170010	767177	18643
UnstrandedReadsAssigned:950902 PositiveStrandReadsAssigned:1334536 NegativeStrandReadsAssigned:451912
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030913 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: SRR5030913-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,548,488 reads, 868,218 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 599 rounds

 109283 SRR5030913.ke.tsv
  52636 SRR5030913.se.tsv
 161919 total
==> SRR5030913.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

==> SRR5030913.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030913 completed mapping pipeline successfully
