Starting /dee2/code/volunteer_pipeline.sh SRR5030932
    current disk space = 160620740608
    free memory = 56713308 
SRR5030932 SRAfilesize
8e78d4b199d9a2766896b55c90d9957f  SRR5030932.sra
SRR5030932.sra file validated
SRR5030932 is single end
SRR5030932 is conventional basespace
SRR5030932 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030932_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	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.4615	33.0	31.0	34.0	31.0	34.0
2	32.75175	34.0	31.0	34.0	31.0	34.0
3	32.84725	34.0	31.0	34.0	31.0	34.0
4	36.2935	37.0	37.0	37.0	35.0	37.0
5	36.36175	37.0	37.0	37.0	35.0	37.0
6	36.10825	37.0	36.0	37.0	35.0	37.0
7	36.168	37.0	35.0	37.0	35.0	37.0
8	36.2845	37.0	37.0	37.0	35.0	37.0
9	37.976	39.0	38.0	39.0	35.0	39.0
10	37.9865	39.0	39.0	39.0	35.0	39.0
11	37.93225	39.0	38.0	39.0	35.0	39.0
12	37.98125	39.0	38.0	39.0	35.0	39.0
13	37.86525	39.0	38.0	39.0	35.0	39.0
14	39.243	41.0	39.0	41.0	36.0	41.0
15	39.3335	41.0	39.0	41.0	36.0	41.0
16	39.33	40.0	39.0	41.0	36.0	41.0
17	39.51925	41.0	39.0	41.0	37.0	41.0
18	39.4815	41.0	39.0	41.0	36.0	41.0
19	39.144	41.0	39.0	41.0	36.0	41.0
20	39.24625	40.0	39.0	41.0	36.0	41.0
21	39.35075	41.0	39.0	41.0	36.0	41.0
22	39.3495	41.0	39.0	41.0	36.0	41.0
23	39.08325	40.0	39.0	41.0	36.0	41.0
24	38.953	40.0	39.0	41.0	36.0	41.0
25	39.13575	41.0	39.0	41.0	36.0	41.0
26	39.25975	41.0	39.0	41.0	36.0	41.0
27	39.26375	41.0	39.0	41.0	36.0	41.0
28	39.146	41.0	39.0	41.0	36.0	41.0
29	38.23525	40.0	38.0	41.0	33.0	41.0
30	38.3825	40.0	38.0	41.0	33.0	41.0
31	38.76475	40.0	38.0	41.0	35.0	41.0
32	39.04525	40.0	39.0	41.0	35.0	41.0
33	38.1455	40.0	38.0	41.0	33.0	41.0
34	38.38325	40.0	38.0	41.0	34.0	41.0
35	38.085	40.0	38.0	41.0	34.0	41.0
36	34.26025	38.0	31.0	40.0	23.0	41.0
37	35.948	38.0	35.0	40.0	30.0	41.0
38	37.29675	39.0	37.0	40.0	33.0	41.0
39	37.29825	39.0	37.0	40.0	32.0	41.0
40	37.21575	39.0	37.0	40.0	32.0	41.0
41	37.263	39.0	37.0	41.0	32.0	41.0
42	37.51125	40.0	37.0	41.0	33.0	41.0
43	37.3015	40.0	37.0	41.0	32.0	41.0
44	37.2555	40.0	37.0	41.0	32.0	41.0
45	36.82525	39.0	36.0	41.0	31.0	41.0
46	35.1225	38.0	34.0	40.0	26.0	41.0
47	35.78225	39.0	35.0	40.0	28.0	41.0
48	36.245	39.0	36.0	41.0	30.0	41.0
49	35.30225	39.0	35.0	40.0	28.0	41.0
50	30.44325	34.0	27.0	39.0	2.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
12	2.0
13	0.0
14	0.0
15	1.0
16	0.0
17	1.0
18	0.0
19	3.0
20	3.0
21	5.0
22	8.0
23	4.0
24	6.0
25	16.0
26	18.0
27	21.0
28	24.0
29	24.0
30	55.0
31	65.0
32	94.0
33	93.0
34	130.0
35	204.0
36	315.0
37	540.0
38	1044.0
39	1324.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.436795994993743	21.90237797246558	53.191489361702125	15.46933667083855
2	26.224999999999998	24.95	21.275	27.55
3	19.025	19.025	20.825	41.125
4	26.275	35.85	13.5	24.375
5	22.025	38.6	26.55	12.825000000000001
6	32.125	16.55	37.875	13.450000000000001
7	15.675	24.425	25.45	34.449999999999996
8	25.15	37.75	15.375	21.725
9	19.225	36.575	31.724999999999998	12.475
10	21.525	19.85	26.0	32.625
11	32.85	13.475000000000001	13.325000000000001	40.35
12	18.775	18.275	23.400000000000002	39.550000000000004
13	20.95	20.95	36.725	21.375
14	32.9	23.474999999999998	28.275	15.35
15	37.675	23.025000000000002	26.8	12.5
16	14.299999999999999	25.85	21.475	38.375
17	23.200000000000003	24.575	36.25	15.975
18	26.900000000000002	18.725	28.9	25.474999999999998
19	37.025000000000006	15.4	29.75	17.825
20	46.550000000000004	17.474999999999998	24.25	11.725
21	24.375	25.5	23.25	26.875
22	31.95	15.0	44.125	8.924999999999999
23	23.775	15.174999999999999	45.800000000000004	15.25
24	50.075	13.825000000000001	26.674999999999997	9.425
25	50.2	22.05	16.625	11.125
26	27.725	44.6	13.025	14.649999999999999
27	14.774999999999999	47.825	22.575	14.825
28	11.5	27.450000000000003	46.400000000000006	14.649999999999999
29	13.975000000000001	12.675	55.875	17.474999999999998
30	11.275	6.825	37.05	44.85
31	13.075000000000001	6.675000000000001	45.800000000000004	34.449999999999996
32	26.25	7.675	23.0	43.075
33	51.349999999999994	8.825	13.425	26.400000000000002
34	60.550000000000004	9.625	14.575	15.25
35	62.324999999999996	8.200000000000001	18.65	10.825
36	44.75	8.975	33.575	12.7
37	44.275	11.35	23.775	20.599999999999998
38	24.65	15.049999999999999	12.525	47.775
39	16.0	24.2	10.15	49.65
40	14.124999999999998	48.75	12.275	24.85
41	21.6	50.125	11.774999999999999	16.5
42	48.575	29.975	11.425	10.025
43	51.300000000000004	27.525	10.299999999999999	10.875
44	30.3	47.15	7.75	14.799999999999999
45	18.875	51.87500000000001	12.075	17.175
46	13.200000000000001	28.15	18.6	40.050000000000004
47	9.375	16.825000000000003	39.825	33.975
48	10.75	12.1	23.075000000000003	54.074999999999996
49	14.274999999999999	19.375	13.925	52.425
50	17.9	36.75	12.725	32.625
>>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	1.0
14	1.0
15	0.5
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	1.5
26	3.0
27	3.5
28	4.0
29	4.0
30	4.0
31	9.0
32	14.0
33	20.0
34	26.0
35	36.0
36	46.0
37	50.0
38	54.0
39	51.5
40	49.0
41	56.0
42	63.0
43	94.0
44	125.0
45	177.5
46	230.0
47	360.5
48	491.0
49	576.0
50	661.0
51	788.0
52	915.0
53	641.0
54	367.0
55	358.0
56	349.0
57	307.0
58	265.0
59	165.5
60	66.0
61	53.5
62	41.0
63	79.0
64	117.0
65	75.0
66	33.0
67	22.5
68	12.0
69	14.5
70	17.0
71	19.5
72	22.0
73	16.0
74	10.0
75	6.5
76	3.0
77	4.5
78	6.0
79	4.5
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	0.125
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	fail
#Total Deduplicated Percentage	40.35
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.5179677819083	30.875000000000004
