Starting /dee2/code/volunteer_pipeline.sh SRR5030941
    current disk space = 160606617600
    free memory = 73927564 
SRR5030941 SRAfilesize
43a2297e7fafddc193c5db369553de24  SRR5030941.sra
SRR5030941.sra file validated
SRR5030941 is single end
SRR5030941 is conventional basespace
SRR5030941 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030941_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	52
>>END_MODULE
>>Per base sequence quality	fail
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.399	34.0	31.0	34.0	31.0	34.0
2	32.74825	34.0	31.0	34.0	31.0	34.0
3	32.8335	34.0	31.0	34.0	31.0	34.0
4	36.2075	37.0	37.0	37.0	35.0	37.0
5	36.17975	37.0	37.0	37.0	35.0	37.0
6	36.04675	37.0	35.0	37.0	35.0	37.0
7	36.15075	37.0	36.0	37.0	35.0	37.0
8	36.176	37.0	36.0	37.0	35.0	37.0
9	37.91225	39.0	38.0	39.0	35.0	39.0
10	37.898	39.0	38.0	39.0	35.0	39.0
11	37.829	39.0	38.0	39.0	35.0	39.0
12	37.876	39.0	38.0	39.0	35.0	39.0
13	37.90175	39.0	38.0	39.0	35.0	39.0
14	39.22125	41.0	39.0	41.0	36.0	41.0
15	39.2705	41.0	39.0	41.0	36.0	41.0
16	39.16	40.0	39.0	41.0	36.0	41.0
17	39.23075	41.0	39.0	41.0	36.0	41.0
18	39.27575	41.0	39.0	41.0	36.0	41.0
19	39.044	40.0	39.0	41.0	35.0	41.0
20	39.14925	40.0	39.0	41.0	36.0	41.0
21	39.10975	40.0	39.0	41.0	36.0	41.0
22	39.13675	41.0	39.0	41.0	36.0	41.0
23	39.1335	40.0	39.0	41.0	36.0	41.0
24	38.422	40.0	38.0	41.0	34.0	41.0
25	38.698	40.0	38.0	41.0	34.0	41.0
26	38.7175	40.0	38.0	41.0	35.0	41.0
27	38.7835	40.0	38.0	41.0	34.0	41.0
28	38.68925	40.0	38.0	41.0	35.0	41.0
29	38.5465	40.0	38.0	41.0	34.0	41.0
30	38.35675	40.0	38.0	41.0	34.0	41.0
31	38.61775	40.0	38.0	41.0	34.0	41.0
32	38.908	40.0	38.0	41.0	35.0	41.0
33	37.1725	40.0	37.0	41.0	30.0	41.0
34	36.70875	40.0	37.0	41.0	30.0	41.0
35	33.22675	38.0	31.0	40.0	15.0	41.0
36	29.58675	37.0	19.0	40.0	8.0	41.0
37	30.0565	36.0	25.0	39.0	6.0	41.0
38	32.4895	37.0	31.0	39.0	15.0	41.0
39	32.2745	37.0	31.0	40.0	9.0	41.0
40	32.92425	38.0	32.0	40.0	9.0	41.0
41	30.73075	36.0	28.0	40.0	2.0	41.0
42	32.11475	37.0	31.0	40.0	2.0	41.0
43	30.74125	37.0	28.0	40.0	2.0	41.0
44	31.7015	37.0	31.0	40.0	2.0	41.0
45	29.57075	37.0	26.0	40.0	2.0	41.0
46	27.64725	35.0	18.0	39.0	2.0	41.0
47	27.6725	35.0	21.0	39.0	2.0	41.0
48	28.06625	35.0	22.0	39.0	2.0	41.0
49	26.15375	34.0	2.0	39.0	2.0	41.0
50	22.57425	29.0	2.0	38.0	2.0	40.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
13	2.0
14	0.0
15	3.0
16	2.0
17	1.0
18	1.0
19	7.0
20	9.0
21	13.0
22	24.0
23	29.0
24	47.0
25	54.0
26	81.0
27	132.0
28	73.0
29	122.0
30	132.0
31	155.0
32	159.0
33	187.0
34	232.0
35	267.0
36	368.0
37	435.0
38	634.0
39	831.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.664580725907383	25.5819774718398	46.958698372966204	15.794743429286608
2	23.599999999999998	27.750000000000004	20.825	27.825
3	25.25	17.724999999999998	22.15	34.875
4	31.4	28.599999999999998	15.45	24.55
5	21.275	38.75	25.2	14.774999999999999
6	26.700000000000003	17.9	41.725	13.675
7	21.3	17.724999999999998	23.400000000000002	37.574999999999996
8	22.825	31.05	15.65	30.475
9	23.200000000000003	32.95	29.45	14.399999999999999
10	26.400000000000002	16.8	31.825	24.975
11	34.4	17.075000000000003	13.825000000000001	34.699999999999996
12	16.1	22.25	31.95	29.7
13	29.075	19.0	29.475	22.45
14	27.375	30.525000000000002	23.1	19.0
15	34.525	22.875	24.55	18.05
16	18.099999999999998	22.125	21.375	38.4
17	24.0	23.150000000000002	36.199999999999996	16.650000000000002
18	24.075	18.075	34.75	23.1
19	33.85	15.275	31.55	19.325
20	42.125	17.325	24.425	16.125
21	23.375	22.675	23.799999999999997	30.15
22	28.875	14.85	43.1	13.175
