Starting /dee2/code/volunteer_pipeline.sh SRR5030922
    current disk space = 160632455168
    free memory = 73944596 
SRR5030922 SRAfilesize
4cb7784fc44b326d013279f1c42bd3f1  SRR5030922.sra
SRR5030922.sra file validated
SRR5030922 is single end
SRR5030922 is conventional basespace
SRR5030922 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030922_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	32.25425	33.0	31.0	34.0	31.0	34.0
2	32.69025	34.0	31.0	34.0	31.0	34.0
3	32.6665	34.0	31.0	34.0	31.0	34.0
4	36.13875	37.0	35.0	37.0	35.0	37.0
5	36.242	37.0	37.0	37.0	35.0	37.0
6	35.90675	37.0	35.0	37.0	35.0	37.0
7	36.03	37.0	35.0	37.0	35.0	37.0
8	36.1	37.0	35.0	37.0	35.0	37.0
9	37.84375	39.0	38.0	39.0	35.0	39.0
10	37.84125	39.0	38.0	39.0	35.0	39.0
11	37.873	39.0	38.0	39.0	35.0	39.0
12	37.927	39.0	38.0	39.0	35.0	39.0
13	37.911	39.0	38.0	39.0	35.0	39.0
14	39.244	41.0	39.0	41.0	36.0	41.0
15	39.34225	41.0	39.0	41.0	36.0	41.0
16	39.0405	40.0	38.0	41.0	36.0	41.0
17	39.289	41.0	39.0	41.0	36.0	41.0
18	39.24275	41.0	39.0	41.0	36.0	41.0
19	39.02075	40.0	39.0	41.0	36.0	41.0
20	39.2095	40.0	39.0	41.0	36.0	41.0
21	39.1265	40.0	39.0	41.0	36.0	41.0
22	39.317	41.0	39.0	41.0	36.0	41.0
23	39.11225	40.0	39.0	41.0	36.0	41.0
24	38.3415	40.0	38.0	41.0	34.0	41.0
25	38.8025	40.0	38.0	41.0	35.0	41.0
26	38.5935	40.0	38.0	41.0	34.0	41.0
27	38.6015	40.0	38.0	41.0	34.0	41.0
28	38.68575	40.0	38.0	41.0	34.0	41.0
29	38.80125	40.0	38.0	41.0	35.0	41.0
30	38.6615	40.0	38.0	41.0	34.0	41.0
31	38.90575	40.0	38.0	41.0	35.0	41.0
32	39.03825	40.0	39.0	41.0	35.0	41.0
33	37.34725	40.0	37.0	41.0	31.0	41.0
34	36.5395	40.0	37.0	41.0	30.0	41.0
35	31.9395	37.0	30.0	40.0	8.0	40.0
36	28.285	36.0	15.0	40.0	8.0	41.0
37	28.55275	35.0	21.0	39.0	6.0	40.0
38	31.39675	36.0	30.0	39.0	7.0	40.0
39	30.97875	37.0	28.0	39.0	2.0	41.0
40	32.07375	37.0	31.0	40.0	2.0	41.0
41	29.533	36.0	24.0	40.0	2.0	41.0
42	31.2895	37.0	30.0	40.0	2.0	41.0
43	29.33675	36.0	24.0	40.0	2.0	41.0
44	30.50575	37.0	30.0	40.0	2.0	41.0
45	28.19275	36.0	18.0	40.0	2.0	41.0
46	26.27525	34.0	7.0	39.0	2.0	41.0
47	26.4355	34.0	2.0	39.0	2.0	41.0
48	27.30575	35.0	2.0	39.0	2.0	41.0
49	25.40475	34.0	2.0	40.0	2.0	41.0
50	22.07175	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
8	1.0
9	0.0
10	0.0
11	0.0
12	0.0
13	1.0
14	1.0
15	1.0
16	2.0
17	0.0
18	1.0
19	7.0
20	12.0
21	19.0
22	19.0
23	21.0
24	50.0
25	71.0
26	115.0
27	166.0
28	78.0
29	140.0
30	160.0
31	176.0
32	157.0
33	185.0
34	218.0
35	289.0
36	317.0
37	399.0
38	580.0
39	814.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.496366825357052	22.174893510398398	55.549987471811576	12.778752192432973
2	23.5	26.6	21.175	28.725
3	19.400000000000002	18.925	20.825	40.849999999999994
4	27.650000000000002	35.8	14.374999999999998	22.175
5	20.525	39.625	28.725	11.125
6	32.0	17.4	39.65	10.95
7	15.675	23.45	24.0	36.875
8	24.3	40.1	14.174999999999999	21.425
9	20.825	38.925	29.675	10.575
10	21.0	18.625	28.449999999999996	31.924999999999997
11	31.8	12.85	13.625000000000002	41.725
12	14.649999999999999	17.025000000000002	27.3	41.025
13	21.375	21.075	36.475	21.075
14	36.5	26.125	25.650000000000002	11.725
15	39.825	20.3	26.700000000000003	13.175
16	12.225	24.625	22.625	40.525
17	24.4	22.625	39.5	13.475000000000001
18	28.999999999999996	17.849999999999998	30.049999999999997	23.1
19	36.525	13.750000000000002	32.375	17.349999999999998
20	50.025	17.424999999999997	21.15	11.4
21	21.0	27.1	23.549999999999997	28.349999999999998
