Starting /dee2/code/volunteer_pipeline.sh SRR5031033
    current disk space = 160535101440
    free memory = 56711728 
SRR5031033 SRAfilesize
8cf9d3b51e549057ef861eabbfa89ad5  SRR5031033.sra
SRR5031033.sra file validated
SRR5031033 is single end
SRR5031033 is conventional basespace
SRR5031033 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031033_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.40925	33.0	31.0	34.0	31.0	34.0
2	32.64675	34.0	31.0	34.0	31.0	34.0
3	32.69825	34.0	31.0	34.0	31.0	34.0
4	36.222	37.0	37.0	37.0	35.0	37.0
5	36.04725	37.0	35.0	37.0	35.0	37.0
6	35.95225	37.0	35.0	37.0	35.0	37.0
7	36.01725	37.0	35.0	37.0	35.0	37.0
8	35.8135	37.0	35.0	37.0	35.0	37.0
9	37.59575	39.0	37.0	39.0	35.0	39.0
10	37.806	39.0	38.0	39.0	35.0	39.0
11	37.7225	39.0	37.0	39.0	35.0	39.0
12	37.693	39.0	37.0	39.0	35.0	39.0
13	37.6775	39.0	37.0	39.0	35.0	39.0
14	39.08475	41.0	38.0	41.0	36.0	41.0
15	39.13625	41.0	38.0	41.0	36.0	41.0
16	39.07125	40.0	38.0	41.0	36.0	41.0
17	38.89175	40.0	38.0	41.0	35.0	41.0
18	39.0925	40.0	38.0	41.0	36.0	41.0
19	38.6375	40.0	38.0	41.0	34.0	41.0
20	38.844	40.0	38.0	41.0	35.0	41.0
21	38.74675	40.0	38.0	41.0	34.0	41.0
22	38.915	40.0	38.0	41.0	35.0	41.0
23	38.71875	40.0	38.0	41.0	34.0	41.0
24	38.83875	40.0	38.0	41.0	35.0	41.0
25	39.15525	41.0	39.0	41.0	36.0	41.0
26	38.65825	40.0	38.0	41.0	34.0	41.0
27	38.84925	40.0	38.0	41.0	35.0	41.0
28	38.63475	40.0	38.0	41.0	34.0	41.0
29	38.19975	40.0	38.0	41.0	33.0	41.0
30	38.10125	40.0	38.0	41.0	33.0	41.0
31	38.32125	40.0	38.0	41.0	33.0	41.0
32	38.3945	40.0	38.0	41.0	34.0	41.0
33	38.46775	40.0	38.0	41.0	34.0	41.0
34	38.46275	40.0	38.0	41.0	34.0	41.0
35	38.3565	40.0	38.0	41.0	34.0	41.0
36	37.87075	40.0	37.0	41.0	33.0	41.0
37	37.3925	39.0	37.0	41.0	31.0	41.0
38	36.59475	39.0	35.0	40.0	30.0	41.0
39	37.2575	39.0	37.0	40.0	31.0	41.0
40	37.59175	40.0	37.0	41.0	32.0	41.0
41	37.70425	40.0	37.0	41.0	33.0	41.0
42	37.89425	40.0	37.0	41.0	33.0	41.0
43	38.11525	40.0	38.0	41.0	33.0	41.0
44	37.7215	40.0	37.0	41.0	33.0	41.0
45	37.56875	39.0	37.0	41.0	33.0	41.0
46	37.5045	40.0	37.0	41.0	33.0	41.0
47	36.86025	40.0	35.0	41.0	30.0	41.0
48	36.37575	39.0	35.0	41.0	30.0	41.0
49	36.6	39.0	35.0	41.0	31.0	41.0
50	36.00725	39.0	35.0	41.0	30.0	41.0
>>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
11	1.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	2.0
18	4.0
19	1.0
20	5.0
21	5.0
22	2.0
23	4.0
24	4.0
25	9.0
26	16.0
27	19.0
28	28.0
29	40.0
30	41.0
31	65.0
32	84.0
33	113.0
34	164.0
35	183.0
36	287.0
37	437.0
38	753.0
39	1733.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.15	24.7	45.550000000000004	18.6
2	23.517638228671505	26.1195896922692	18.21366024518389	32.1491118338754
3	24.125	16.925	20.9	38.05
4	36.15	27.200000000000003	14.000000000000002	22.650000000000002
5	20.25	39.074999999999996	26.1	14.575
6	27.474999999999998	13.900000000000002	39.725	18.9
7	18.0	19.5	20.424999999999997	42.075
8	21.6	27.474999999999998	19.3	31.624999999999996
9	26.575	30.5	23.724999999999998	19.2
10	23.599999999999998	20.849999999999998	29.125	26.424999999999997
11	32.925	14.325	16.625	36.125
12	15.825	20.275000000000002	31.825	32.074999999999996
13	27.375	16.5	35.05	21.075
14	27.400000000000002	31.374999999999996	18.25	22.975
15	35.75	24.175	25.85	14.224999999999998
16	19.5	21.15	21.475	37.875
17	28.675	22.675	33.725	14.924999999999999