2	9.603469640644361	7.75
3	3.593556381660471	4.35
4	2.478314745972739	4.0
5	1.4250309789343247	2.875
6	0.9913258983890955	2.4
7	0.8054522924411399	2.275
8	0.6195786864931847	2.0
9	0.18587360594795538	0.675
>10	3.3457249070631967	25.25
>50	0.18587360594795538	4.8
>100	0.24783147459727387	12.75
>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
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	152	3.8	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	130	3.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	124	3.1	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	104	2.6	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	70	1.7500000000000002	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGC	65	1.625	RNA PCR Primer, Index 15 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	57	1.425	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	42	1.05	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 33bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTC	21	0.525	RNA PCR Primer, Index 15 (100% over 44bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	21	0.525	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAT	15	0.375	RNA PCR Primer, Index 1 (100% over 35bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	12	0.3	No Hit
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	10	0.25	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	10	0.25	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	10	0.25	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	9	0.22499999999999998	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	8	0.2	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	8	0.2	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	8	0.2	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	8	0.2	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	8	0.2	No Hit
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	7	0.17500000000000002	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	6	0.15	No Hit
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
TTAAGGCACGCGGTGAATTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	6	0.15	RNA PCR Primer, Index 1 (100% over 32bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATTTAAGCATATTATGG	6	0.15	No Hit
CTGGGCTACACATTTTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	6	0.15	RNA PCR Primer, Index 1 (100% over 33bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAAGGCACGCGGTGAATGAAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTAATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
ATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGCCGCGCC	5	0.125	No Hit
AGATACCCGTCGCCGCGCTCTCCCTCTCCCCCCGTCCGCCTCCCGGGCGG	5	0.125	No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	5	0.125	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	5	0.125	No Hit
TAGCAGCACAGAAATATTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	5	0.125	No Hit
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
GCACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGC	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	1.9	0.0	0.0	0.0
2	0.0	1.9	0.0	0.0	0.0
3	0.0	2.025	0.0	0.0	0.0
4	0.0	2.075	0.0	0.0	0.0
5	0.0	2.125	0.0	0.0	0.0
6	0.0	2.175	0.0	0.0	0.0
7	0.0	2.775	0.0	0.0	0.0
8	0.0	2.85	0.0	0.0	0.0
9	0.0	2.925	0.0	0.0	0.0
10	0.0	3.075	0.0	0.0	0.0
11	0.0	3.35	0.0	0.0	0.0
12	0.0	3.575	0.0	0.0	0.0
13	0.0	3.85	0.0	0.0	0.0
14	0.0	4.025	0.0	0.0	0.0
15	0.0	4.3	0.0	0.0	0.0
16	0.0	5.125	0.0	0.0	0.0
17	0.0	5.725	0.0	0.0	0.0
18	0.0	7.075	0.0	0.0	0.0
19	0.0	7.825	0.0	0.0	0.0
20	0.0	8.975	0.0	0.0	0.0
21	0.0	13.125	0.0	0.0	0.0
22	0.0	22.925	0.0	0.0	0.0
23	0.0	52.05	0.0	0.0	0.0
24	0.0	65.7	0.0	0.0	0.0
25	0.0	71.125	0.0	0.0	0.0
26	0.0	72.075	0.0	0.0	0.0
27	0.0	72.675	0.0	0.0	0.0
28	0.0	73.1	0.0	0.0	0.0
29	0.0	73.675	0.0	0.0	0.0
30	0.0	74.075	0.0	0.0	0.0
31	0.0	74.875	0.0	0.0	0.0
32	0.0	76.075	0.0	0.0	0.0
33	0.0	76.975	0.0	0.0	0.0
34	0.0	79.8	0.0	0.0	0.0
35	0.0	80.6	0.0	0.0	0.0
36	0.0	81.225	0.0	0.0	0.0
37	0.0	81.975	0.0	0.0	0.0
38	0.0	82.375	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGAGACC	20	6.952051E-4	44.000004	5
CTGAGCT	45	2.728484E-10	44.000004	11
CTGAGAC	20	6.952051E-4	44.000004	4
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
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
CGGATCC	45	2.728484E-10	44.000004	2
GATCCGT	45	2.728484E-10	44.000004	4
GGCTTTG	20	6.952051E-4	44.000004	19
GGCTTGG	20	6.952051E-4	44.000004	19
CCCTGAG	20	6.952051E-4	44.000004	2
GCTTGGC	40	5.315087E-9	44.000004	15
TCCGTCT	45	2.728484E-10	44.000004	6
ATCCGTC	45	2.728484E-10	44.000004	5
AGACCCT	20	6.952051E-4	44.000004	7
CTTTGGA	20	6.952051E-4	44.000004	21
GCTTTGG	20	6.952051E-4	44.000004	20
>>END_MODULE
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319289 spots for SRR5030932.sra
Written 319289 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
Read 319278 spots for SRR5030932.sra
Written 319278 spots for SRR5030932.sra
SRR ids: ['SRR5030932.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_03pl1uw_
SRR5030932.sra spots: 3831347
blocks: [[1, 319278], [319279, 638556], [638557, 957834], [957835, 1277112], [1277113, 1596390], [1596391, 1915668], [1915669, 2234946], [2234947, 2554224], [2554225, 2873502], [2873503, 3192780], [3192781, 3512058], [3512059, 3831347]]
SRR5030932 file size 662983
SRR5030932 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030932 SRR5030932_1.fastq
Input file:	SRR5030932_1.fastq
trimmed:	SRR5030932-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 06:48:23 2020 >> started

