Starting /dee2/code/volunteer_pipeline.sh SRR5030991
    current disk space = 160573997056
    free memory = 73950404 
SRR5030991 SRAfilesize
cc2f895cef426c9ecfe76ca4d38ec644  SRR5030991.sra
SRR5030991.sra file validated
SRR5030991 is single end
SRR5030991 is conventional basespace
SRR5030991 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030991_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	32.255	33.0	31.0	34.0	30.0	34.0
2	32.4395	34.0	31.0	34.0	31.0	34.0
3	32.369	34.0	31.0	34.0	30.0	34.0
4	36.05825	37.0	35.0	37.0	35.0	37.0
5	36.03475	37.0	35.0	37.0	35.0	37.0
6	35.71175	37.0	35.0	37.0	33.0	37.0
7	35.8705	37.0	35.0	37.0	35.0	37.0
8	35.91325	37.0	35.0	37.0	35.0	37.0
9	37.5295	39.0	37.0	39.0	35.0	39.0
10	37.36375	39.0	37.0	39.0	34.0	39.0
11	37.118	39.0	37.0	39.0	33.0	39.0
12	37.50425	39.0	37.0	39.0	34.0	39.0
13	37.461	39.0	37.0	39.0	34.0	39.0
14	38.885	40.0	38.0	41.0	35.0	41.0
15	38.839	40.0	38.0	41.0	35.0	41.0
16	38.725	40.0	38.0	41.0	34.0	41.0
17	38.96	40.0	38.0	41.0	35.0	41.0
18	38.79825	40.0	38.0	41.0	34.0	41.0
19	38.6505	40.0	38.0	41.0	34.0	41.0
20	38.6365	40.0	38.0	41.0	34.0	41.0
21	38.76375	40.0	38.0	41.0	34.0	41.0
22	38.79025	40.0	38.0	41.0	35.0	41.0
23	38.32175	40.0	38.0	41.0	33.0	41.0
24	38.7155	40.0	38.0	41.0	35.0	41.0
25	38.82325	40.0	38.0	41.0	34.0	41.0
26	38.8215	40.0	38.0	41.0	35.0	41.0
27	38.95225	40.0	38.0	41.0	35.0	41.0
28	38.77675	40.0	38.0	41.0	35.0	41.0
29	38.562	40.0	38.0	41.0	34.0	41.0
30	38.53	40.0	38.0	41.0	34.0	41.0
31	38.67525	40.0	38.0	41.0	34.0	41.0
32	38.657	40.0	38.0	41.0	34.0	41.0
33	38.454	40.0	38.0	41.0	34.0	41.0
34	38.436	40.0	38.0	41.0	34.0	41.0
35	38.1745	40.0	38.0	41.0	33.0	41.0
36	37.9385	40.0	38.0	41.0	33.0	41.0
37	37.5035	40.0	37.0	41.0	31.0	41.0
38	37.4065	40.0	37.0	41.0	32.0	41.0
39	37.891	40.0	37.0	41.0	33.0	41.0
40	37.9515	40.0	38.0	41.0	33.0	41.0
41	38.19775	40.0	38.0	41.0	33.0	41.0
42	38.103	40.0	38.0	41.0	33.0	41.0
43	37.82575	40.0	38.0	41.0	33.0	41.0
44	38.13625	40.0	38.0	41.0	33.0	41.0
45	38.1715	40.0	38.0	41.0	33.0	41.0
46	37.80975	40.0	37.0	41.0	33.0	41.0
47	37.27	40.0	37.0	41.0	31.0	41.0
48	36.78925	40.0	36.0	41.0	31.0	41.0
49	36.89325	40.0	36.0	41.0	31.0	41.0
50	36.43225	39.0	36.0	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
13	1.0
14	0.0
15	0.0
16	1.0
17	0.0
18	2.0
19	2.0
20	5.0
21	3.0
22	2.0
23	8.0
24	6.0
25	10.0
26	18.0
27	21.0
28	27.0
29	36.0
30	37.0
31	65.0
32	89.0
33	102.0
34	178.0
35	174.0
36	271.0
37	407.0
38	714.0
39	1821.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.9750000000000005	23.0	56.89999999999999	13.125
2	24.347389558232933	26.28012048192771	23.970883534136547	25.40160642570281
3	17.325	19.0	20.349999999999998	43.325
4	27.275	37.824999999999996	13.225000000000001	21.675
5	23.95	37.55	27.950000000000003	10.549999999999999
6	36.5	15.225	36.199999999999996	12.075
7	12.174999999999999	25.05	25.55	37.225
8	23.5	41.6	14.174999999999999	20.724999999999998
9	17.1	38.125	30.75	14.025000000000002
10	18.95	20.674999999999997	27.125	33.25
11	31.6	11.175	14.35	42.875
12	16.05	15.950000000000001	24.099999999999998	43.9
13	20.849999999999998	22.375	38.0	18.775
14	39.4	21.85	24.7	14.05
15	38.574999999999996	19.8	29.099999999999998	12.525
16	12.55	25.45	22.95	39.050000000000004
17	26.174999999999997	21.725	38.7	13.4
18	29.375	19.45	26.724999999999998	24.45
19	39.074999999999996	14.000000000000002	29.95	16.975
20	50.724999999999994	17.65	21.099999999999998	10.525
21	20.349999999999998	26.424999999999997	24.975	28.249999999999996
22	32.475	11.55	47.675	8.3
23	23.7	11.75	50.875	13.675
24	52.675000000000004	12.25	29.099999999999998	5.975
25	57.825	21.575	13.325000000000001	7.2749999999999995
26	31.275	49.4	11.025	8.3
27	14.075	55.1	21.099999999999998	9.725
28	9.75	27.250000000000004	51.324999999999996	11.675
29	8.95	11.375	62.2	17.474999999999998
30	9.275	5.1	38.95	46.675
31	11.675	4.15	47.949999999999996	36.225
32	23.75	4.7	24.6	46.949999999999996
33	55.800000000000004	6.425	11.625	26.150000000000002
34	68.89999999999999	6.8500000000000005	11.975	12.275
35	69.95	6.4750000000000005	16.675	6.9
36	43.175000000000004	6.275	39.775	10.775
37	47.25	8.95	23.849999999999998	19.950000000000003
38	25.424999999999997	13.5	10.45	50.625
39	13.075000000000001	21.0	7.825	58.099999999999994
40	12.3	50.449999999999996	8.799999999999999	28.449999999999996
41	21.875	56.525000000000006	6.875000000000001	14.725
42	51.075	31.825	8.6	8.5
43	58.599999999999994	25.900000000000002	6.75	8.75
44	32.35	50.375	6.375	10.9
45	15.0	56.8	10.875	17.325
46	9.925	28.575	16.1	45.4
47	7.000000000000001	12.775	41.55	38.675
48	8.6	9.675	23.35	58.375
49	11.85	17.25	11.725	59.175
50	18.175	39.574999999999996	9.725	32.525
>>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	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	1.0
20	2.0
21	1.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	2.0
30	4.0
31	4.0
32	4.0
33	6.5
34	9.0
35	14.5
36	20.0
37	21.0
38	22.0
39	25.5
40	29.0
41	36.0
42	43.0
43	81.0
44	119.0
45	179.5
46	240.0
47	452.5
48	665.0
49	627.5
50	590.0
51	776.5
52	963.0
53	652.0
54	341.0
55	348.0
56	355.0
57	322.0
58	289.0
59	190.5
60	92.0
61	65.0
62	38.0
63	62.5
64	87.0
65	53.0
66	19.0
67	15.0
68	11.0
69	13.0
70	15.0
71	28.0
72	41.0
73	20.5
74	0.0
75	0.5
76	1.0
77	0.5
78	0.0
79	0.5
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	0.4
