Starting /dee2/code/volunteer_pipeline.sh SRR5030924
    current disk space = 160630259712
    free memory = 1046785864 
SRR5030924 SRAfilesize
3ac1db98da4f3c1452a52740b1a8e70e  SRR5030924.sra
SRR5030924.sra file validated
SRR5030924 is single end
SRR5030924 is conventional basespace
SRR5030924 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5030924_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	32.3065	33.0	31.0	34.0	31.0	34.0
2	32.697	34.0	31.0	34.0	31.0	34.0
3	32.7125	34.0	31.0	34.0	31.0	34.0
4	36.2105	37.0	35.0	37.0	35.0	37.0
5	36.27075	37.0	37.0	37.0	35.0	37.0
6	35.875	37.0	35.0	37.0	35.0	37.0
7	36.07375	37.0	35.0	37.0	35.0	37.0
8	36.19375	37.0	36.0	37.0	35.0	37.0
9	37.89425	39.0	38.0	39.0	35.0	39.0
10	37.95425	39.0	38.0	39.0	35.0	39.0
11	37.83525	39.0	38.0	39.0	35.0	39.0
12	37.86875	39.0	38.0	39.0	35.0	39.0
13	37.884	39.0	38.0	39.0	35.0	39.0
14	39.3375	41.0	39.0	41.0	36.0	41.0
15	39.38075	41.0	39.0	41.0	36.0	41.0
16	39.19975	40.0	39.0	41.0	36.0	41.0
17	39.2545	40.0	39.0	41.0	36.0	41.0
18	39.2635	41.0	39.0	41.0	36.0	41.0
19	38.901	40.0	38.0	41.0	35.0	41.0
20	39.10625	40.0	39.0	41.0	36.0	41.0
21	39.19475	40.0	39.0	41.0	36.0	41.0
22	39.25025	41.0	39.0	41.0	36.0	41.0
23	39.17725	40.0	39.0	41.0	36.0	41.0
24	38.3015	40.0	38.0	41.0	34.0	41.0
25	38.5325	40.0	38.0	41.0	34.0	41.0
26	38.46225	40.0	38.0	41.0	34.0	41.0
27	38.549	40.0	38.0	41.0	34.0	41.0
28	38.665	40.0	38.0	41.0	34.0	41.0
29	38.72175	40.0	38.0	41.0	35.0	41.0
30	38.56525	40.0	38.0	41.0	34.0	41.0
31	38.94125	40.0	39.0	41.0	35.0	41.0
32	39.079	41.0	39.0	41.0	35.0	41.0
33	37.64275	40.0	38.0	41.0	32.0	41.0
34	37.2925	40.0	38.0	41.0	31.0	41.0
35	32.78225	38.0	31.0	40.0	13.0	41.0
36	29.40575	37.0	16.0	40.0	8.0	41.0
37	29.02225	35.0	22.0	39.0	6.0	40.0
38	32.1415	37.0	30.0	39.0	12.0	41.0
39	31.09775	37.0	28.0	40.0	2.0	41.0
40	32.31375	38.0	31.0	40.0	2.0	41.0
41	29.91175	36.0	25.0	40.0	2.0	41.0
42	31.7215	37.0	31.0	40.0	2.0	41.0
43	30.02675	37.0	26.0	40.0	2.0	41.0
44	30.99075	37.0	30.0	40.0	2.0	41.0
45	28.84475	36.0	24.0	40.0	2.0	41.0
46	26.7805	35.0	8.0	39.0	2.0	41.0
47	26.811	34.0	9.0	40.0	2.0	41.0
48	27.54125	35.0	2.0	40.0	2.0	41.0
49	25.6435	34.0	2.0	40.0	2.0	41.0
50	22.5275	30.0	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
15	2.0
16	2.0
17	5.0
18	4.0
19	7.0
20	10.0
21	12.0
22	22.0
23	28.0
24	46.0
25	58.0
26	97.0
27	178.0
28	83.0
29	113.0
30	129.0
31	163.0
32	173.0
33	157.0
34	237.0
35	303.0
36	327.0
37	387.0
38	612.0
39	845.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	10.035035035035035	23.673673673673672	51.97697697697697	14.314314314314313
2	27.075	26.275	21.85	24.8
3	15.5	20.674999999999997	19.875	43.95
4	26.325	36.525	14.75	22.400000000000002
