Starting /dee2/code/volunteer_pipeline.sh SRR5030953
    current disk space = 160605519872
    free memory = 73949572 
SRR5030953 SRAfilesize
f5e2689f32404c55196b7356f451bf7a  SRR5030953.sra
SRR5030953.sra file validated
SRR5030953 is single end
SRR5030953 is conventional basespace
SRR5030953 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030953_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	32.3475	33.0	31.0	34.0	31.0	34.0
2	32.72375	34.0	31.0	34.0	31.0	34.0
3	32.79525	34.0	31.0	34.0	31.0	34.0
4	36.23375	37.0	37.0	37.0	35.0	37.0
5	36.259	37.0	37.0	37.0	35.0	37.0
6	36.099	37.0	35.0	37.0	35.0	37.0
7	36.16375	37.0	36.0	37.0	35.0	37.0
8	36.184	37.0	36.0	37.0	35.0	37.0
9	37.9355	39.0	38.0	39.0	35.0	39.0
10	37.96275	39.0	38.0	39.0	35.0	39.0
11	37.83575	39.0	38.0	39.0	35.0	39.0
12	37.8895	39.0	38.0	39.0	35.0	39.0
13	37.84125	39.0	38.0	39.0	35.0	39.0
14	39.1815	41.0	39.0	41.0	36.0	41.0
15	39.27	41.0	39.0	41.0	36.0	41.0
16	39.1605	40.0	39.0	41.0	36.0	41.0
17	39.231	41.0	39.0	41.0	36.0	41.0
18	39.248	41.0	39.0	41.0	36.0	41.0
19	38.88425	40.0	38.0	41.0	35.0	41.0
20	39.027	40.0	39.0	41.0	35.0	41.0
21	39.1085	40.0	39.0	41.0	35.0	41.0
22	39.0715	40.0	39.0	41.0	36.0	41.0
23	39.00475	40.0	39.0	41.0	35.0	41.0
24	38.093	40.0	38.0	41.0	33.0	41.0
25	38.34	40.0	38.0	41.0	34.0	41.0
26	38.39675	40.0	38.0	41.0	34.0	41.0
27	38.38075	40.0	38.0	41.0	34.0	41.0
28	38.419	40.0	38.0	41.0	34.0	41.0
29	38.36225	40.0	38.0	41.0	34.0	41.0
30	37.981	40.0	38.0	41.0	32.0	41.0
31	38.463	40.0	38.0	41.0	34.0	41.0
32	38.6775	40.0	38.0	41.0	35.0	41.0
33	37.1945	40.0	37.0	41.0	31.0	41.0
34	36.52675	40.0	37.0	41.0	30.0	41.0
35	33.112	38.0	31.0	40.0	15.0	41.0
36	29.242	37.0	18.0	40.0	8.0	41.0
37	29.921	35.0	25.0	39.0	7.0	40.0
38	32.3735	37.0	30.0	39.0	16.0	40.0
39	32.00625	37.0	30.0	40.0	9.0	41.0
40	32.6605	37.0	32.0	40.0	8.0	41.0
41	30.42075	36.0	26.0	40.0	2.0	41.0
42	32.08575	37.0	31.0	40.0	2.0	41.0
43	30.83025	37.0	28.0	40.0	2.0	41.0
44	31.66	37.0	31.0	40.0	2.0	41.0
45	29.7855	37.0	26.0	40.0	2.0	41.0
46	27.66025	34.0	18.0	39.0	2.0	41.0
47	27.66875	35.0	21.0	39.0	2.0	41.0
48	28.445	35.0	24.0	39.0	2.0	41.0
49	26.22575	35.0	2.0	39.0	2.0	41.0
50	22.7075	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
14	1.0
15	0.0
16	4.0
17	0.0
18	4.0
19	6.0
20	10.0
21	20.0
22	9.0
23	28.0
24	46.0
25	64.0
26	94.0
27	130.0
28	91.0
29	91.0
30	134.0
31	166.0
32	153.0
33	205.0
34	257.0
35	246.0
36	367.0
37	486.0
38	652.0
39	736.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	12.647132481843226	24.64312546957175	47.458051590283	15.251690458302027
2	22.625	27.725	21.2	28.449999999999996
3	24.025	18.325	22.375	35.275
4	30.575000000000003	29.75	15.25	24.425
5	20.4	39.125	25.7	14.774999999999999
6	28.625	16.950000000000003	40.65	13.775
7	20.974999999999998	19.825	23.775	35.425000000000004
8	23.849999999999998	32.175	15.8	28.175
9	22.7	32.625	30.2	14.475
10	25.775	18.075	30.45	25.7
11	32.525	17.575	14.575	35.325
12	16.325	20.674999999999997	31.900000000000002	31.1
13	25.974999999999998	20.225	31.574999999999996	22.225
14	27.35	30.0	22.55	20.1
15	35.175	22.6	25.900000000000002	16.325
16	15.7	24.0	22.35	37.95
17	24.65	23.599999999999998	35.8	15.950000000000001
18	24.525	16.925	33.95	24.6
19	33.625	16.025	32.074999999999996	18.275
20	41.825	17.150000000000002	25.05	15.975
21	23.400000000000002	22.1	25.924999999999997	28.575
22	28.825	14.799999999999999	44.55	11.825
23	25.025	14.85	44.2	15.925
24	47.575	16.175	24.95	11.3
25	47.075	22.175	16.650000000000002	14.099999999999998
26	27.725	43.75	15.2	13.325000000000001
27	17.349999999999998	45.4	22.85	14.399999999999999
28	15.125	25.85	44.45	14.575
29	11.1	14.35	55.474999999999994	19.075
30	11.325000000000001	9.2	34.65	44.824999999999996
31	14.524999999999999	7.575	45.75	32.15
32	26.974999999999998	8.0	22.925	42.1
33	50.849999999999994	10.125	15.85	23.175
34	58.62500000000001	8.35	15.575	17.45
35	58.15	9.55	18.975	13.325000000000001
36	57.9	11.475	16.8	13.825000000000001
37	41.025	12.55	21.975	24.45
38	24.925	16.125	13.975000000000001	44.975
39	17.275	25.75	10.9	46.075
40	16.125	44.75	13.05	26.075
41	25.15	44.85	12.2	17.8
42	47.625	29.75	11.799999999999999	10.825
43	45.574999999999996	33.550000000000004	10.625	10.25
44	29.225	46.800000000000004	8.95	15.024999999999999
45	20.225	47.0	12.950000000000001	19.825
46	13.525	29.175	22.5	34.8
47	11.450000000000001	16.275000000000002	35.099999999999994	37.175000000000004
48	11.625	13.4	21.6	53.37499999999999
49	14.524999999999999	24.3	13.900000000000002	47.275
50	27.700000000000003	26.5	11.675	34.125
>>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	0.0
14	0.0
15	0.0
16	0.0
17	1.0
18	2.0
19	1.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	2.5
26	4.0
27	3.5
28	3.0
29	4.5
30	6.0
31	13.5
32	21.0
33	34.0
34	47.0
35	56.0
36	65.0
37	76.5
38	88.0
39	80.0
40	72.0
41	76.0
42	80.0
43	99.0
44	118.0
45	159.0
46	200.0
47	266.0
48	332.0
49	416.0
50	500.0
51	622.0
52	744.0
53	612.5
54	481.0
55	428.0
56	375.0
57	381.5
58	388.0
59	282.5
60	177.0
61	130.0
62	83.0
63	92.0
64	101.0
65	63.5
66	26.0
67	20.0
68	14.0
69	16.0
70	18.0
71	29.5
72	41.0
73	22.5
74	4.0
75	2.5
76	1.0
77	2.5
78	4.0
79	3.5
80	3.0
81	2.0
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	0.17500000000000002
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	51.725
#Duplication Level	Percentage of deduplicated	Percentage of total
1	79.0720154664089	40.9
2	8.651522474625423	8.95
3	4.156597390043499	6.45
4	1.9333011116481391	4.0
5	1.4983083615273078	3.875
6	0.7249879168680522	2.25
7	0.5316578057032383	1.925
8	0.3383276945384244	1.4000000000000001
9	0.2416626389560174	1.125
>10	2.7549540840985984	25.174999999999997
>50	0.04833252779120348	1.375
>100	0.04833252779120348	2.5749999999999997