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	35.575
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.89599437807449	27.0
2	9.557273366127898	6.800000000000001
3	4.2164441321152495	4.5
4	2.178496134926212	3.1
5	1.1243851018973998	2.0
6	1.3352073085031624	2.85
7	0.6324666198172875	1.575
8	0.7730147575544624	2.1999999999999997
9	0.35137034434293746	1.125
>10	3.3731553056921992	25.3
>50	0.28109627547434995	5.625
>100	0.28109627547434995	17.925
>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	287	7.175	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	186	4.65	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	139	3.4750000000000005	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	105	2.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	59	1.4749999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	57	1.425	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	57	1.425	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	52	1.3	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	46	1.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	45	1.125	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	42	1.05	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGG	33	0.8250000000000001	RNA PCR Primer, Index 2 (97% over 35bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	32	0.8	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	30	0.75	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTC	22	0.5499999999999999	RNA PCR Primer, Index 11 (100% over 44bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	19	0.475	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	17	0.42500000000000004	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	9	0.22499999999999998	No Hit
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	8	0.2	RNA PCR Primer, Index 1 (100% over 31bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGC	8	0.2	RNA PCR Primer, Index 11 (100% over 50bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	6	0.15	No Hit
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
CATTGCACTTGTCTCGGTCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCTCCCAACCCTTGTACCAGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGC	6	0.15	RNA PCR Primer, Index 6 (97% over 36bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	5	0.125	No Hit
CAACGGAATCCCAAAAGCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC	5	0.125	No Hit
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTGGACTTGGAGTCAGAAGGCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
CTGCGTTCGCGCTCTCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ATCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGATGGAATTCTCGGGTGC	5	0.125	No Hit
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>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	0.225	0.0	0.0	0.0
2	0.0	0.25	0.0	0.0	0.0
3	0.0	0.375	0.0	0.0	0.0
4	0.0	0.375	0.0	0.0	0.0
5	0.0	0.4	0.0	0.0	0.0
6	0.0	0.525	0.0	0.0	0.0
7	0.0	1.175	0.0	0.0	0.0
8	0.0	1.4	0.0	0.0	0.0
9	0.0	1.475	0.0	0.0	0.0
10	0.0	1.625	0.0	0.0	0.0
11	0.0	1.825	0.0	0.0	0.0
12	0.0	1.95	0.0	0.0	0.0
13	0.0	2.275	0.0	0.0	0.0
14	0.0	2.475	0.0	0.0	0.0
15	0.0	2.95	0.0	0.0	0.0
16	0.0	4.325	0.0	0.0	0.0
17	0.0	5.1	0.0	0.0	0.0
18	0.0	6.225	0.0	0.0	0.0
19	0.0	6.625	0.0	0.0	0.0
20	0.0	7.65	0.0	0.0	0.0
21	0.0	12.0	0.0	0.0	0.0
22	0.0	22.875	0.0	0.0	0.0
23	0.0	56.775	0.0	0.0	0.0
24	0.0	74.35	0.0	0.0	0.0
25	0.0	79.875	0.0	0.0	0.0
26	0.0	80.825	0.0	0.0	0.0
27	0.0	81.325	0.0	0.0	0.0
28	0.0	81.7	0.0	0.0	0.0
29	0.0	82.325	0.0	0.0	0.0
30	0.0	82.675	0.0	0.0	0.0
31	0.0	83.45	0.0	0.0	0.0
32	0.0	84.4	0.0	0.0	0.0
33	0.0	85.125	0.0	0.0	0.0
34	0.0	87.2	0.0	0.0	0.0
35	0.0	88.175	0.0	0.0	0.0
36	0.0	88.75	0.0	0.0	0.0
37	0.0	89.575	0.0	0.0	0.0
38	0.0	90.025	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ATCCCCG	20	6.952051E-4	44.000004	8
AACGCTG	20	6.952051E-4	44.000004	8
GTTTGGA	20	6.952051E-4	44.000004	20
AAGTAAT	45	2.728484E-10	44.000004	4
TCAAGTA	45	2.728484E-10	44.000004	2
ACGCTGT	20	6.952051E-4	44.000004	9
AATCCAG	40	5.315087E-9	44.000004	8
ATCCAGG	40	5.315087E-9	44.000004	9
TTCAAGT	45	2.728484E-10	44.000004	1
TTCAACG	20	6.952051E-4	44.000004	5
AGGATAG	45	2.728484E-10	44.000004	13
TCGGTGA	20	6.952051E-4	44.000004	15
CATCCCC	20	6.952051E-4	44.000004	7
ATAGGCT	40	5.315087E-9	44.000004	16
CATTCAA	20	6.952051E-4	44.000004	3
TCAACGC	20	6.952051E-4	44.000004	6
TCCAGGA	40	5.315087E-9	44.000004	10
ACATCCC	20	6.952051E-4	44.000004	6
ACATTCA	20	6.952051E-4	44.000004	2
GGATAGG	45	2.728484E-10	44.000004	14
>>END_MODULE
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337593 spots for SRR5030991.sra
Written 337593 spots for SRR5030991.sra
Read 337604 spots for SRR5030991.sra
Written 337604 spots for SRR5030991.sra
SRR ids: ['SRR5030991.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_js9fh8re
SRR5030991.sra spots: 4051127
blocks: [[1, 337593], [337594, 675186], [675187, 1012779], [1012780, 1350372], [1350373, 1687965], [1687966, 2025558], [2025559, 2363151], [2363152, 2700744], [2700745, 3038337], [3038338, 3375930], [3375931, 3713523], [3713524, 4051127]]
SRR5030991 file size 701084
SRR5030991 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030991 SRR5030991_1.fastq
Input file:	SRR5030991_1.fastq
trimmed:	SRR5030991-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 07:01:01 2020 >> started

