Starting /dee2/code/volunteer_pipeline.sh SRR5031029
    current disk space = 160545472512
    free memory = 73929960 
SRR5031029 SRAfilesize
dde4f68bebc2c03a57e4c218f352c05f  SRR5031029.sra
SRR5031029.sra file validated
SRR5031029 is single end
SRR5031029 is conventional basespace
SRR5031029 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031029_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	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.29075	33.0	31.0	34.0	30.0	34.0
2	32.52725	34.0	31.0	34.0	31.0	34.0
3	32.59025	34.0	31.0	34.0	31.0	34.0
4	36.132	37.0	35.0	37.0	35.0	37.0
5	35.933	37.0	35.0	37.0	35.0	37.0
6	35.728	37.0	35.0	37.0	33.0	37.0
7	35.872	37.0	35.0	37.0	35.0	37.0
8	35.7435	37.0	35.0	37.0	33.0	37.0
9	37.4945	39.0	37.0	39.0	34.0	39.0
10	37.747	39.0	37.0	39.0	35.0	39.0
11	37.569	39.0	37.0	39.0	35.0	39.0
12	37.4855	39.0	37.0	39.0	35.0	39.0
13	37.54925	39.0	37.0	39.0	35.0	39.0
14	38.9505	40.0	38.0	41.0	35.0	41.0
15	38.903	40.0	38.0	41.0	35.0	41.0
16	38.94475	40.0	38.0	41.0	35.0	41.0
17	38.84925	40.0	38.0	41.0	34.0	41.0
18	38.88275	40.0	38.0	41.0	35.0	41.0
19	38.645	40.0	38.0	41.0	34.0	41.0
20	38.80575	40.0	38.0	41.0	34.0	41.0
21	38.6965	40.0	38.0	41.0	34.0	41.0
22	38.901	40.0	38.0	41.0	35.0	41.0
23	38.678	40.0	38.0	41.0	35.0	41.0
24	38.75875	40.0	38.0	41.0	34.0	41.0
25	38.9875	41.0	39.0	41.0	35.0	41.0
26	38.738	40.0	38.0	41.0	34.0	41.0
27	38.6245	40.0	38.0	41.0	34.0	41.0
28	38.52225	40.0	38.0	41.0	34.0	41.0
29	37.97375	40.0	38.0	41.0	32.0	41.0
30	38.1455	40.0	38.0	41.0	33.0	41.0
31	38.35275	40.0	38.0	41.0	34.0	41.0
32	38.2615	40.0	38.0	41.0	33.0	41.0
33	38.2125	40.0	38.0	41.0	33.0	41.0
34	38.341	40.0	38.0	41.0	34.0	41.0
35	38.26	40.0	38.0	41.0	34.0	41.0
36	37.88675	40.0	37.0	41.0	33.0	41.0
37	37.44175	40.0	37.0	41.0	31.0	41.0
38	36.85475	39.0	36.0	41.0	30.0	41.0
39	37.20475	39.0	37.0	41.0	31.0	41.0
40	37.40925	40.0	37.0	41.0	32.0	41.0
41	37.576	40.0	37.0	41.0	33.0	41.0
42	37.79975	40.0	37.0	41.0	33.0	41.0
43	38.02325	40.0	38.0	41.0	33.0	41.0
44	37.68125	40.0	37.0	41.0	33.0	41.0
45	37.62025	40.0	37.0	41.0	33.0	41.0
46	37.64525	40.0	37.0	41.0	33.0	41.0
47	37.1485	40.0	37.0	41.0	31.0	41.0
48	36.76825	40.0	36.0	41.0	31.0	41.0
49	36.92525	40.0	36.0	41.0	31.0	41.0
50	36.35325	39.0	35.0	41.0	31.0	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
10	1.0
11	1.0
12	0.0
13	0.0
14	1.0
15	1.0
16	0.0
17	1.0
18	1.0
19	5.0
20	6.0
21	4.0
22	6.0
23	6.0
24	6.0
25	15.0
26	13.0
27	20.0
28	25.0
29	33.0
30	40.0
31	86.0
32	73.0
33	106.0
34	170.0
35	181.0
36	306.0
37	423.0
38	750.0
39	1720.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.65	24.8	50.849999999999994	14.7
2	25.243932949712285	26.26970227670753	19.239429572179134	29.246935201401055
3	23.150000000000002	19.1	21.125	36.625
4	36.4	29.425	13.15	21.025
5	22.5	37.824999999999996	26.974999999999998	12.7
6	27.675	16.925	41.125	14.274999999999999
7	16.475	22.45	20.0	41.075
8	24.0	28.9	17.45	29.65
9	23.375	32.025	27.925	16.675
10	22.1	22.275	29.95	25.674999999999997
11	35.925000000000004	10.875	15.825	37.375
12	15.4	23.275000000000002	30.525000000000002	30.8
13	26.275	17.1	37.45	19.175
14	30.25	28.749999999999996	24.15	16.85
15	37.724999999999994	22.15	25.874999999999996	14.249999999999998
16	18.8	17.675	26.5	37.025000000000006
17	26.525	26.075	34.075	13.325000000000001
18	26.825	16.1	32.574999999999996	24.5
19	35.875	15.75	33.324999999999996	15.049999999999999
20	46.075	14.774999999999999	24.3	14.85
21	24.525	21.375	25.900000000000002	28.199999999999996
22	30.675	11.65	47.75	9.925
23	25.35	12.725	45.65	16.275000000000002
24	50.949999999999996	14.025000000000002	26.275	8.75
25	50.675000000000004	23.875	15.975	9.475
26	27.700000000000003	46.125	14.124999999999998	12.049999999999999
27	15.325	47.699999999999996	24.275	12.7
28	12.075	24.349999999999998	47.699999999999996	15.875
29	12.975	13.3	55.725	18.0
30	9.35	7.475	35.875	47.3
31	14.224999999999998	6.0249999999999995	47.275	32.475
32	27.425	5.800000000000001	23.325000000000003	43.45
33	53.6	8.975	14.224999999999998	23.200000000000003
34	60.4	7.825	16.225	15.55
35	65.3	6.45	18.775	9.475
36	42.225	7.475	36.475	13.825000000000001
37	46.2	10.825	20.45	22.525000000000002
38	25.15	16.5	11.75	46.6
39	16.375	22.975	11.0	49.65
40	16.1	48.0	10.775	25.124999999999996
41	23.575	49.7	9.275	17.45
42	48.025	29.675	11.675	10.625
43	51.4	28.675	8.450000000000001	11.475
44	30.7	48.25	6.825	14.224999999999998
45	18.9	50.4	13.275	17.424999999999997
46	14.000000000000002	24.9	17.45	43.65
47	10.35	14.975	39.675	35.0
48	11.3	13.0	19.85	55.85
49	13.750000000000002	19.400000000000002	13.25	53.6
50	17.525	37.6	13.775	31.1
>>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	0.5
12	1.0
13	0.5
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	2.5
32	5.0
33	8.5
34	12.0
35	16.5
36	21.0
37	33.5
38	46.0
39	45.5
40	45.0
41	47.0
42	49.0
43	105.0
44	161.0
45	181.0
46	201.0
47	318.0
48	435.0
49	547.0
50	659.0
51	756.5
52	854.0
53	627.5
54	401.0
55	463.5
56	526.0
57	373.5
58	221.0
59	147.0
60	73.0
61	62.5
62	52.0
63	88.0
64	124.0
65	75.5
66	27.0
67	19.0
68	11.0
69	16.5
70	22.0
71	35.0
72	48.0
73	25.5
74	3.0
75	2.5
76	2.0
77	1.0
78	0.0
79	0.0
80	0.0
81	0.5
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	0.0
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	38.550000000000004
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.68093385214007	29.175
2	9.014267185473411	6.950000000000001
3	4.863813229571985	5.625
4	2.529182879377432	3.9
5	1.4267185473411155	2.75
6	1.6861219195849546	3.9
7	0.7133592736705577	1.925
8	0.38910505836575876	1.2
9	0.38910505836575876	1.35
>10	2.7237354085603114	19.900000000000002
>50	0.38910505836575876	14.025000000000002
>100	0.19455252918287938	9.3