18	25.624999999999996	16.125	31.275	26.974999999999998
19	37.35	15.125	30.2	17.325
20	44.625	14.774999999999999	26.35	14.249999999999998
21	27.650000000000002	20.9	22.2	29.25
22	31.05	15.7	42.175000000000004	11.075
23	24.525	14.75	41.525	19.2
24	50.24999999999999	16.1	24.8	8.85
25	46.025	25.3	16.425	12.25
26	26.724999999999998	42.525	14.000000000000002	16.75
27	16.175	43.35	22.8	17.675
28	12.825000000000001	23.775	43.925	19.475
29	16.325	13.600000000000001	51.675000000000004	18.4
30	11.525	7.95	32.65	47.875
31	14.149999999999999	6.5	47.599999999999994	31.75
32	28.7	8.0	21.075	42.225
33	50.125	12.775	15.375	21.725
34	54.725	10.174999999999999	18.325	16.775000000000002
35	61.75000000000001	7.9750000000000005	18.6	11.675
36	40.225	10.125	36.449999999999996	13.200000000000001
37	44.65	14.35	19.275000000000002	21.725
38	23.425	20.1	13.625000000000002	42.85
39	18.25	21.925	13.0	46.825
40	15.950000000000001	45.574999999999996	15.25	23.225
41	23.1	44.45	11.625	20.825
42	45.525	27.125	15.825	11.525
43	48.449999999999996	26.55	10.75	14.249999999999998
44	32.574999999999996	43.5	9.075	14.85
45	22.7	46.125	14.374999999999998	16.8
46	17.925	24.15	17.549999999999997	40.375
47	12.075	16.025	40.6	31.3
48	16.1	12.2	19.35	52.349999999999994
49	14.975	19.6	15.35	50.075
50	17.8	35.75	12.65	33.800000000000004
>>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	0.0
10	0.0
11	0.0
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	0.0
24	0.0
25	0.0
26	0.0
27	1.5
28	3.0
29	3.0
30	3.0
31	11.5
32	20.0
33	19.0
34	18.0
35	22.5
36	27.0
37	34.5
38	42.0
39	48.0
40	54.0
41	56.0
42	58.0
43	75.0
44	92.0
45	115.0
46	138.0
47	247.0
48	356.0
49	445.0
50	534.0
51	687.0
52	840.0
53	644.5
54	449.0
55	511.0
56	573.0
57	431.0
58	289.0
59	177.5
60	66.0
61	63.0
62	60.0
63	136.0
64	212.0
65	126.0
66	40.0
67	29.0
68	18.0
69	18.5
70	19.0
71	49.0
72	79.0
73	41.5
74	4.0
75	3.5
76	3.0
77	2.0
78	1.0
79	1.0
80	1.0
81	0.5
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	0.0
2	0.075
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	0.0
30	0.0
31	0.0
32	0.0
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.0
41	0.0
42	0.0
43	0.0
44	0.0
45	0.0
46	0.0
47	0.0
48	0.0
49	0.0
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	39.4
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.69796954314721	29.825000000000003
2	9.200507614213198	7.249999999999999
3	5.1395939086294415	6.075
4	2.284263959390863	3.5999999999999996
5	1.8401015228426396	3.6249999999999996
6	0.5710659898477157	1.35
7	0.7614213197969544	2.1
8	0.7614213197969544	2.4
9	0.4441624365482234	1.575
>10	2.728426395939086	18.7
>50	0.31725888324873097	9.525
>100	0.25380710659898476	13.975000000000001
>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
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	175	4.375	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	167	4.175	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	112	2.8000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	105	2.625	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	93	2.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	91	2.275	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	78	1.95	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	64	1.6	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	55	1.