23	23.825	15.25	44.074999999999996	16.85
24	46.225	14.549999999999999	26.75	12.475
25	48.375	20.525	17.175	13.925
26	29.075	41.3	14.75	14.875
27	18.975	45.625	20.95	14.45
28	15.049999999999999	26.6	42.875	15.475
29	11.675	15.85	54.900000000000006	17.575
30	11.15	9.375	35.175	44.3
31	15.0	7.95	45.800000000000004	31.25
32	25.474999999999998	8.05	24.099999999999998	42.375
33	48.375	10.85	15.55	25.224999999999998
34	56.25	7.575	16.7	19.475
35	58.8	8.95	18.575	13.675
36	59.8	10.375	16.85	12.975
37	40.775	13.100000000000001	22.3	23.825
38	26.224999999999998	14.549999999999999	15.525	43.7
39	19.55	22.875	11.475	46.1
40	17.2	43.1	13.425	26.275
41	25.025	43.45	12.25	19.275000000000002
42	46.7	29.675	12.55	11.075
43	46.175	32.475	10.5	10.85
44	31.3	45.475	9.275	13.950000000000001
45	20.65	45.775	11.600000000000001	21.975
46	15.65	30.5	21.45	32.4
47	11.275	19.05	34.275	35.4
48	12.625	13.075000000000001	22.35	51.949999999999996
49	15.35	22.6	15.875	46.175
50	27.450000000000003	25.825	11.725	35.0
>>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	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	1.5
28	2.0
29	4.0
30	6.0
31	12.0
32	18.0
33	24.0
34	30.0
35	46.0
36	62.0
37	73.5
38	85.0
39	87.0
40	89.0
41	89.0
42	89.0
43	110.0
44	131.0
45	162.0
46	193.0
47	242.0
48	291.0
49	382.0
50	473.0
51	578.0
52	683.0
53	592.0
54	501.0
55	446.0
56	391.0
57	410.5
58	430.0
59	296.5
60	163.0
61	123.0
62	83.0
63	101.0
64	119.0
65	79.0
66	39.0
67	28.0
68	17.0
69	22.0
70	27.0
71	38.5
72	50.0
73	30.0
74	10.0
75	6.0
76	2.0
77	3.0
78	4.0
79	4.5
80	5.0
81	5.0
82	5.0
83	2.5
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	warn
#Total Deduplicated Percentage	52.1
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.27831094049904	41.825
2	8.253358925143955	8.6
3	3.5508637236084453	5.55
4	1.583493282149712	3.3000000000000003
5	1.3435700575815739	3.5000000000000004
6	0.8157389635316697	2.55
7	0.47984644913627633	1.7500000000000002
8	0.7197696737044146	3.0
9	0.23992322456813817	1.125
>10	2.5911708253358925	23.0
>50	0.09596928982725528	2.775
>100	0.04798464491362764	3.025
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	121	3.025	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	58	1.4500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	53	1.325	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	49	1.225	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	24	0.6	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	24	0.6	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	23	0.575	RNA PCR Primer, Index 1 (100% over 30bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	20	0.5	RNA PCR Primer, Index 1 (100% over 33bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 29bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	18	0.44999999999999996	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGC	18	0.44999999999999996	RNA PCR Primer, Index 22 (100% over 50bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	17	0.42500000000000004	No Hit
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	17	0.42500000000000004	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	16	0.4	RNA PCR Primer, Index 2 (100% over 35bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	15	0.375	No Hit
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	15	0.375	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	15	0.375	No Hit
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	14	0.35000000000000003	No Hit
