Starting /dee2/code/volunteer_pipeline.sh SRR5030842
    current disk space = 160655474688
    free memory = 73947956 
SRR5030842 SRAfilesize
32043193d472938a8e9c93a667e67749  SRR5030842.sra
SRR5030842.sra file validated
SRR5030842 is single end
SRR5030842 is conventional basespace
SRR5030842 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030842_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	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.302	33.0	31.0	34.0	31.0	34.0
2	32.6675	34.0	31.0	34.0	31.0	34.0
3	32.7015	34.0	31.0	34.0	31.0	34.0
4	36.2	37.0	35.0	37.0	35.0	37.0
5	36.14475	37.0	35.0	37.0	35.0	37.0
6	35.931	37.0	35.0	37.0	35.0	37.0
7	36.01025	37.0	35.0	37.0	35.0	37.0
8	36.089	37.0	35.0	37.0	35.0	37.0
9	37.82025	39.0	38.0	39.0	35.0	39.0
10	37.80275	39.0	38.0	39.0	35.0	39.0
11	37.72525	39.0	37.0	39.0	35.0	39.0
12	37.77875	39.0	38.0	39.0	35.0	39.0
13	37.76125	39.0	38.0	39.0	35.0	39.0
14	39.17025	41.0	39.0	41.0	36.0	41.0
15	39.1545	41.0	39.0	41.0	36.0	41.0
16	39.06225	40.0	38.0	41.0	36.0	41.0
17	39.25825	41.0	39.0	41.0	36.0	41.0
18	39.20025	41.0	39.0	41.0	36.0	41.0
19	38.943	40.0	38.0	41.0	35.0	41.0
20	39.0995	40.0	39.0	41.0	36.0	41.0
21	39.143	40.0	39.0	41.0	36.0	41.0
22	39.20125	41.0	39.0	41.0	36.0	41.0
23	39.084	40.0	39.0	41.0	36.0	41.0
24	38.3175	40.0	38.0	41.0	34.0	41.0
25	38.619	40.0	38.0	41.0	34.0	41.0
26	38.7085	40.0	38.0	41.0	34.0	41.0
27	38.689	40.0	38.0	41.0	34.0	41.0
28	38.73825	40.0	38.0	41.0	34.0	41.0
29	38.7015	40.0	38.0	41.0	34.0	41.0
30	38.438	40.0	38.0	41.0	34.0	41.0
31	38.8495	40.0	38.0	41.0	35.0	41.0
32	38.97525	40.0	39.0	41.0	35.0	41.0
33	37.62775	40.0	38.0	41.0	32.0	41.0
34	36.36725	40.0	37.0	41.0	28.0	41.0
35	32.03375	38.0	30.0	40.0	8.0	41.0
36	29.01225	37.0	16.0	40.0	8.0	41.0
37	29.04725	35.0	22.0	39.0	6.0	41.0
38	31.713	37.0	30.0	40.0	6.0	41.0
39	30.8465	37.0	28.0	40.0	2.0	41.0
40	31.92275	37.0	31.0	40.0	2.0	41.0
41	29.576	36.0	24.0	40.0	2.0	41.0
42	31.33	37.0	30.0	40.0	2.0	41.0
43	29.5275	36.0	26.0	40.0	2.0	41.0
44	30.612	37.0	30.0	40.0	2.0	41.0
45	28.32225	36.0	21.0	40.0	2.0	41.0
46	26.329	34.0	7.0	39.0	2.0	41.0
47	26.303	34.0	2.0	39.0	2.0	41.0
48	27.06225	35.0	2.0	40.0	2.0	41.0
49	25.26175	34.0	2.0	40.0	2.0	41.0
50	21.97175	29.0	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
12	1.0
13	0.0
14	0.0
15	0.0
16	4.0
17	1.0
18	2.0
19	4.0
20	9.0
21	13.0
22	28.0
23	34.0
24	54.0
25	68.0
26	121.0
27	171.0
28	82.0
29	110.0
30	156.0
31	186.0
32	152.0
33	193.0
34	236.0
35	276.0
36	299.0
37	390.0
38	557.0
39	853.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.734734734734735	25.350350350350347	51.4014014014014	13.513513513513514
2	23.674999999999997	26.325	18.55	31.45
3	24.525	21.85	23.1	30.525000000000002
4	29.45	28.849999999999998	15.275	26.424999999999997
5	20.474999999999998	42.425000000000004	25.900000000000002	11.200000000000001
6	34.675	18.15	35.699999999999996	11.475
7	18.05	18.75	26.174999999999997	37.025000000000006
8	26.525	30.049999999999997	14.825	28.599999999999998
9	19.275000000000002	36.775000000000006	30.675	13.275
10	23.05	22.8	28.625	25.525
11	30.675	11.425	17.424999999999997	40.475
12	15.85	18.875	29.825000000000003	35.449999999999996
13	32.300000000000004	18.75	29.675	19.275000000000002
14	31.775	31.874999999999996	21.375	14.975
15	34.2	24.0	28.199999999999996	13.600000000000001
16	16.825000000000003	20.674999999999997	22.525000000000002	39.975
17	22.925	21.4	40.8	14.875
18	24.825	18.7	29.25	27.224999999999998
19	34.775	14.674999999999999	32.725	17.825
20	40.849999999999994	17.150000000000002	28.225	13.775
21	22.375	19.825	30.95	26.85
22	29.799999999999997	12.325	46.875	11.0
23	28.325	14.7	42.375	14.6
24	50.24999999999999	15.225	24.925	9.6
25	48.8	24.95	15.075	11.175
26	26.875	45.9	15.925	11.3
27	15.075	46.175	25.874999999999996	12.875
28	11.675	24.75	48.199999999999996	15.375
29	9.825000000000001	13.4	56.725	20.05
30	10.125	7.85	37.2	44.824999999999996
31	15.325	5.5	44.275	34.9
32	29.475	6.375	22.125	42.025
33	54.50000000000001	8.5	14.149999999999999	22.85
34	62.35000000000001	6.275	14.774999999999999	16.6
35	58.650000000000006	6.425	23.175	11.75
36	63.14999999999999	8.425	14.099999999999998	14.325
37	37.875	10.825	20.25	31.05
38	25.05	15.45	12.925	46.575
39	18.425	28.175	9.825000000000001	43.575
40	17.575	47.875	10.625	23.925
41	31.2	43.25	10.625	14.924999999999999
42	49.2	30.25	9.775	10.775
43	44.95	36.8	9.275	8.975
44	28.749999999999996	49.175000000000004	7.8	14.274999999999999
45	18.35	43.675000000000004	11.95	26.025
46	11.975	27.800000000000004	27.85	32.375
47	10.725	15.825	30.325000000000003	43.125
48	10.725	13.675	21.3	54.300000000000004
49	15.925	25.35	13.25	45.475
50	34.2	22.675	11.175	31.95
>>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	0.5
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.5
26	2.0
27	1.0
28	0.0
29	2.0
30	4.0
31	9.0
32	14.0
33	20.5
34	27.0
35	34.5
36	42.0
37	60.0
38	78.0
39	66.5
40	55.0
41	51.0
42	47.0
43	67.0
44	87.0
45	160.5
46	234.0
47	281.0
48	328.0
49	417.0
50	506.0
51	696.0
52	886.0
53	714.0
54	542.0
55	474.0
56	406.0
57	350.5
58	295.0
59	213.5
60	132.0
61	108.5
62	85.0
63	91.0
64	97.0
65	63.5
66	30.0
67	21.0
68	12.0
69	20.5
70	29.0
71	37.5
72	46.0
73	26.0
74	6.0
75	4.5
76	3.0
77	2.0
78	1.0
79	2.0
80	3.0
81	1.5
82	0.0
83	0.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.1
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	51.24999999999999