>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	103	2.5749999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	55	1.375	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	40	1.0	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	27	0.675	RNA PCR Primer, Index 1 (100% over 33bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTC	23	0.575	RNA PCR Primer, Index 36 (100% over 44bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	20	0.5	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	19	0.475	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	18	0.44999999999999996	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	18	0.44999999999999996	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCC	17	0.42500000000000004	RNA PCR Primer, Index 5 (97% over 35bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	17	0.42500000000000004	No Hit
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	15	0.375	RNA PCR Primer, Index 1 (96% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGC	14	0.35000000000000003	RNA PCR Primer, Index 36 (100% over 50bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	14	0.35000000000000003	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	13	0.325	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	12	0.3	RNA PCR Primer, Index 1 (96% over 27bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	12	0.3	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	12	0.3	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	12	0.3	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	12	0.3	RNA PCR Primer, Index 1 (96% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	10	0.25	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	9	0.22499999999999998	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	8	0.2	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	8	0.2	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	8	0.2	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TACCATGATGATAACATAGTTCAGCAGACTTAACTCTGATGAACAATCAT	7	0.17500000000000002	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	7	0.17500000000000002	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	7	0.17500000000000002	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	7	0.17500000000000002	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCC	6	0.15	RNA PCR Primer, Index 5 (97% over 35bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	6	0.15	No Hit
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	6	0.15	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	6	0.15	No Hit
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCTGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	5	0.125	No Hit
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	5	0.125	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	5	0.125	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTAT	5	0.125	RNA PCR Primer, Index 36 (100% over 48bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	5	0.125	No Hit
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GAGCAATGATGACCCCAACATGCCATCTGAGTGGCTTTGCTGAAATCCAG	5	0.125	No Hit
ACATGTGATGAGAAACTGTTTCGGTCCCAGTTGATGGCCACTGATAACAT	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	0.375	0.0	0.0	0.0
2	0.0	0.375	0.0	0.0	0.0
3	0.0	0.55	0.0	0.0	0.0
4	0.0	0.575	0.0	0.0	0.0
5	0.0	0.65	0.0	0.0	0.0
6	0.0	0.7	0.0	0.0	0.0
7	0.0	1.35	0.0	0.0	0.0
8	0.0	1.475	0.0	0.0	0.0
9	0.0	1.475	0.0	0.0	0.0
10	0.0	1.65	0.0	0.0	0.0
11	0.0	1.725	0.0	0.0	0.0
12	0.0	1.85	0.0	0.0	0.0
13	0.0	2.075	0.0	0.0	0.0
14	0.0	2.175	0.0	0.0	0.0
15	0.0	2.45	0.0	0.0	0.0
16	0.0	3.3	0.0	0.0	0.0
17	0.0	3.95	0.0	0.0	0.0
18	0.0	5.05	0.0	0.0	0.0
19	0.0	5.35	0.0	0.0	0.0
20	0.0	6.075	0.0	0.0	0.0
21	0.0	10.8	0.0	0.0	0.0
22	0.0	20.15	0.0	0.0	0.0
23	0.0	46.825	0.0	0.0	0.0
24	0.0	58.55	0.0	0.0	0.0
25	0.0	63.95	0.0	0.0	0.0
26	0.0	65.45	0.0	0.0	0.0
27	0.0	66.175	0.0	0.0	0.0
28	0.0	66.625	0.0	0.0	0.0
29	0.0	66.875	0.0	0.0	0.0
30	0.0	67.075	0.0	0.0	0.0
31	0.0	67.825	0.0	0.0	0.0
32	0.0	69.25	0.0	0.0	0.0
33	0.0	70.325	0.0	0.0	0.0
34	0.0	72.3	0.0	0.0	0.0
35	0.0	73.425	0.0	0.0	0.0
36	0.0	74.05	0.0	0.0	0.0
37	0.0	75.075	0.0	0.0	0.0
38	0.0	75.425	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
AACGCTG	20	6.952051E-4	44.000004	8
GTTGAAG	20	6.952051E-4	44.000004	10
ACGCTGT	20	6.952051E-4	44.000004	9
CAGTTGA	20	6.952051E-4	44.000004	8
AGCTTGG	45	2.728484E-10	44.000004	14
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
TTCAACG	20	6.952051E-4	44.000004	5
GAGCTTG	45	2.728484E-10	44.000004	13
GGATCCG	45	2.728484E-10	44.000004	3
CCGTCTG	45	2.728484E-10	44.000004	7
TCGGATC	45	2.728484E-10	44.000004	1
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
CGGATCC	45	2.728484E-10	44.000004	2
GAAGAAC	20	6.952051E-4	44.000004	13
GCCAGTT	20	6.952051E-4	44.000004	6
CTTGGTG	20	6.952051E-4	44.000004	16
AACTCCG	20	6.952051E-4	44.000004	44
>>END_MODULE
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367300 spots for SRR5030953.sra
Written 367300 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
Read 367298 spots for SRR5030953.sra
Written 367298 spots for SRR5030953.sra
SRR ids: ['SRR5030953.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_6ngh4yxi
SRR5030953.sra spots: 4407578
blocks: [[1, 367298], [367299, 734596], [734597, 1101894], [1101895, 1469192], [1469193, 1836490], [1836491, 2203788], [2203789, 2571086], [2571087, 2938384], [2938385, 3305682], [3305683, 3672980], [3672981, 4040278], [4040279, 4407578]]
SRR5030953 file size 762853
SRR5030953 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030953 SRR5030953_1.fastq
Input file:	SRR5030953_1.fastq
trimmed:	SRR5030953-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 06:52:54 2020 >> started