Wed Mar  4 07:01:04 2020 >> done (2.802s)
4051127 reads processed; of these:
    245 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
4050873 (99.99%) reads available; of these:
 222308 ( 5.49%) trimmed reads available after processing
3828565 (94.51%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     74	  0.00%
 19	     89	  0.00%
 20	    161	  0.00%
 21	    244	  0.01%
 22	    449	  0.01%
 23	    497	  0.01%
 24	    496	  0.01%
 25	    625	  0.02%
 26	    551	  0.01%
 27	    742	  0.02%
 28	    828	  0.02%
 29	   1570	  0.04%
 30	    897	  0.02%
 31	    918	  0.02%
 32	   1033	  0.03%
 33	   1358	  0.03%
 34	   1724	  0.04%
 35	   3486	  0.09%
 36	   2978	  0.07%
 37	   3390	  0.08%
 38	   3273	  0.08%
 39	   3674	  0.09%
 40	   4215	  0.10%
 41	   4584	  0.11%
 42	   5986	  0.15%
 43	   8571	  0.21%
 44	  12613	  0.31%
 45	  16931	  0.42%
 46	  21933	  0.54%
 47	  27522	  0.68%
 48	  43442	  1.07%
 49	  47454	  1.17%
 50	3828565	 94.51%
4050873 reads passed initial QC