Wed Mar  4 06:48:26 2020 >> done (2.382s)
3831347 reads processed; of these:
    129 ( 0.00%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
3831209 (100.00%) reads available; of these:
 216116 ( 5.64%) trimmed reads available after processing
3615093 (94.36%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     44	  0.00%
 19	     58	  0.00%
 20	    120	  0.00%
 21	    182	  0.00%
 22	    308	  0.01%
 23	    340	  0.01%
 24	    383	  0.01%
 25	    452	  0.01%
 26	    423	  0.01%
 27	    560	  0.01%
 28	    791	  0.02%
 29	   1274	  0.03%
 30	    861	  0.02%
 31	   1046	  0.03%
 32	   1178	  0.03%
 33	   1398	  0.04%
 34	   3490	  0.09%
 35	   3203	  0.08%
 36	   2398	  0.06%
 37	   2653	  0.07%
 38	   2868	  0.07%
 39	   3276	  0.09%
 40	   3627	  0.09%
 41	   3993	  0.10%
 42	   5406	  0.14%
 43	   7074	  0.18%
 44	  12318	  0.32%
 45	  15114	  0.39%
 46	  13787	  0.36%
 47	  19797	  0.52%
 48	  41915	  1.09%
 49	  65779	  1.72%
 50	3615093	 94.36%
3831209 reads passed initial QC


