Starting /dee2/code/volunteer_pipeline.sh SRR5030844
    current disk space = 160676462592
    free memory = 73943564 
SRR5030844 SRAfilesize
876702b40403d7041608c5d99129c8f2  SRR5030844.sra
SRR5030844.sra file validated
SRR5030844 is single end
SRR5030844 is conventional basespace
SRR5030844 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030844_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	32.38175	33.0	31.0	34.0	31.0	34.0
2	32.762	34.0	31.0	34.0	31.0	34.0
3	32.808	34.0	31.0	34.0	31.0	34.0
4	36.26125	37.0	37.0	37.0	35.0	37.0
5	36.27675	37.0	37.0	37.0	35.0	37.0
6	36.05275	37.0	35.0	37.0	35.0	37.0
7	36.14125	37.0	35.0	37.0	35.0	37.0
8	36.179	37.0	36.0	37.0	35.0	37.0
9	37.92675	39.0	38.0	39.0	35.0	39.0
10	37.8935	39.0	38.0	39.0	35.0	39.0
11	37.847	39.0	38.0	39.0	35.0	39.0
12	37.887	39.0	38.0	39.0	35.0	39.0
13	37.92725	39.0	38.0	39.0	35.0	39.0
14	39.31975	41.0	39.0	41.0	36.0	41.0
15	39.1775	41.0	39.0	41.0	36.0	41.0
16	39.26275	40.0	39.0	41.0	36.0	41.0
17	39.3395	41.0	39.0	41.0	36.0	41.0
18	39.375	41.0	39.0	41.0	36.0	41.0
19	39.129	40.0	39.0	41.0	36.0	41.0
20	39.137	40.0	39.0	41.0	36.0	41.0
21	39.219	40.0	39.0	41.0	36.0	41.0
22	39.19675	41.0	39.0	41.0	36.0	41.0
23	39.13	41.0	39.0	41.0	36.0	41.0
24	38.53375	40.0	38.0	41.0	34.0	41.0
25	38.7655	40.0	38.0	41.0	35.0	41.0
26	38.66925	40.0	38.0	41.0	34.0	41.0
27	38.77825	40.0	38.0	41.0	35.0	41.0
28	38.72375	40.0	38.0	41.0	34.0	41.0
29	38.44525	40.0	38.0	41.0	34.0	41.0
30	38.25425	40.0	38.0	41.0	33.0	41.0
31	38.6295	40.0	38.0	41.0	34.0	41.0
32	38.8795	40.0	38.0	41.0	35.0	41.0
33	37.376	40.0	37.0	41.0	31.0	41.0
34	36.66725	40.0	37.0	41.0	30.0	41.0
35	33.19225	38.0	31.0	40.0	16.0	41.0
36	29.22225	37.0	16.0	40.0	8.0	41.0
37	29.993	36.0	24.0	39.0	6.0	41.0
38	32.65525	37.0	31.0	40.0	18.0	41.0
39	32.21175	37.0	31.0	40.0	9.0	41.0
40	33.0145	38.0	33.0	40.0	8.0	41.0
41	30.81925	37.0	27.0	40.0	2.0	41.0
42	32.525	38.0	31.0	40.0	2.0	41.0
43	30.6955	37.0	28.0	40.0	2.0	41.0
44	31.71025	38.0	31.0	40.0	2.0	41.0
45	29.71375	37.0	26.0	40.0	2.0	41.0
46	27.57675	35.0	17.0	40.0	2.0	41.0
47	27.75675	35.0	21.0	39.0	2.0	41.0
48	28.54375	36.0	24.0	40.0	2.0	41.0
49	26.43425	35.0	2.0	40.0	2.0	41.0
50	22.608	30.0	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	2.0
15	1.0
16	0.0
17	0.0
18	3.0
19	7.0
20	9.0
21	20.0
22	21.0
23	26.0
24	45.0
25	59.0
26	83.0
27	125.0
28	71.0
29	106.0
30	149.0
31	155.0
32	133.0
33	187.0
34	242.0
35	292.0
36	340.0
37	473.0
38	622.0
39	828.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.091637456184277	25.41311967951928	49.47421131697546	14.02103154732098
2	24.6	26.875	19.7	28.825
3	24.45	22.175	20.65	32.725
4	27.800000000000004	28.275	15.725	28.199999999999996
5	21.025	41.075	25.724999999999998	12.174999999999999
6	34.825	17.175	34.875	13.125
7	17.95	19.35	27.525	35.175
8	26.424999999999997	31.5	15.25	26.825
9	19.775000000000002	36.725	30.225	13.275
10	24.825	20.9	29.475	24.8
11	31.75	12.475	17.75	38.025
12	16.1	19.925	31.05	32.925
13	30.525000000000002	20.724999999999998	29.25	19.5
14	31.275	31.5	22.675	14.549999999999999
15	33.550000000000004	25.525	26.125	14.799999999999999
16	19.3	22.45	21.9	36.35
17	22.325	23.225	38.425	16.025
18	24.275	21.775	28.799999999999997	25.15
19	33.475	15.675	32.675	18.175
20	40.2	17.0	28.325	14.475
21	23.75	20.150000000000002	28.849999999999998	27.250000000000004
22	27.675	13.200000000000001	46.050000000000004	13.075000000000001
23	26.55	14.05	44.2	15.2
24	49.7	13.0	26.200000000000003	11.1
25	49.475	22.8	16.35	11.375
26	27.05	44.824999999999996	14.45	13.675
27	16.725	46.6	23.724999999999998	12.950000000000001
28	13.225000000000001	25.974999999999998	46.325	14.475
29	11.25	14.249999999999998	56.074999999999996	18.425
30	10.5	7.625	37.35	44.525
31	15.075	7.55	43.824999999999996	33.550000000000004
32	26.75	7.425	22.650000000000002	43.175000000000004
33	52.575	9.35	14.549999999999999	23.525
34	59.824999999999996	8.05	14.825	17.299999999999997
35	58.099999999999994	7.8	21.725	12.375
36	60.3	9.525	16.825000000000003	13.350000000000001
37	41.75	11.225	20.974999999999998	26.05
38	24.975	15.075	12.9	47.05
39	18.2	25.25	10.15	46.400000000000006
40	15.65	48.15	11.475	24.725
41	27.800000000000004	44.95	11.375	15.875
42	48.65	30.2	10.424999999999999	10.725
43	45.050000000000004	34.449999999999996	10.15	10.35
44	28.275	48.25	8.275	15.2
45	18.75	46.975	11.825	22.45
46	12.45	28.275	24.474999999999998	34.8
47	10.325	17.275	33.800000000000004	38.6
48	11.675	12.75	21.725	53.849999999999994
49	14.85	24.425	13.825000000000001	46.9
50	28.925	26.825	11.450000000000001	32.800000000000004
>>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	0.0
12	0.0
13	0.5
14	1.0
15	1.0
16	1.0
17	0.5
18	0.0
19	0.5
20	1.0
21	0.5
22	0.0
23	0.5
24	1.0
25	1.5
26	2.0
27	1.0
28	0.0
29	1.0
30	2.0
31	8.0
32	14.0
33	16.5
34	19.0
35	39.5
36	60.0
37	78.0
38	96.0
39	86.0
40	76.0
41	67.0
42	58.0
43	84.0
44	110.0
45	161.0
46	212.0
47	271.5
48	331.0
49	427.5
50	524.0
51	692.0
52	860.0
53	675.5
54	491.0
55	442.5
56	394.0
57	365.0
58	336.0
59	236.0
60	136.0
61	113.0
62	90.0
63	95.0
64	100.0
65	63.0
66	26.0
67	20.5
68	15.0
69	12.0
70	9.0
71	16.5
72	24.0
73	12.5
74	1.0
75	0.5
76	0.0
77	3.0
78	6.0
79	5.0
80	4.0
81	2.0
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	0.15
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	50.475
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.18821198613175	40.475
2	8.221892025755324	8.3
3	3.7642397226349678	5.7
4	1.8821198613174839	3.8
5	1.0896483407627537	2.75
6	0.8420009905894007	2.55