>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	143	3.5749999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	124	3.1	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	105	2.625	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	99	2.475	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	97	2.4250000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	93	2.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	93	2.325	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	90	2.25	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	89	2.225	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	47	1.175	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	42	1.05	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	26	0.65	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	23	0.575	RNA PCR Primer, Index 1 (100% over 30bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGC	23	0.575	RNA PCR Primer, Index 1 (100% over 50bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	21	0.525	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	20	0.5	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	20	0.5	RNA PCR Primer, Index 1 (100% over 35bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (100% over 28bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	16	0.4	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	15	0.375	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	13	0.325	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	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)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 25bp)
AACATTCAACGCTGTCGGTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 44bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGGGCTAGGGCTAACAGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGACACAAGGGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA	6	0.15	RNA PCR Primer, Index 1 (100% over 34bp)
TACCCTGTAGATCCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTAGTTCAATGGTAGAATTCTCGCCTCCCTGGAATTCTCGGGTG	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AAGGGATTCTGATGTTGGTCACACTCTGGAATTCTCGGGTGCCAAGGAAC	6	0.15	RNA PCR Primer, Index 1 (100% over 24bp)
TCCAGCATCAGTGATTTTGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTGCC	6	0.15	No Hit
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	6	0.15	No Hit
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGGAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	6	0.15	No Hit
CGCGACCTCAGATCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (100% over 33bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	6	0.15	No Hit
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
ACCATTCGTAGACGACCTGCTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	5	0.125	No Hit
ATCATGATGGGCTCCTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATGGAATTCTCGGGTGCCAAG	5	0.125	No Hit
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	5	0.125	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTG	5	0.125	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ATAGTGGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTTAACCCAATTTTTTGAGGTCCTGCTCGTGCAGGGCTTGGAATTCTC	5	0.125	No Hit
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
>>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	0.6	0.0	0.0	0.0
2	0.0	0.625	0.0	0.0	0.0
3	0.0	0.675	0.0	0.0	0.0
4	0.0	0.7	0.0	0.0	0.0
5	0.0	0.725	0.0	0.0	0.0
6	0.0	0.75	0.0	0.0	0.0
7	0.0	1.1	0.0	0.0	0.0
8	0.0	1.375	0.0	0.0	0.0
9	0.0	1.45	0.0	0.0	0.0
10	0.0	1.575	0.0	0.0	0.0
11	0.0	1.9	0.0	0.0	0.0
12	0.0	2.05	0.0	0.0	0.0
13	0.0	2.275	0.0	0.0	0.0
14	0.0	2.525	0.0	0.0	0.0
15	0.0	2.725	0.0	0.0	0.0
16	0.0	3.775	0.0	0.0	0.0
17	0.0	4.4	0.0	0.0	0.0
18	0.0	5.325	0.0	0.0	0.0
19	0.0	5.9	0.0	0.0	0.0
20	0.0	6.7	0.0	0.0	0.0
21	0.0	12.3	0.0	0.0	0.0
22	0.0	22.675	0.0	0.0	0.0
23	0.0	52.675	0.0	0.0	0.0
24	0.0	65.95	0.0	0.0	0.0
25	0.0	72.025	0.0	0.0	0.0
26	0.0	73.575	0.0	0.0	0.0
27	0.0	74.675	0.0	0.0	0.0
28	0.0	75.475	0.0	0.0	0.0
29	0.0	75.95	0.0	0.0	0.0
30	0.0	76.675	0.0	0.0	0.0
31	0.0	77.575	0.0	0.0	0.0
32	0.0	78.55	0.0	0.0	0.0
33	0.0	79.65	0.0	0.0	0.0
34	0.0	83.3	0.0	0.0	0.0
35	0.0	84.475	0.0	0.0	0.0
36	0.0	85.475	0.0	0.0	0.0
37	0.0	86.85	0.0	0.0	0.0
38	0.0	87.475	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCTCG	20	6.952051E-4	44.000004	8
TCCTCGA	20	6.952051E-4	44.000004	9
GGTGAGT	20	6.952051E-4	44.000004	17
TCGACTG	20	6.952051E-4	44.000004	12
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
GCGACCC	20	6.952051E-4	44.000004	22
CATCCTC	20	6.952051E-4	44.000004	7
CCTCGAC	20	6.952051E-4	44.000004	10
CCGCTGA	20	6.952051E-4	44.000004	27
GGCGACC	20	6.952051E-4	44.000004	21
ACCCGCT	20	6.952051E-4	44.000004	25
ACATCCT	20	6.952051E-4	44.000004	6
CCCGCTG	20	6.952051E-4	44.000004	26
CTTGGCT	40	5.315087E-9	44.000004	16
CGTGGCG	20	6.952051E-4	44.000004	18
ATCAGAC	20	6.952051E-4	44.000004	12
AGACGTG	20	6.952051E-4	44.000004	15
GACGTGG	20	6.952051E-4	44.000004	16
TCAGACG	20	6.952051E-4	44.000004	13
>>END_MODULE
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192407 spots for SRR5031029.sra
Written 192407 spots for SRR5031029.sra
Read 192415 spots for SRR5031029.sra
Written 192415 spots for SRR5031029.sra
SRR ids: ['SRR5031029.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_b0_nl8zs
SRR5031029.sra spots: 2308892
blocks: [[1, 192407], [192408, 384814], [384815, 577221], [577222, 769628], [769629, 962035], [962036, 1154442], [1154443, 1346849], [1346850, 1539256], [1539257, 1731663], [1731664, 1924070], [1924071, 2116477], [2116478, 2308892]]
SRR5031029 file size 399113
SRR5031029 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031029 SRR5031029_1.fastq
Input file:	SRR5031029_1.fastq
trimmed:	SRR5031029-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 07:09:27 2020 >> started