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	13	0.325	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	13	0.325	RNA PCR Primer, Index 1 (96% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTC	13	0.325	RNA PCR Primer, Index 22 (100% over 44bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	12	0.3	RNA PCR Primer, Index 1 (100% over 32bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	11	0.27499999999999997	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	11	0.27499999999999997	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	11	0.27499999999999997	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGAAGAAAGGT	11	0.27499999999999997	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	10	0.25	RNA PCR Primer, Index 1 (96% over 27bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	10	0.25	No Hit
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	10	0.25	No Hit
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	10	0.25	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	10	0.25	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	9	0.22499999999999998	No Hit
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	9	0.22499999999999998	No Hit
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	8	0.2	No Hit
GCATGTGATGACATTATTTAGCGACCAAAGTCTGATAAAGATGATTGTGA	8	0.2	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	8	0.2	RNA PCR Primer, Index 1 (100% over 25bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	8	0.2	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	8	0.2	No Hit
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	8	0.2	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	8	0.2	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TTTGGCAATGGTAGAACTCACACCGTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATATGGA	7	0.17500000000000002	No Hit
CTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCTA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCGG	7	0.17500000000000002	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
ATATATGATGACTTTCATAGAATCTCGTTCGGCTGATGATTGCTGTTGAG	6	0.15	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	6	0.15	No Hit
ACGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	6	0.15	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTCTGTGATGAGGCTCTGGAATGTGCGCTGGGCACAGCGCCCGAGAGAG	6	0.15	No Hit
CCTGCATGATGACGAACAAATACTGACTACCTGAAGATCTTATTAGCTCT	6	0.15	No Hit
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	6	0.15	RNA PCR Primer, Index 1 (100% over 25bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	6	0.15	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	6	0.15	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTATTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
GGTCAATGATGACAACCCAATGTCATGAAGAAAGGTGATGACATAAAATT	5	0.125	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTATTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	5	0.125	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CCCCTATGATGAGGACCTTTTCACAGACCTGTACTGATATATCTGTGAGG	5	0.125	No Hit
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	5	0.125	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
>>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	0.5	0.0	0.0	0.0
2	0.0	0.5	0.0	0.0	0.0
3	0.0	0.55	0.0	0.0	0.0
4	0.0	0.55	0.0	0.0	0.0
5	0.0	0.55	0.0	0.0	0.0
6	0.0	0.6	0.0	0.0	0.0
7	0.0	0.975	0.0	0.0	0.0
8	0.0	1.15	0.0	0.0	0.0
9	0.0	1.225	0.0	0.0	0.0
10	0.0	1.275	0.0	0.0	0.0
11	0.0	1.325	0.0	0.0	0.0
12	0.0	1.5	0.0	0.0	0.0
13	0.0	1.7	0.0	0.0	0.0
14	0.0	1.975	0.0	0.0	0.0
15	0.0	2.35	0.0	0.0	0.0
16	0.0	3.175	0.0	0.0	0.0
17	0.0	3.725	0.0	0.0	0.0
18	0.0	4.7	0.0	0.0	0.0
19	0.0	5.425	0.0	0.0	0.0
20	0.0	6.2	0.0	0.0	0.0
21	0.0	10.225	0.0	0.0	0.0