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	49	1.225	RNA PCR Primer, Index 5 (100% over 35bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	31	0.775	RNA PCR Primer, Index 1 (100% over 33bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	27	0.675	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGC	27	0.675	RNA PCR Primer, Index 5 (100% over 50bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTC	20	0.5	RNA PCR Primer, Index 5 (100% over 44bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	17	0.42500000000000004	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	17	0.42500000000000004	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	15	0.375	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	11	0.27499999999999997	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	10	0.25	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
AACCCGTAGATCCGAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	9	0.22499999999999998	No Hit
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	9	0.22499999999999998	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	8	0.2	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	8	0.2	No Hit
ACTAATCCTAGCCCTAGCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	8	0.2	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	8	0.2	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	7	0.17500000000000002	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	6	0.15	No Hit
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	6	0.15	No Hit
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGTG	6	0.15	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	6	0.15	No Hit
TTTAGCTGTTAACTAAATTTTCGTAGGTTTAATTCCTGCCAATCTAGCCA	6	0.15	No Hit
CACCCAGAAGATTTCATGACCAATGAACACTCTGACCATGGAATTCTCGG	6	0.15	No Hit
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
CTCAATAGGATTACGCTGAGGCCCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	5	0.125	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
CGCTAAACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
TGAGGTAGTAGGTTGTGTGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	5	0.125	No Hit
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	5	0.125	No Hit
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	5	0.125	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CTGCGTTCGCGCTCTCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	5	0.125	No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTAT	5	0.125	RNA PCR Primer, Index 5 (100% over 48bp)
TACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	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	0.875	0.0	0.0	0.0
2	0.0	0.875	0.0	0.0	0.0
3	0.0	1.05	0.0	0.0	0.0
4	0.0	1.1	0.0	0.0	0.0
5	0.0	1.1	0.0	0.0	0.0
6	0.0	1.175	0.0	0.0	0.0
7	0.0	1.85	0.0	0.0	0.0
8	0.0	2.05	0.0	0.0	0.0
9	0.0	2.175	0.0	0.0	0.0
10	0.0	2.275	0.0	0.0	0.0
11	0.0	2.425	0.0	0.0	0.0
12	0.0	2.55	0.0	0.0	0.0
13	0.0	2.725	0.0	0.0	0.0
14	0.0	2.85	0.0	0.0	0.0
15	0.0	3.075	0.0	0.0	0.0
16	0.0	4.725	0.0	0.0	0.0
17	0.0	5.075	0.0	0.0	0.0
18	0.0	6.325	0.0	0.0	0.0
19	0.0	6.775	0.0	0.0	0.0
20	0.0	7.6	0.0	0.0	0.0
21	0.0	12.225	0.0	0.0	0.0
22	0.0	21.325	0.0	0.0	0.0
23	0.0	48.3	0.0	0.0	0.0
24	0.0	59.025	0.0	0.0	0.0
25	0.0	64.75	0.0	0.0	0.0
26	0.0	65.9	0.0	0.0	0.0
27	0.0	66.825	0.0	0.0	0.0
28	0.0	67.7	0.0	0.0	0.0
29	0.0	68.5	0.0	0.0	0.0
30	0.0	69.25	0.0	0.0	0.0
31	0.0	70.3	0.0	0.0	0.0
32	0.0	71.55	0.0	0.0	0.0