22	32.2	12.6	47.325	7.875
23	23.125	14.875	49.1	12.9
24	49.9	12.925	30.099999999999998	7.074999999999999
25	56.525000000000006	20.375	14.725	8.375
26	31.125000000000004	46.675	12.625	9.575
27	13.450000000000001	54.55	21.875	10.125
28	9.35	28.675	49.525000000000006	12.45
29	8.625	11.5	62.425	17.45
30	8.575000000000001	5.65	39.65	46.125
31	12.55	4.925	45.85	36.675000000000004
32	23.974999999999998	4.775	26.0	45.25
33	54.05	5.875	13.425	26.650000000000002
34	69.45	5.475	11.475	13.600000000000001
35	65.05	6.15	19.2	9.6
36	66.875	7.75	14.05	11.325000000000001
37	38.675	10.35	24.825	26.150000000000002
38	27.075	12.625	11.95	48.35
39	14.924999999999999	23.549999999999997	8.275	53.25
40	14.499999999999998	48.225	8.85	28.425
41	25.55	52.1	8.825	13.525
42	50.949999999999996	33.324999999999996	7.575	8.15
43	51.15	33.825	7.3	7.725
44	32.550000000000004	49.0	6.2	12.25
45	16.075	51.6	10.274999999999999	22.05
46	9.825000000000001	30.475	25.474999999999998	34.225
47	8.5	13.900000000000002	33.625	43.974999999999994
48	9.2	10.725	24.224999999999998	55.85
49	12.8	23.625	11.450000000000001	52.125
50	32.875	24.375	8.7	34.050000000000004
>>END_MODULE
>>Per sequence GC content	warn
#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	0.5
10	1.0
11	0.5
12	0.0
13	1.0
14	2.0
15	1.5
16	1.0
17	0.5
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	1.0
26	2.0
27	1.5
28	1.0
29	2.0
30	3.0
31	3.5
32	4.0
33	16.5
34	29.0
35	31.0
36	33.0
37	43.5
38	54.0
39	55.0
40	56.0
41	57.0
42	58.0
43	79.5
44	101.0
45	168.0
46	235.0
47	304.5
48	374.0
49	478.0
50	582.0
51	742.0
52	902.0
53	696.5
54	491.0
55	422.0
56	353.0
57	352.0
58	351.0
59	234.5
60	118.0
61	100.0
62	82.0
63	79.5
64	77.0
65	47.5
66	18.0
67	15.5
68	13.0
69	16.0
70	19.0
71	23.0
72	27.0
73	17.5
74	8.0
75	4.5
76	1.0
77	1.0
78	1.0
79	2.0
80	3.0
81	1.5
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	0.22499999999999998
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	49.9
#Duplication Level	Percentage of deduplicated	Percentage of total
1	80.56112224448898	40.2
2	7.865731462925851	7.85
3	3.5571142284569137	5.325
4	2.004008016032064	4.0
5	1.0521042084168337	2.625
6	0.6513026052104208	1.95
7	0.4008016032064128	1.4000000000000001
8	0.5511022044088176	2.1999999999999997
9	0.501002004008016	2.25
>10	2.755511022044088	25.5
>50	0.0501002004008016	2.0500000000000003
>100	0.0501002004008016	4.65
>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	186	4.65	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	82	2.0500000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	49	1.225	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	40	1.0	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	31	0.775	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	26	0.65	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	26	0.65	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	23	0.575	RNA PCR Primer, Index 1 (96% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	21	0.525	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	20	0.5	RNA PCR Primer, Index 1 (96% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	16	0.4	RNA PCR Primer, Index 1 (96% over 29bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	16	0.4	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGC	15	0.375	RNA PCR Primer, Index 24 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	13	0.325	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	13	0.325	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	13	0.325	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 26bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGG	10	0.25	RNA PCR Primer, Index 2 (97% over 35bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	10	0.25	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (95% over 23bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 33bp)
CACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGT	9	0.22499999999999998	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	9	0.22499999999999998	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	9	0.22499999999999998	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	9	0.22499999999999998	RNA PCR Primer, Index 1 (96% over 27bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	8	0.2	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	8	0.2	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (96% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	7	0.17500000000000002	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	7	0.17500000000000002	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	7	0.17500000000000002	No Hit
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	7	0.17500000000000002	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 27bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCCAGGAACTCCAGTCACGG	6	0.15	RNA PCR Primer, Index 11 (97% over 35bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	6	0.15	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	6	0.15	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	6	0.15	No Hit
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	6	0.15	No Hit
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GGTTAATTCCGATAACGAACGAGACTCTGGCATGCTAACTAGTTACGCGA	5	0.125	No Hit
GGTCCATGATGAAACCCATTATCAGTGGACATCTATGGATGAGAAATGCG	5	0.125	No Hit
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGGGCCAAGGAACTCCG	5	0.125	RNA PCR Primer, Index 1 (96% over 27bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	5	0.125	RNA PCR Primer, Index 6 (100% over 34bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAATTCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
GCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	5	0.125	No Hit
CAAAGAATTCTCCTTTTGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	5	0.125	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATCCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
ATACATGATGATCTCACACAACTTGAACTCTCTCACTGATTACTTGATGA	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGGGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (96% over 30bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	5	0.125	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	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	0.375	0.0	0.0	0.0
2	0.0	0.375	0.0	0.0	0.0
3	0.0	0.45	0.0	0.0	0.0
4	0.0	0.45	0.0	0.0	0.0
5	0.0	0.45	0.0	0.0	0.0
6	0.0	0.5	0.0	0.0	0.0
7	0.0	0.7	0.0	0.0	0.0
8	0.0	0.8	0.0	0.0	0.0
9	0.0	0.8	0.0	0.0	0.0
10	0.0	0.875	0.0	0.0	0.0
11	0.0	0.95	0.0	0.0	0.0
12	0.0	1.05	0.0	0.0	0.0
13	0.0	1.175	0.0	0.0	0.0
14	0.0	1.325	0.0	0.0	0.0
15	0.0	1.5	0.0	0.0	0.0
16	0.0	2.2	0.0	0.0	0.0
17	0.0	2.7	0.0	0.0	0.0
18	0.0	3.25	0.0	0.0	0.0
19	0.0	3.6	0.0	0.0	0.0
20	0.0	4.725	0.0	0.0	0.0
21	0.0	9.525	0.0	0.0	0.0
22	0.0	19.55	0.0	0.0	0.0
23	0.0	51.35	0.0	0.0	0.0
24	0.0	68.9	0.0	0.0	0.0
25	0.0	74.45	0.0	0.0	0.0
26	0.0	75.375	0.0	0.0	0.0
27	0.0	75.775	0.0	0.0	0.0