22	0.0	18.525	0.0	0.0	0.0
23	0.0	44.4	0.0	0.0	0.0
24	0.0	56.7	0.0	0.0	0.0
25	0.0	63.025	0.0	0.0	0.0
26	0.0	65.0	0.0	0.0	0.0
27	0.0	65.65	0.0	0.0	0.0
28	0.0	66.15	0.0	0.0	0.0
29	0.0	66.5	0.0	0.0	0.0
30	0.0	66.8	0.0	0.0	0.0
31	0.0	67.25	0.0	0.0	0.0
32	0.0	68.525	0.0	0.0	0.0
33	0.0	69.15	0.0	0.0	0.0
34	0.0	71.5	0.0	0.0	0.0
35	0.0	72.375	0.0	0.0	0.0
36	0.0	73.25	0.0	0.0	0.0
37	0.0	73.775	0.0	0.0	0.0
38	0.0	74.125	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GTAGATT	20	6.952051E-4	44.000004	8
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
AATCCAG	20	6.952051E-4	44.000004	8
ATCCAGG	20	6.952051E-4	44.000004	9
TTCAAGT	20	6.952051E-4	44.000004	1
AGTAGAT	20	6.952051E-4	44.000004	7
AGGATAG	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
GATTGTA	20	6.952051E-4	44.000004	11
TCCAGGA	20	6.952051E-4	44.000004	10
GGATAGG	20	6.952051E-4	44.000004	14
AGTAATC	20	6.952051E-4	44.000004	5
GGCTTGG	20	6.952051E-4	44.000004	19
TAATCCA	20	6.952051E-4	44.000004	7
CAGGATA	20	6.952051E-4	44.000004	12
AGATTGT	20	6.952051E-4	44.000004	10
GTAATCC	20	6.952051E-4	44.000004	6
TAGATTG	20	6.952051E-4	44.000004	9
GATAGGC	20	6.952051E-4	44.000004	15
>>END_MODULE
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271036 spots for SRR5030941.sra
Written 271036 spots for SRR5030941.sra
Read 271044 spots for SRR5030941.sra
Written 271044 spots for SRR5030941.sra
SRR ids: ['SRR5030941.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_w5l2cc6i
SRR5030941.sra spots: 3252440
blocks: [[1, 271036], [271037, 542072], [542073, 813108], [813109, 1084144], [1084145, 1355180], [1355181, 1626216], [1626217, 1897252], [1897253, 2168288], [2168289, 2439324], [2439325, 2710360], [2710361, 2981396], [2981397, 3252440]]
SRR5030941 file size 562642
SRR5030941 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030941 SRR5030941_1.fastq
Input file:	SRR5030941_1.fastq
trimmed:	SRR5030941-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 06:50:25 2020 >> started

Wed Mar  4 06:50:27 2020 >> done (2.408s)
3252440 reads processed; of these:
    220 ( 0.01%) short reads filtered out after trimming by size control
     12 ( 0.00%) empty reads filtered out after trimming by size control
3252208 (99.99%) reads available; of these:
 403104 (12.39%) trimmed reads available after processing
2849104 (87.61%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     75	  0.00%
 19	     86	  0.00%
 20	    147	  0.00%
 21	    194	  0.01%
 22	    342	  0.01%
 23	    436	  0.01%
 24	    443	  0.01%
 25	    616	  0.02%
 26	    542	  0.02%
 27	    699	  0.02%
 28	    892	  0.03%
 29	   1368	  0.04%
 30	    998	  0.03%
 31	   1424	  0.04%
 32	   3783	  0.12%
 33	  11892	  0.37%
 34	  25262	  0.78%
 35	   6416	  0.20%
 36	   6904	  0.21%
 37	   4170	  0.13%
 38	   7692	  0.24%
 39	   7929	  0.24%
 40	  15346	  0.47%
 41	   7969	  0.25%
 42	  20441	  0.63%
 43	   9431	  0.29%
 44	  37086	  1.14%
 45	  24825	  0.76%
 46	  23905	  0.74%
 47	  27505	  0.85%
 48	  72560	  2.23%
 49	  81726	  2.51%
 50	2849104	 87.61%
3252208 reads passed initial QC


criterion=sequence-density
sequence-density=72.66
sequence-density-rank=1
fanout-score=20.76
fanout-score-rank=2
prefix-density=75.34
prefix-fanout=20.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC


criterion=fanout-score
sequence-density=3.49
sequence-density-rank=3
fanout-score=65.85
fanout-score-rank=1
prefix-density=74.57
prefix-fanout=3.1
sequence=GAATTCTCGGGGGCCAAGGAACT
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC -o SRR5030941 -
Input file:	STDIN