criterion=sequence-density
sequence-density=81.97
sequence-density-rank=1
fanout-score=19.47
fanout-score-rank=1
prefix-density=82.23
prefix-fanout=19.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC


criterion=fanout-score
sequence-density=81.97
sequence-density-rank=1
fanout-score=19.47
fanout-score-rank=1
prefix-density=82.23
prefix-fanout=19.4
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC -o SRR5030932 -
Input file:	STDIN
trimmed:	SRR5030932-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGTCAATCTCGTATGCC
-- 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 06:48:42 2020 >> started

Wed Mar  4 06:48:48 2020 >> done (6.127s)
3737765 reads processed; of these:
 173783 ( 4.65%) short reads filtered out after trimming by size control
  70643 ( 1.89%) empty reads filtered out after trimming by size control
3493339 (93.46%) reads available; of these:
3111531 (89.07%) trimmed reads available after processing
 381808 (10.93%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  21726	  0.62%
 19	  43394	  1.24%
 20	 171873	  4.92%
 21	 375534	 10.75%
 22	1106756	 31.68%
 23	 535435	 15.33%
 24	 201986	  5.78%
 25	  36036	  1.03%
 26	  18928	  0.54%
 27	  18030	  0.52%
 28	  21106	  0.60%
 29	  16445	  0.47%
 30	  28536	  0.82%
 31	  40575	  1.16%
 32	  42636	  1.22%
 33	  97963	  2.80%
 34	  36974	  1.06%
 35	  24914	  0.71%
 36	  26567	  0.76%
 37	  16898	  0.48%
 38	  18419	  0.53%
 39	  18012	  0.52%
 40	  24132	  0.69%
 41	  33482	  0.96%
 42	  36068	  1.03%
 43	  27422	  0.78%
 44	  24401	  0.70%
 45	  28533	  0.82%
 46	  22072	  0.63%
 47	  18804	  0.54%
 48	   3889	  0.11%
 49	  14435	  0.41%
 50	 341358	  9.77%


criterion=sequence-density
sequence-density=3.55
sequence-density-rank=1
fanout-score=1.00
fanout-score-rank=18
prefix-density=0.01
prefix-fanout=1.0
sequence=TGTAAACATCCT


criterion=fanout-score
sequence-density=1.07
sequence-density-rank=11
fanout-score=2.71
fanout-score-rank=1
prefix-density=2.90
prefix-fanout=1.0
sequence=GTAGGTTGTATAGTT
                                 Started job on |	Mar 04 06:49:09
                             Started mapping on |	Mar 04 06:49:09
                                    Finished on |	Mar 04 06:49:33
       Mapping speed, Million of reads per hour |	538.02

                          Number of input reads |	3586783
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1864622
                        Uniquely mapped reads % |	51.99%
                          Average mapped length |	27.29
                       Number of splices: Total |	1670
            Number of splices: Annotated (sjdb) |	248
                       Number of splices: GT/AG |	1508
                       Number of splices: GC/AG |	19
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	143
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.50
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.08
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1298259
             % of reads mapped to multiple loci |	36.20%
        Number of reads mapped to too many loci |	98139
             % of reads mapped to too many loci |	2.74%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.36%
                     % of reads unmapped: other |	0.73%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	423902	423902	423902
N_multimapping	1298259	1298259	1298259
N_noFeature	80467	98621	1441259
N_ambiguous	1019447	661213	17091
UnstrandedReadsAssigned:764708 PositiveStrandReadsAssigned:1104788 NegativeStrandReadsAssigned:406272
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030932 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: SRR5030932-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,586,783 reads, 766,350 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 927 rounds

 109283 SRR5030932.ke.tsv
  52636 SRR5030932.se.tsv
 161919 total
==> SRR5030932.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

==> SRR5030932.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030932 completed mapping pipeline successfully