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.04878048780488	41.025
2	9.073170731707316	9.3
3	2.731707317073171	4.2
4	2.3902439024390243	4.9
5	0.8292682926829269	2.125
6	0.6829268292682927	2.1
7	0.5365853658536586	1.925
8	0.7317073170731708	3.0
9	0.1951219512195122	0.8999999999999999
>10	2.6341463414634148	23.825
>50	0.04878048780487805	1.3
>100	0.0975609756097561	5.4
>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	109	2.725	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	107	2.675	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	52	1.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	47	1.175	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 26bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	40	1.0	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	23	0.575	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	21	0.525	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT	19	0.475	RNA PCR Primer, Index 1 (97% over 35bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGC	18	0.44999999999999996	RNA PCR Primer, Index 17 (100% over 50bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	17	0.42500000000000004	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	16	0.4	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	16	0.4	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	16	0.4	RNA PCR Primer, Index 1 (96% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	16	0.4	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	13	0.325	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	13	0.325	RNA PCR Primer, Index 1 (96% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	13	0.325	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (96% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	13	0.325	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTC	13	0.325	RNA PCR Primer, Index 17 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	12	0.3	RNA PCR Primer, Index 1 (100% over 33bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	12	0.3	RNA PCR Primer, Index 1 (96% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	12	0.3	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	11	0.27499999999999997	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	10	0.25	RNA PCR Primer, Index 1 (100% over 25bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	9	0.22499999999999998	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	8	0.2	No Hit
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	8	0.2	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (96% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	8	0.2	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	8	0.2	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	7	0.17500000000000002	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	5	0.125	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	5	0.125	No Hit
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	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	0.5	0.0	0.0	0.0
2	0.0	0.525	0.0	0.0	0.0
3	0.0	0.6	0.0	0.0	0.0
4	0.0	0.6	0.0	0.0	0.0
5	0.0	0.65	0.0	0.0	0.0
6	0.0	0.75	0.0	0.0	0.0
7	0.0	1.125	0.0	0.0	0.0
8	0.0	1.2	0.0	0.0	0.0
9	0.0	1.3	0.0	0.0	0.0
10	0.0	1.375	0.0	0.0	0.0
11	0.0	1.6	0.0	0.0	0.0
12	0.0	1.725	0.0	0.0	0.0
13	0.0	1.975	0.0	0.0	0.0
14	0.0	2.15	0.0	0.0	0.0
15	0.0	2.525	0.0	0.0	0.0
16	0.0	3.3	0.0	0.0	0.0
17	0.0	3.6	0.0	0.0	0.0
18	0.0	4.2	0.0	0.0	0.0
19	0.0	4.75	0.0	0.0	0.0
20	0.0	5.65	0.0	0.0	0.0
21	0.0	11.65	0.0	0.0	0.0
22	0.0	23.775	0.0	0.0	0.0
23	0.0	51.3	0.0	0.0	0.0
24	0.0	64.0	0.0	0.0	0.0
25	0.0	69.575	0.0	0.0	0.0
26	0.0	71.225	0.0	0.0	0.0
27	0.0	72.075	0.0	0.0	0.0
28	0.0	72.525	0.0	0.0	0.0
29	0.0	72.75	0.0	0.0	0.0
30	0.0	73.15	0.0	0.0	0.0
31	0.0	73.85	0.0	0.0	0.0
32	0.0	74.425	0.0	0.0	0.0
33	0.0	75.525	0.0	0.0	0.0
34	0.0	77.575	0.0	0.0	0.0
35	0.0	78.55	0.0	0.0	0.0
36	0.0	79.15	0.0	0.0	0.0
37	0.0	79.925	0.0	0.0	0.0
38	0.0	80.225	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGATT	20	6.952051E-4	44.000004	8
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
AATCCAG	20	6.952051E-4	44.000004	8
TAAACAT	20	6.952051E-4	44.000004	3
ATCCAGG	20	6.952051E-4	44.000004	9
TTGTATA	20	6.952051E-4	44.000004	13
AAACATC	20	6.952051E-4	44.000004	4
TTCAAGT	20	6.952051E-4	44.000004	1
AGTAGAT	20	6.952051E-4	44.000004	7
AGGATAG	20	6.952051E-4	44.000004	13
TCGGTGC	20	6.952051E-4	44.000004	31
ATAGGCT	20	6.952051E-4	44.000004	16
AGTGGAA	40	5.315087E-9	44.000004	21
GATTGTA	20	6.952051E-4	44.000004	11
TCCAGGA	20	6.952051E-4	44.000004	10
GTATAGT	20	6.952051E-4	44.000004	15
GGATAGG	20	6.952051E-4	44.000004	14
CTTGGCT	20	6.952051E-4	44.000004	16
AACTCCG	20	6.952051E-4	44.000004	44
>>END_MODULE
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
Read 297691 spots for SRR5030842.sra
Written 297691 spots for SRR5030842.sra
SRR ids: ['SRR5030842.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_wumh2hr8
SRR5030842.sra spots: 3572292
blocks: [[1, 297691], [297692, 595382], [595383, 893073], [893074, 1190764], [1190765, 1488455], [1488456, 1786146], [1786147, 2083837], [2083838, 2381528], [2381529, 2679219], [2679220, 2976910], [2976911, 3274601], [3274602, 3572292]]
SRR5030842 file size 618082
SRR5030842 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030842 SRR5030842_1.fastq
Input file:	SRR5030842_1.fastq
trimmed:	SRR5030842-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 06:25:58 2020 >> started