Wed Mar  4 07:09:29 2020 >> done (1.634s)
2308892 reads processed; of these:
    209 ( 0.01%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
2308677 (99.99%) reads available; of these:
 117359 ( 5.08%) trimmed reads available after processing
2191318 (94.92%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     46	  0.00%
 19	     75	  0.00%
 20	    158	  0.01%
 21	    191	  0.01%
 22	    308	  0.01%
 23	    370	  0.02%
 24	    368	  0.02%
 25	    473	  0.02%
 26	    423	  0.02%
 27	    578	  0.03%
 28	    641	  0.03%
 29	   1058	  0.05%
 30	    608	  0.03%
 31	    674	  0.03%
 32	    707	  0.03%
 33	    971	  0.04%
 34	   1091	  0.05%
 35	   2263	  0.10%
 36	   2016	  0.09%
 37	   2068	  0.09%
 38	   2032	  0.09%
 39	   2107	  0.09%
 40	   2583	  0.11%
 41	   2617	  0.11%
 42	   3365	  0.15%
 43	   5019	  0.22%
 44	   6571	  0.28%
 45	   7868	  0.34%
 46	  12061	  0.52%
 47	  14811	  0.64%
 48	  21303	  0.92%
 49	  21935	  0.95%
 50	2191318	 94.92%
2308677 reads passed initial QC