7	0.44576523031203563	1.575
8	0.396235760277365	1.6
9	0.3467062902426944	1.575
>10	2.674591381872214	25.424999999999997
>50	0.09905894006934125	3.4250000000000003
>100	0.04952947003467063	2.825
>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	113	2.825	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	85	2.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	52	1.3	RNA PCR Primer, Index 1 (96% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	50	1.25	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	38	0.95	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGC	32	0.8	RNA PCR Primer, Index 38 (100% over 50bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	31	0.775	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	19	0.475	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	16	0.4	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	16	0.4	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	15	0.375	No Hit
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	15	0.375	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 33bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	14	0.35000000000000003	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	13	0.325	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	13	0.325	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTC	13	0.325	RNA PCR Primer, Index 38 (100% over 44bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	12	0.3	RNA PCR Primer, Index 1 (97% over 35bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	12	0.3	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	11	0.27499999999999997	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	10	0.25	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	9	0.22499999999999998	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	9	0.22499999999999998	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	9	0.22499999999999998	No Hit
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	8	0.2	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	8	0.2	No Hit
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	8	0.2	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	7	0.17500000000000002	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCT	6	0.15	RNA PCR Primer, Index 1 (97% over 35bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	6	0.15	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	6	0.15	RNA PCR Primer, Index 1 (95% over 23bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	5	0.125	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	5	0.125	No Hit
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	5	0.125	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AAGAAAGATTGCAAGAACTGCTAATTCATGCTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	5	0.125	No Hit
ATTCATGATGAAATAGATCCTTGACTGAAGCTGATGATGCGTCTGTGTAA	5	0.125	No Hit
ACATGTGATGAGAAACTGTTTCGGTCCCAGTTGATGGCCACTGATAACAT	5	0.125	No Hit
AGCAGCATTGTACAGGGCTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.825	0.0	0.0	0.0
2	0.0	0.825	0.0	0.0	0.0
3	0.0	0.925	0.0	0.0	0.0
4	0.0	0.95	0.0	0.0	0.0
5	0.0	0.975	0.0	0.0	0.0
6	0.0	1.025	0.0	0.0	0.0
7	0.0	1.425	0.0	0.0	0.0
8	0.0	1.55	0.0	0.0	0.0
9	0.0	1.65	0.0	0.0	0.0
10	0.0	1.85	0.0	0.0	0.0
11	0.0	2.0	0.0	0.0	0.0
12	0.0	2.15	0.0	0.0	0.0
13	0.0	2.525	0.0	0.0	0.0
14	0.0	2.8	0.0	0.0	0.0
15	0.0	3.225	0.0	0.0	0.0
16	0.0	4.225	0.0	0.0	0.0
17	0.0	4.925	0.0	0.0	0.0
18	0.0	5.575	0.0	0.0	0.0
19	0.0	6.075	0.0	0.0	0.0
20	0.0	6.825	0.0	0.0	0.0
21	0.0	11.675	0.0	0.0	0.0
22	0.0	22.6	0.0	0.0	0.0
23	0.0	50.275	0.0	0.0	0.0
24	0.0	62.75	0.0	0.0	0.0
25	0.0	68.6	0.0	0.0	0.0
26	0.0	70.025	0.0	0.0	0.0
27	0.0	70.825	0.0	0.0	0.0
28	0.0	71.4	0.0	0.0	0.0
29	0.0	71.75	0.0	0.0	0.0
30	0.0	72.125	0.0	0.0	0.0
31	0.0	72.7	0.0	0.0	0.0
32	0.0	73.45	0.0	0.0	0.0
33	0.0	74.175	0.0	0.0	0.0
34	0.0	76.175	0.0	0.0	0.0
35	0.0	77.25	0.0	0.0	0.0
36	0.0	77.825	0.0	0.0	0.0
37	0.0	79.05	0.0	0.0	0.0
38	0.0	79.45	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACTGTTG	20	6.952051E-4	44.000004	18
AAGTAAT	20	6.952051E-4	44.000004	4
GTTGAAG	20	6.952051E-4	44.000004	10
TCAAGTA	20	6.952051E-4	44.000004	2
AATCCAG	20	6.952051E-4	44.000004	8
CAGTTGA	20	6.952051E-4	44.000004	8
ATCCAGG	20	6.952051E-4	44.000004	9
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
TTCAAGT	20	6.952051E-4	44.000004	1
AGGATAG	20	6.952051E-4	44.000004	13
CATTCAA	20	6.952051E-4	44.000004	3
TCCAGGA	20	6.952051E-4	44.000004	10
GCCAGTT	20	6.952051E-4	44.000004	6
ACATTCA	20	6.952051E-4	44.000004	2
GGATAGG	20	6.952051E-4	44.000004	14
CTTGGCT	20	6.952051E-4	44.000004	16
GCTGCCA	20	6.952051E-4	44.000004	3
AGTAATC	20	6.952051E-4	44.000004	5
GAACTGT	20	6.952051E-4	44.000004	16
>>END_MODULE
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214383 spots for SRR5030844.sra
Written 214383 spots for SRR5030844.sra
Read 214387 spots for SRR5030844.sra
Written 214387 spots for SRR5030844.sra
SRR ids: ['SRR5030844.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_e8ooz4lc
SRR5030844.sra spots: 2572600
blocks: [[1, 214383], [214384, 428766], [428767, 643149], [643150, 857532], [857533, 1071915], [1071916, 1286298], [1286299, 1500681], [1500682, 1715064], [1715065, 1929447], [1929448, 2143830], [2143831, 2358213], [2358214, 2572600]]
SRR5030844 file size 444811
SRR5030844 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030844 SRR5030844_1.fastq
Input file:	SRR5030844_1.fastq
trimmed:	SRR5030844-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 06:26:27 2020 >> started