33	0.0	72.775	0.0	0.0	0.0
34	0.0	78.425	0.0	0.0	0.0
35	0.0	80.075	0.0	0.0	0.0
36	0.0	81.725	0.0	0.0	0.0
37	0.0	83.125	0.0	0.0	0.0
38	0.0	83.875	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CGCGACC	20	6.952051E-4	44.000004	1
CGCTGAT	20	6.952051E-4	44.000004	28
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
ATCCAGG	20	6.952051E-4	44.000004	9
GCGACCT	20	6.952051E-4	44.000004	2
GCGACCC	20	6.952051E-4	44.000004	22
TTCAAGT	20	6.952051E-4	44.000004	1
AGGATAG	20	6.952051E-4	44.000004	13
CCGCTGA	20	6.952051E-4	44.000004	27
ATAGGCT	20	6.952051E-4	44.000004	16
GGCGACC	20	6.952051E-4	44.000004	21
ACCCGCT	20	6.952051E-4	44.000004	25
CTGATGG	20	6.952051E-4	44.000004	30
TCCAGGA	20	6.952051E-4	44.000004	10
GGATAGG	20	6.952051E-4	44.000004	14
CCCGCTG	20	6.952051E-4	44.000004	26
CTTGGCT	45	2.728484E-10	44.000004	16
CGTGGCG	20	6.952051E-4	44.000004	18
ATCAGAC	20	6.952051E-4	44.000004	12
>>END_MODULE
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369498 spots for SRR5031033.sra
Written 369498 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
Read 369495 spots for SRR5031033.sra
Written 369495 spots for SRR5031033.sra
SRR ids: ['SRR5031033.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_j1xjzal1
SRR5031033.sra spots: 4433943
blocks: [[1, 369495], [369496, 738990], [738991, 1108485], [1108486, 1477980], [1477981, 1847475], [1847476, 2216970], [2216971, 2586465], [2586466, 2955960], [2955961, 3325455], [3325456, 3694950], [3694951, 4064445], [4064446, 4433943]]
SRR5031033 file size 767446
SRR5031033 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031033 SRR5031033_1.fastq
Input file:	SRR5031033_1.fastq
trimmed:	SRR5031033-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 07:10:19 2020 >> started

Wed Mar  4 07:10:22 2020 >> done (2.581s)
4433943 reads processed; of these:
    365 ( 0.01%) short reads filtered out after trimming by size control
     13 ( 0.00%) empty reads filtered out after trimming by size control
4433565 (99.99%) reads available; of these:
 243396 ( 5.49%) trimmed reads available after processing
4190169 (94.51%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    112	  0.00%
 19	    138	  0.00%
 20	    270	  0.01%
 21	    306	  0.01%
 22	    498	  0.01%
 23	    630	  0.01%
 24	    676	  0.02%
 25	    951	  0.02%
 26	    741	  0.02%
 27	    964	  0.02%
 28	   1102	  0.02%
 29	   1685	  0.04%
 30	   1214	  0.03%
 31	   1408	  0.03%
 32	   1614	  0.04%
 33	   1953	  0.04%
 34	   2187	  0.05%
 35	   4545	  0.10%
 36	   3960	  0.09%
 37	   4333	  0.10%
 38	   4303	  0.10%
 39	   4531	  0.10%
 40	   5184	  0.12%
 41	   5112	  0.12%
 42	   6626	  0.15%
 43	   9699	  0.22%
 44	  12455	  0.28%
 45	  16282	  0.37%
 46	  25725	  0.58%
 47	  30366	  0.68%
 48	  45642	  1.03%
 49	  48184	  1.09%
 50	4190169	 94.51%
4433565 reads passed initial QC


criterion=sequence-density
sequence-density=82.32
sequence-density-rank=1
fanout-score=21.16
fanout-score-rank=1
prefix-density=84.61
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC


criterion=fanout-score
sequence-density=82.32
sequence-density-rank=1
fanout-score=21.16
fanout-score-rank=1
prefix-density=84.61
prefix-fanout=20.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC -o SRR5031033 -
Input file:	STDIN
trimmed:	SRR5031033-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 07:10:44 2020 >> started