trimmed:	SRR5030941-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTACGATCTCGTATGCC
-- 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 06:50:44 2020 >> started

Wed Mar  4 06:50:49 2020 >> done (4.805s)
3163107 reads processed; of these:
 137470 ( 4.35%) short reads filtered out after trimming by size control
  15213 ( 0.48%) empty reads filtered out after trimming by size control
3010424 (95.17%) reads available; of these:
2450825 (81.41%) trimmed reads available after processing
 559599 (18.59%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  21946	  0.73%
 19	  24026	  0.80%
 20	 140600	  4.67%
 21	 286716	  9.52%
 22	 786808	 26.14%
 23	 373115	 12.39%
 24	 184231	  6.12%
 25	  51607	  1.71%
 26	  25636	  0.85%
 27	  20491	  0.68%
 28	  22313	  0.74%
 29	  17831	  0.59%
 30	  24421	  0.81%
 31	  40560	  1.35%
 32	  30439	  1.01%
 33	  75906	  2.52%
 34	  29355	  0.98%
 35	  22273	  0.74%
 36	  27264	  0.91%
 37	  16683	  0.55%
 38	  19271	  0.64%
 39	  19536	  0.65%
 40	  32681	  1.09%
 41	  35665	  1.18%
 42	  45315	  1.51%
 43	  30156	  1.00%
 44	  27787	  0.92%
 45	  35559	  1.18%
 46	  28227	  0.94%
 47	  21046	  0.70%
 48	   9168	  0.30%
 49	  17383	  0.58%
 50	 466409	 15.49%


criterion=sequence-density
sequence-density=6.72
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.55
sequence-density-rank=30
fanout-score=14.73
fanout-score-rank=1
prefix-density=8.17
prefix-fanout=1.0
sequence=TGAGCTTGGCTT
                                 Started job on |	Mar 04 06:51:12
                             Started mapping on |	Mar 04 06:51:12
                                    Finished on |	Mar 04 06:51:35
       Mapping speed, Million of reads per hour |	485.14

                          Number of input reads |	3099525
                      Average input read length |	30
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1805386
                        Uniquely mapped reads % |	58.25%
                          Average mapped length |	29.08
                       Number of splices: Total |	2067
            Number of splices: Annotated (sjdb) |	277
                       Number of splices: GT/AG |	1936
                       Number of splices: GC/AG |	17
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	113
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.26
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.06
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	839815
             % of reads mapped to multiple loci |	27.09%
        Number of reads mapped to too many loci |	64915
             % of reads mapped to too many loci |	2.09%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.73%
                     % of reads unmapped: other |	0.84%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	454324	454324	454324
N_multimapping	839815	839815	839815
N_noFeature	88119	111248	1285849
N_ambiguous	979237	521934	17671
UnstrandedReadsAssigned:738030 PositiveStrandReadsAssigned:1172204 NegativeStrandReadsAssigned:501866
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030941 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: SRR5030941-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,099,525 reads, 753,154 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 757 rounds

 109283 SRR5030941.ke.tsv
  52636 SRR5030941.se.tsv
 161919 total
==> SRR5030941.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

==> SRR5030941.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	3
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030941 completed mapping pipeline successfully