Wed Mar  4 06:26:30 2020 >> done (2.961s)
2572600 reads processed; of these:
    163 ( 0.01%) short reads filtered out after trimming by size control
      3 ( 0.00%) empty reads filtered out after trimming by size control
2572434 (99.99%) reads available; of these:
 303521 (11.80%) trimmed reads available after processing
2268913 (88.20%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     34	  0.00%
 19	     56	  0.00%
 20	    100	  0.00%
 21	    137	  0.01%
 22	    269	  0.01%
 23	    326	  0.01%
 24	    355	  0.01%
 25	    475	  0.02%
 26	    417	  0.02%
 27	    545	  0.02%
 28	    696	  0.03%
 29	   1182	  0.05%
 30	    845	  0.03%
 31	   1125	  0.04%
 32	   2832	  0.11%
 33	   8772	  0.34%
 34	  21178	  0.82%
 35	   4842	  0.19%
 36	   5472	  0.21%
 37	   3074	  0.12%
 38	   5925	  0.23%
 39	   5411	  0.21%
 40	  10690	  0.42%
 41	   5965	  0.23%
 42	  15485	  0.60%
 43	   6532	  0.25%
 44	  28757	  1.12%
 45	  18078	  0.70%
 46	  16448	  0.64%
 47	  19020	  0.74%
 48	  56138	  2.18%
 49	  62340	  2.42%
 50	2268913	 88.20%
2572434 reads passed initial QC