criterion=sequence-density
sequence-density=89.66
sequence-density-rank=1
fanout-score=17.61
fanout-score-rank=1
prefix-density=91.19
prefix-fanout=17.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC


criterion=fanout-score
sequence-density=89.66
sequence-density-rank=1
fanout-score=17.61
fanout-score-rank=1
prefix-density=91.19
prefix-fanout=17.3
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC -o SRR5030991 -
Input file:	STDIN
trimmed:	SRR5030991-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC
-- 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 07:01:21 2020 >> started

Wed Mar  4 07:01:27 2020 >> done (5.359s)
3960854 reads processed; of these:
 217331 ( 5.49%) short reads filtered out after trimming by size control
  11611 ( 0.29%) empty reads filtered out after trimming by size control
3731912 (94.22%) reads available; of these:
3613055 (96.82%) trimmed reads available after processing
 118857 ( 3.18%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  20235	  0.54%
 19	  44453	  1.19%
 20	 170653	  4.57%
 21	 443656	 11.89%
 22	1355504	 36.32%
 23	 689623	 18.48%
 24	 243379	  6.52%
 25	  41580	  1.11%
 26	  21648	  0.58%
 27	  20921	  0.56%
 28	  23025	  0.62%
 29	  17050	  0.46%
 30	  30351	  0.81%
 31	  44018	  1.18%
 32	  39692	  1.06%
 33	  75710	  2.03%
 34	  34194	  0.92%
 35	  25237	  0.68%
 36	  27461	  0.74%
 37	  17103	  0.46%
 38	  18374	  0.49%
 39	  17463	  0.47%
 40	  22102	  0.59%
 41	  33014	  0.88%
 42	  37838	  1.01%
 43	  30632	  0.82%
 44	  25017	  0.67%
 45	  25193	  0.68%
 46	  19477	  0.52%
 47	  14122	  0.38%
 48	   1261	  0.03%
 49	   2344	  0.06%
 50	  99582	  2.67%


criterion=sequence-density
sequence-density=10.45
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=22
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.43
sequence-density-rank=31
fanout-score=8.60
fanout-score-rank=1
prefix-density=3.72
prefix-fanout=1.0
sequence=TAGTAGGTTGTGTGGTTTT
                                 Started job on |	Mar 04 07:01:47
                             Started mapping on |	Mar 04 07:01:48
                                    Finished on |	Mar 04 07:02:13
       Mapping speed, Million of reads per hour |	550.36

                          Number of input reads |	3821931
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1775787
                        Uniquely mapped reads % |	46.46%
                          Average mapped length |	24.18
                       Number of splices: Total |	1910
            Number of splices: Annotated (sjdb) |	244
                       Number of splices: GT/AG |	1740
                       Number of splices: GC/AG |	13
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	157
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.04
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1656872
             % of reads mapped to multiple loci |	43.35%
        Number of reads mapped to too many loci |	89475
             % of reads mapped to too many loci |	2.34%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	6.93%
                     % of reads unmapped: other |	0.91%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	389272	389272	389272
N_multimapping	1656872	1656872	1656872
N_noFeature	93564	110145	1366276
N_ambiguous	937612	591200	12896
UnstrandedReadsAssigned:744611 PositiveStrandReadsAssigned:1074442 NegativeStrandReadsAssigned:396615
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5030991 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: SRR5030991-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,821,931 reads, 713,797 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 784 rounds

 109283 SRR5030991.ke.tsv
  52636 SRR5030991.se.tsv
 161919 total
==> SRR5030991.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

==> SRR5030991.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030991 completed mapping pipeline successfully