Wed Mar  4 06:26:00 2020 >> done (2.130s)
3572292 reads processed; of these:
    163 ( 0.00%) short reads filtered out after trimming by size control
     11 ( 0.00%) empty reads filtered out after trimming by size control
3572118 (100.00%) reads available; of these:
 433887 (12.15%) trimmed reads available after processing
3138231 (87.85%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     54	  0.00%
 19	     71	  0.00%
 20	    151	  0.00%
 21	    194	  0.01%
 22	    362	  0.01%
 23	    478	  0.01%
 24	    451	  0.01%
 25	    636	  0.02%
 26	    581	  0.02%
 27	    711	  0.02%
 28	    915	  0.03%
 29	   1432	  0.04%
 30	   1035	  0.03%
 31	   1469	  0.04%
 32	   4078	  0.11%
 33	  13486	  0.38%
 34	  30729	  0.86%
 35	   7358	  0.21%
 36	   8522	  0.24%
 37	   4434	  0.12%
 38	   9096	  0.25%
 39	   7875	  0.22%
 40	  15961	  0.45%
 41	   8363	  0.23%
 42	  21763	  0.61%
 43	   9480	  0.27%
 44	  44565	  1.25%
 45	  25197	  0.71%
 46	  22984	  0.64%
 47	  25044	  0.70%
 48	  77624	  2.17%
 49	  88788	  2.49%
 50	3138231	 87.85%
3572118 reads passed initial QC