criterion=sequence-density
sequence-density=78.48
sequence-density-rank=1
fanout-score=20.69
fanout-score-rank=3
prefix-density=81.14
prefix-fanout=20.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC


criterion=fanout-score
sequence-density=1.42
sequence-density-rank=4
fanout-score=522.27
fanout-score-rank=1
prefix-density=80.28
prefix-fanout=9.3
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC -o SRR5030844 -
Input file:	STDIN
trimmed:	SRR5030844-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTAGCTATCTCGTATGCC
-- 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 06:26:52 2020 >> started

Wed Mar  4 06:26:58 2020 >> done (6.355s)
2507309 reads processed; of these:
 116548 ( 4.65%) short reads filtered out after trimming by size control
  13425 ( 0.54%) empty reads filtered out after trimming by size control
2377336 (94.82%) reads available; of these:
2049305 (86.20%) trimmed reads available after processing
 328031 (13.80%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  14396	  0.61%
 19	  23418	  0.99%
 20	 116627	  4.91%
 21	 290704	 12.23%
 22	 677502	 28.50%
 23	 324671	 13.66%
 24	 159555	  6.71%
 25	  38864	  1.63%
 26	  19638	  0.83%
 27	  15310	  0.64%
 28	  15518	  0.65%
 29	  12804	  0.54%
 30	  16907	  0.71%
 31	  19781	  0.83%
 32	  22712	  0.96%
 33	  55529	  2.34%
 34	  23890	  1.00%
 35	  19892	  0.84%
 36	  27312	  1.15%
 37	  11148	  0.47%
 38	  12860	  0.54%
 39	  12950	  0.54%
 40	  20482	  0.86%
 41	  23438	  0.99%
 42	  31063	  1.31%
 43	  20390	  0.86%
 44	  19956	  0.84%
 45	  19350	  0.81%
 46	  15103	  0.64%
 47	  12993	  0.55%
 48	   5357	  0.23%
 49	  10302	  0.43%
 50	 266914	 11.23%


criterion=sequence-density
sequence-density=6.77
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=21
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=41
fanout-score=318.13
fanout-score-rank=1
prefix-density=1.79
prefix-fanout=1.7
sequence=TTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 06:27:30
                             Started mapping on |	Mar 04 06:27:31
                                    Finished on |	Mar 04 06:27:54
       Mapping speed, Million of reads per hour |	382.30

                          Number of input reads |	2442461
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1335396
                        Uniquely mapped reads % |	54.67%
                          Average mapped length |	27.60
                       Number of splices: Total |	1137
            Number of splices: Annotated (sjdb) |	114
                       Number of splices: GT/AG |	1029
                       Number of splices: GC/AG |	22
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	86
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.17
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.07
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	800044
             % of reads mapped to multiple loci |	32.76%
        Number of reads mapped to too many loci |	46697
             % of reads mapped to too many loci |	1.91%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.11%
                     % of reads unmapped: other |	0.54%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	307021	307021	307021
N_multimapping	800044	800044	800044
N_noFeature	59368	74464	992431
N_ambiguous	720996	426187	13944
UnstrandedReadsAssigned:555032 PositiveStrandReadsAssigned:834745 NegativeStrandReadsAssigned:329021
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030844 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: SRR5030844-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,442,461 reads, 604,714 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 611 rounds

 109283 SRR5030844.ke.tsv
  52636 SRR5030844.se.tsv
 161919 total
==> SRR5030844.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

==> SRR5030844.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030844 completed mapping pipeline successfully