Wed Mar  4 07:10:51 2020 >> done (6.860s)
4326732 reads processed; of these:
 271251 ( 6.27%) short reads filtered out after trimming by size control
  51358 ( 1.19%) empty reads filtered out after trimming by size control
4004123 (92.54%) reads available; of these:
3753506 (93.74%) trimmed reads available after processing
 250617 ( 6.26%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  21631	  0.54%
 19	  39059	  0.98%
 20	 218646	  5.46%
 21	 400262	 10.00%
 22	1094583	 27.34%
 23	 475693	 11.88%
 24	 235842	  5.89%
 25	  74828	  1.87%
 26	  39493	  0.99%
 27	  32570	  0.81%
 28	  38668	  0.97%
 29	  29769	  0.74%
 30	  42145	  1.05%
 31	  56228	  1.40%
 32	  59575	  1.49%
 33	 225770	  5.64%
 34	  73066	  1.82%
 35	  62355	  1.56%
 36	  67819	  1.69%
 37	  34942	  0.87%
 38	  39978	  1.00%
 39	  35250	  0.88%
 40	  52172	  1.30%
 41	  61757	  1.54%
 42	  68593	  1.71%
 43	  47430	  1.18%
 44	  37507	  0.94%
 45	  50614	  1.26%
 46	  37567	  0.94%
 47	  28588	  0.71%
 48	   2619	  0.07%
 49	   3835	  0.10%
 50	 215269	  5.38%


criterion=sequence-density
sequence-density=6.41
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=0.82
sequence-density-rank=16
fanout-score=11.30
fanout-score-rank=1
prefix-density=9.20
prefix-fanout=1.0
sequence=TGAGCTTGGCTAT
                                 Started job on |	Mar 04 07:11:13
                             Started mapping on |	Mar 04 07:11:14
                                    Finished on |	Mar 04 07:11:48
       Mapping speed, Million of reads per hour |	435.28

                          Number of input reads |	4110956
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2187002
                        Uniquely mapped reads % |	53.20%
                          Average mapped length |	25.76
                       Number of splices: Total |	2926
            Number of splices: Annotated (sjdb) |	517
                       Number of splices: GT/AG |	2735
                       Number of splices: GC/AG |	42
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	147
                      Mismatch rate per base, % |	0.23%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.80
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1212552
             % of reads mapped to multiple loci |	29.50%
        Number of reads mapped to too many loci |	115741
             % of reads mapped to too many loci |	2.82%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.31%
                     % of reads unmapped: other |	1.18%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	711402	711402	711402
N_multimapping	1212552	1212552	1212552
N_noFeature	111813	152567	1425706
N_ambiguous	1197373	536470	23955
UnstrandedReadsAssigned:877816 PositiveStrandReadsAssigned:1497965 NegativeStrandReadsAssigned:737341
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031033 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: SRR5031033-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,110,956 reads, 1,018,876 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 884 rounds

 109283 SRR5031033.ke.tsv
  52636 SRR5031033.se.tsv
 161919 total
==> SRR5031033.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

==> SRR5031033.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031033 completed mapping pipeline successfully