criterion=sequence-density
sequence-density=79.08
sequence-density-rank=1
fanout-score=20.67
fanout-score-rank=2
prefix-density=81.43
prefix-fanout=20.1
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC


criterion=fanout-score
sequence-density=4.31
sequence-density-rank=2
fanout-score=54.28
fanout-score-rank=1
prefix-density=81.37
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC -o SRR5030842 -
Input file:	STDIN
trimmed:	SRR5030842-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTAGAGATCTCGTATGCC
-- 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 06:26:21 2020 >> started

Wed Mar  4 06:26:26 2020 >> done (4.655s)
3482815 reads processed; of these:
 136874 ( 3.93%) short reads filtered out after trimming by size control
  18605 ( 0.53%) empty reads filtered out after trimming by size control
3327336 (95.54%) reads available; of these:
2875903 (86.43%) trimmed reads available after processing
 451433 (13.57%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  20354	  0.61%
 19	  30844	  0.93%
 20	 174531	  5.25%
 21	 415121	 12.48%
 22	 971390	 29.19%
 23	 455241	 13.68%
 24	 219255	  6.59%
 25	  52520	  1.58%
 26	  25831	  0.78%
 27	  20403	  0.61%
 28	  20344	  0.61%
 29	  15985	  0.48%
 30	  23626	  0.71%
 31	  27148	  0.82%
 32	  29772	  0.89%
 33	  77305	  2.32%
 34	  32104	  0.96%
 35	  25289	  0.76%
 36	  37558	  1.13%
 37	  14542	  0.44%
 38	  17516	  0.53%
 39	  16727	  0.50%
 40	  24718	  0.74%
 41	  30965	  0.93%
 42	  39902	  1.20%
 43	  25390	  0.76%
 44	  24930	  0.75%
 45	  29379	  0.88%
 46	  22534	  0.68%
 47	  16833	  0.51%
 48	   7470	  0.22%
 49	  12754	  0.38%
 50	 369055	 11.09%


criterion=sequence-density
sequence-density=5.97
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=41
fanout-score=382.89
fanout-score-rank=1
prefix-density=2.31
prefix-fanout=1.7
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:26:51
                             Started mapping on |	Mar 04 06:26:52
                                    Finished on |	Mar 04 06:27:20
       Mapping speed, Million of reads per hour |	439.28

                          Number of input reads |	3416639
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1863381
                        Uniquely mapped reads % |	54.54%
                          Average mapped length |	27.05
                       Number of splices: Total |	1982
            Number of splices: Annotated (sjdb) |	284
                       Number of splices: GT/AG |	1864
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	98
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.31
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1113893
             % of reads mapped to multiple loci |	32.60%
        Number of reads mapped to too many loci |	58908
             % of reads mapped to too many loci |	1.72%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.74%
                     % of reads unmapped: other |	0.40%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	439365	439365	439365
N_multimapping	1113893	1113893	1113893
N_noFeature	74084	93058	1341947
N_ambiguous	1033080	578423	16723
UnstrandedReadsAssigned:756217 PositiveStrandReadsAssigned:1191900 NegativeStrandReadsAssigned:504711
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030842 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: SRR5030842-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,416,639 reads, 861,274 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 830 rounds

 109283 SRR5030842.ke.tsv
  52636 SRR5030842.se.tsv
 161919 total
==> SRR5030842.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

==> SRR5030842.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030842 completed mapping pipeline successfully