Wed Mar  4 06:52:57 2020 >> done (2.913s)
4407578 reads processed; of these:
    282 ( 0.01%) short reads filtered out after trimming by size control
     14 ( 0.00%) empty reads filtered out after trimming by size control
4407282 (99.99%) reads available; of these:
 524594 (11.90%) trimmed reads available after processing
3882688 (88.10%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    110	  0.00%
 19	    115	  0.00%
 20	    224	  0.01%
 21	    325	  0.01%
 22	    540	  0.01%
 23	    754	  0.02%
 24	    721	  0.02%
 25	    876	  0.02%
 26	    808	  0.02%
 27	   1066	  0.02%
 28	   1299	  0.03%
 29	   2166	  0.05%
 30	   1402	  0.03%
 31	   2092	  0.05%
 32	   4541	  0.10%
 33	  14699	  0.33%
 34	  33403	  0.76%
 35	   8442	  0.19%
 36	   9873	  0.22%
 37	   5273	  0.12%
 38	  10553	  0.24%
 39	   9479	  0.22%
 40	  19262	  0.44%
 41	   9694	  0.22%
 42	  25864	  0.59%
 43	  11521	  0.26%
 44	  46762	  1.06%
 45	  32480	  0.74%
 46	  29035	  0.66%
 47	  33922	  0.77%
 48	  95577	  2.17%
 49	 111716	  2.53%
 50	3882688	 88.10%
4407282 reads passed initial QC