criterion=sequence-density
sequence-density=86.86
sequence-density-rank=1
fanout-score=22.43
fanout-score-rank=1
prefix-density=88.96
prefix-fanout=21.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC


criterion=fanout-score
sequence-density=86.86
sequence-density-rank=1
fanout-score=22.43
fanout-score-rank=1
prefix-density=88.96
prefix-fanout=21.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC -o SRR5031029 -
Input file:	STDIN
trimmed:	SRR5031029-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCC
-- 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 07:09:42 2020 >> started

Wed Mar  4 07:09:46 2020 >> done (3.653s)
2255604 reads processed; of these:
 116417 ( 5.16%) short reads filtered out after trimming by size control
  15287 ( 0.68%) empty reads filtered out after trimming by size control
2123900 (94.16%) reads available; of these:
2025738 (95.38%) trimmed reads available after processing
  98162 ( 4.62%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  13338	  0.63%
 19	  22289	  1.05%
 20	 118492	  5.58%
 21	 260848	 12.28%
 22	 664364	 31.28%
 23	 305421	 14.38%
 24	 129721	  6.11%
 25	  35118	  1.65%
 26	  18572	  0.87%
 27	  17579	  0.83%
 28	  17997	  0.85%
 29	  15410	  0.73%
 30	  19624	  0.92%
 31	  27276	  1.28%
 32	  29054	  1.37%
 33	  89314	  4.21%
 34	  30418	  1.43%
 35	  26401	  1.24%
 36	  29297	  1.38%
 37	  12829	  0.60%
 38	  16573	  0.78%
 39	  12620	  0.59%
 40	  17525	  0.83%
 41	  19640	  0.92%
 42	  21575	  1.02%
 43	  15468	  0.73%
 44	  12611	  0.59%
 45	  16411	  0.77%
 46	  11378	  0.54%
 47	  10660	  0.50%
 48	    883	  0.04%
 49	   1203	  0.06%
 50	  83991	  3.95%


criterion=sequence-density
sequence-density=3.50
sequence-density-rank=1
fanout-score=1.66
fanout-score-rank=10
prefix-density=0.03
prefix-fanout=1.7
sequence=TGAGGTAGTAGATTGTATAGTT


criterion=fanout-score
sequence-density=0.60
sequence-density-rank=24
fanout-score=12.69
fanout-score-rank=1
prefix-density=7.56
prefix-fanout=1.0
sequence=TGAGCTTGGCTAT
                                 Started job on |	Mar 04 07:10:08
                             Started mapping on |	Mar 04 07:10:08
                                    Finished on |	Mar 04 07:10:34
       Mapping speed, Million of reads per hour |	301.43

                          Number of input reads |	2176973
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1116168
                        Uniquely mapped reads % |	51.27%
                          Average mapped length |	24.38
                       Number of splices: Total |	1425
            Number of splices: Annotated (sjdb) |	303
                       Number of splices: GT/AG |	1348
                       Number of splices: GC/AG |	15
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	62
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.74
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	762015
             % of reads mapped to multiple loci |	35.00%
        Number of reads mapped to too many loci |	56456
             % of reads mapped to too many loci |	2.59%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.12%
                     % of reads unmapped: other |	1.02%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	298790	298790	298790
N_multimapping	762015	762015	762015
N_noFeature	55154	69925	732750
N_ambiguous	623316	280382	8004
UnstrandedReadsAssigned:437698 PositiveStrandReadsAssigned:765861 NegativeStrandReadsAssigned:375414
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031029 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: SRR5031029-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,176,973 reads, 561,605 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,118 rounds

 109283 SRR5031029.ke.tsv
  52636 SRR5031029.se.tsv
 161919 total
==> SRR5031029.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

==> SRR5031029.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031029 completed mapping pipeline successfully