28	0.0	76.25	0.0	0.0	0.0
29	0.0	76.325	0.0	0.0	0.0
30	0.0	76.65	0.0	0.0	0.0
31	0.0	77.05	0.0	0.0	0.0
32	0.0	78.25	0.0	0.0	0.0
33	0.0	79.175	0.0	0.0	0.0
34	0.0	80.85	0.0	0.0	0.0
35	0.0	81.6	0.0	0.0	0.0
36	0.0	81.875	0.0	0.0	0.0
37	0.0	82.4	0.0	0.0	0.0
38	0.0	82.675	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AAGTAAT	40	5.315087E-9	44.000004	4
TCAAGTA	40	5.315087E-9	44.000004	2
TTCAAGT	40	5.315087E-9	44.000004	1
AGGATAG	40	5.315087E-9	44.000004	13
GAGTTGG	20	6.952051E-4	44.000004	20
GGATAGG	40	5.315087E-9	44.000004	14
CTGGAAG	20	6.952051E-4	44.000004	16
GGCTTGG	45	2.728484E-10	44.000004	19
GCTTGGC	40	5.315087E-9	44.000004	15
CAGGATA	40	5.315087E-9	44.000004	12
CAAGTAA	40	5.315087E-9	44.000004	3
TGAGACC	35	1.02281774E-7	44.0	5
AACGCTG	55	0.0	44.0	8
GAGGTAG	30	1.9515464E-6	44.0	2
ACGCTGT	55	0.0	44.0	9
CTGAGCT	50	1.4551915E-11	44.0	11
CTGAGAC	35	1.02281774E-7	44.0	4
TAAACAT	30	1.9515464E-6	44.0	3
ATCCAGG	35	1.02281774E-7	44.0	9
CTTTAAC	25	3.6958358E-5	44.0	12
>>END_MODULE
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421295 spots for SRR5030922.sra
Written 421295 spots for SRR5030922.sra
Read 421306 spots for SRR5030922.sra
Written 421306 spots for SRR5030922.sra
SRR ids: ['SRR5030922.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_hle0wthv
SRR5030922.sra spots: 5055551
blocks: [[1, 421295], [421296, 842590], [842591, 1263885], [1263886, 1685180], [1685181, 2106475], [2106476, 2527770], [2527771, 2949065], [2949066, 3370360], [3370361, 3791655], [3791656, 4212950], [4212951, 4634245], [4634246, 5055551]]
SRR5030922 file size 875164
SRR5030922 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5030922 SRR5030922_1.fastq
Input file:	SRR5030922_1.fastq
trimmed:	SRR5030922-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 06:45:45 2020 >> started

Wed Mar  4 06:45:48 2020 >> done (2.111s)
5055551 reads processed; of these:
    209 ( 0.00%) short reads filtered out after trimming by size control
      6 ( 0.00%) empty reads filtered out after trimming by size control
5055336 (100.00%) reads available; of these:
 618946 (12.24%) trimmed reads available after processing
4436390 (87.76%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     66	  0.00%
 19	     94	  0.00%
 20	    218	  0.00%
 21	    266	  0.01%
 22	    522	  0.01%
 23	    667	  0.01%
 24	    586	  0.01%
 25	    821	  0.02%
 26	    711	  0.01%
 27	    925	  0.02%
 28	   1123	  0.02%
 29	   2113	  0.04%
 30	   1560	  0.03%
 31	   2057	  0.04%
 32	   6004	  0.12%
 33	  17277	  0.34%
 34	  45077	  0.89%
 35	   9201	  0.18%
 36	  11375	  0.23%
 37	   5672	  0.11%
 38	  11665	  0.23%
 39	   9852	  0.19%
 40	  22570	  0.45%
 41	  11724	  0.23%
 42	  36702	  0.73%
 43	  12221	  0.24%
 44	  65062	  1.29%
 45	  37551	  0.74%
 46	  31297	  0.62%
 47	  35685	  0.71%
 48	 112461	  2.22%
 49	 125821	  2.49%
 50	4436390	 87.76%
5055336 reads passed initial QC


criterion=sequence-density
sequence-density=80.98
sequence-density-rank=1
fanout-score=19.72
fanout-score-rank=3
prefix-density=83.86
prefix-fanout=19.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=1.79
sequence-density-rank=7
fanout-score=424.98
fanout-score-rank=1
prefix-density=83.05
prefix-fanout=9.2
sequence=GGAATTCTCGGTGCCAAGGA
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC -o SRR5030922 -
Input file:	STDIN
trimmed:	SRR5030922-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC
-- 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 06:46:07 2020 >> started

Wed Mar  4 06:46:12 2020 >> done (5.233s)
4930513 reads processed; of these:
 136615 ( 2.77%) short reads filtered out after trimming by size control
  14170 ( 0.29%) empty reads filtered out after trimming by size control
4779728 (96.94%) reads available; of these:
4199160 (87.85%) trimmed reads available after processing
 580568 (12.15%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  30404	  0.64%
 19	  48180	  1.01%
 20	 236537	  4.95%
 21	 529491	 11.08%
 22	1516718	 31.73%
 23	 826373	 17.29%
 24	 292410	  6.12%
 25	  49505	  1.04%
 26	  23679	  0.50%
 27	  22327	  0.47%
 28	  25753	  0.54%
 29	  22149	  0.46%
 30	  35744	  0.75%
 31	  48369	  1.01%
 32	  50442	  1.06%
 33	  93887	  1.96%
 34	  43659	  0.91%
 35	  28046	  0.59%
 36	  38246	  0.80%
 37	  18377	  0.38%
 38	  23218	  0.49%
 39	  20587	  0.43%
 40	  32802	  0.69%
 41	  35898	  0.75%
 42	  44496	  0.93%
 43	  28550	  0.60%
 44	  35817	  0.75%
 45	  34258	  0.72%
 46	  27087	  0.57%
 47	  20328	  0.43%
 48	   9988	  0.21%
 49	  17570	  0.37%
 50	 468833	  9.81%


criterion=sequence-density
sequence-density=5.13
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=21
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.57
sequence-density-rank=26
fanout-score=15.81
fanout-score-rank=1
prefix-density=8.99
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 06:46:34
                             Started mapping on |	Mar 04 06:46:34
                                    Finished on |	Mar 04 06:47:15
       Mapping speed, Million of reads per hour |	430.64

                          Number of input reads |	4904551
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	2517447
                        Uniquely mapped reads % |	51.33%
                          Average mapped length |	26.77
                       Number of splices: Total |	2582
            Number of splices: Annotated (sjdb) |	312
                       Number of splices: GT/AG |	2325
                       Number of splices: GC/AG |	28
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	227
                      Mismatch rate per base, % |	0.16%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.34
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.11
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1836312
             % of reads mapped to multiple loci |	37.44%
        Number of reads mapped to too many loci |	96514
             % of reads mapped to too many loci |	1.97%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.78%
                     % of reads unmapped: other |	0.48%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	550792	550792	550792
N_multimapping	1836312	1836312	1836312
N_noFeature	93632	113160	1840250
N_ambiguous	1403999	794838	18843
UnstrandedReadsAssigned:1019816 PositiveStrandReadsAssigned:1609449 NegativeStrandReadsAssigned:658354
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030922 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: SRR5030922-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,904,551 reads, 1,108,000 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,153 rounds

 109283 SRR5030922.ke.tsv
  52636 SRR5030922.se.tsv
 161919 total
==> SRR5030922.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

==> SRR5030922.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030922 completed mapping pipeline successfully