criterion=sequence-density
sequence-density=73.04
sequence-density-rank=1
fanout-score=21.17
fanout-score-rank=2
prefix-density=75.76
prefix-fanout=20.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC


criterion=fanout-score
sequence-density=3.61
sequence-density-rank=3
fanout-score=64.75
fanout-score-rank=1
prefix-density=75.35
prefix-fanout=3.1
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC -o SRR5030953 -
Input file:	STDIN
trimmed:	SRR5030953-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCAACAATCTCGTATGCC
-- 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 06:53:16 2020 >> started

Wed Mar  4 06:53:22 2020 >> done (5.567s)
4288166 reads processed; of these:
 193127 ( 4.50%) short reads filtered out after trimming by size control
  22243 ( 0.52%) empty reads filtered out after trimming by size control
4072796 (94.98%) reads available; of these:
3345369 (82.14%) trimmed reads available after processing
 727427 (17.86%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  20990	  0.52%
 19	  30538	  0.75%
 20	 173330	  4.26%
 21	 389312	  9.56%
 22	1075808	 26.41%
 23	 519185	 12.75%
 24	 255962	  6.28%
 25	  74594	  1.83%
 26	  36386	  0.89%
 27	  27695	  0.68%
 28	  29323	  0.72%
 29	  24566	  0.60%
 30	  34572	  0.85%
 31	  53420	  1.31%
 32	  47033	  1.15%
 33	  94498	  2.32%
 34	  46980	  1.15%
 35	  35501	  0.87%
 36	  46193	  1.13%
 37	  25214	  0.62%
 38	  28231	  0.69%
 39	  28985	  0.71%
 40	  45484	  1.12%
 41	  48836	  1.20%
 42	  60101	  1.48%
 43	  39608	  0.97%
 44	  37826	  0.93%
 45	  46364	  1.14%
 46	  36423	  0.89%
 47	  27070	  0.66%
 48	  11880	  0.29%
 49	  22687	  0.56%
 50	 598201	 14.69%


criterion=sequence-density
sequence-density=2.80
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=17
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.55
sequence-density-rank=28
fanout-score=13.73
fanout-score-rank=1
prefix-density=7.58
prefix-fanout=1.0
sequence=TGAGCTTGGCTT
                                 Started job on |	Mar 04 06:53:46
                             Started mapping on |	Mar 04 06:53:46
                                    Finished on |	Mar 04 06:54:27
       Mapping speed, Million of reads per hour |	368.07

                          Number of input reads |	4191912
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2432737
                        Uniquely mapped reads % |	58.03%
                          Average mapped length |	29.20
                       Number of splices: Total |	2380
            Number of splices: Annotated (sjdb) |	400
                       Number of splices: GT/AG |	2176
                       Number of splices: GC/AG |	39
                       Number of splices: AT/AC |	3
               Number of splices: Non-canonical |	162
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.22
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1201500
             % of reads mapped to multiple loci |	28.66%
        Number of reads mapped to too many loci |	98328
             % of reads mapped to too many loci |	2.35%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.05%
                     % of reads unmapped: other |	0.91%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	557675	557675	557675
N_multimapping	1201500	1201500	1201500
N_noFeature	114615	146041	1777816
N_ambiguous	1272318	704499	21210
UnstrandedReadsAssigned:1045804 PositiveStrandReadsAssigned:1582197 NegativeStrandReadsAssigned:633711
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030953 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: SRR5030953-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,191,912 reads, 999,381 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,161 rounds

 109283 SRR5030953.ke.tsv
  52636 SRR5030953.se.tsv
 161919 total
==> SRR5030953.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

==> SRR5030953.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030953 completed mapping pipeline successfully