5	23.7	36.3	28.549999999999997	11.450000000000001
6	32.475	15.1	39.550000000000004	12.875
7	16.875	24.525	24.65	33.95
8	26.375	40.150000000000006	14.975	18.5
9	16.225	38.45	32.925	12.4
10	21.0	22.375	25.650000000000002	30.975
11	37.0	13.625000000000002	12.425	36.95
12	17.625	18.7	22.275	41.4
13	18.05	21.675	40.300000000000004	19.975
14	36.6	20.9	27.575	14.924999999999999
15	38.4	20.7	28.4	12.5
16	14.674999999999999	24.6	23.1	37.625
17	26.174999999999997	25.2	34.525	14.099999999999998
18	28.475	18.375	27.6	25.55
19	35.175	14.799999999999999	33.275	16.75
20	48.125	17.625	22.7	11.55
21	22.575	26.525	24.575	26.325
22	33.025	12.825000000000001	44.725	9.425
23	23.1	14.6	48.0	14.299999999999999
24	49.425000000000004	11.875	28.925	9.775
25	54.800000000000004	20.45	14.575	10.174999999999999
26	30.8	44.074999999999996	11.825	13.3
27	14.174999999999999	52.349999999999994	21.125	12.35
28	10.925	28.799999999999997	46.275	14.000000000000002
29	12.174999999999999	12.475	59.199999999999996	16.150000000000002
30	9.025	7.025	39.1	44.85
31	13.25	5.800000000000001	45.800000000000004	35.15
32	23.95	5.35	27.05	43.65
33	51.075	9.025	13.375	26.525
34	64.14999999999999	6.825	13.450000000000001	15.575
35	63.2	6.800000000000001	18.9	11.1
36	67.25	8.0	14.35	10.4
37	39.5	11.65	24.55	24.3
38	28.1	13.200000000000001	13.100000000000001	45.6
39	15.675	23.724999999999998	10.475	50.125
40	13.575000000000001	46.675	10.975	28.775000000000002
41	25.275	49.15	9.5	16.075
42	48.225	31.85	11.05	8.875
43	51.449999999999996	29.625	9.0	9.925
44	33.6	46.925	7.95	11.525
45	17.8	50.3	9.45	22.45
46	12.35	31.225	25.05	31.374999999999996
47	9.975000000000001	13.925	33.4	42.699999999999996
48	10.174999999999999	10.825	25.650000000000002	53.349999999999994
49	12.025	23.674999999999997	12.55	51.74999999999999
50	30.15	25.124999999999996	8.975	35.75
>>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	0.5
10	1.0
11	0.5
12	0.0
13	0.5
14	1.0
15	1.0
16	1.0
17	1.0
18	1.0
19	0.5
20	0.0
21	0.5
22	1.0
23	0.5
24	0.0
25	0.5
26	1.0
27	1.0
28	1.0
29	1.5
30	2.0
31	3.5
32	5.0
33	10.0
34	15.0
35	26.0
36	37.0
37	61.0
38	85.0
39	73.5
40	62.0
41	52.5
42	43.0
43	70.0
44	97.0
45	170.0
46	243.0
47	319.5
48	396.0
49	483.5
50	571.0
51	731.5
52	892.0
53	672.0
54	452.0
55	407.5
56	363.0
57	336.5
58	310.0
59	209.5
60	109.0
61	94.5
62	80.0
63	104.5
64	129.0
65	77.0
66	25.0
67	19.0
68	13.0
69	15.5
70	18.0
71	26.0
72	34.0
73	18.5
74	3.0
75	3.0
76	3.0
77	3.5
78	4.0
79	3.0
80	2.0
81	1.0
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	0.1
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	51.15
#Duplication Level	Percentage of deduplicated	Percentage of total
1	82.74682306940372	42.325
2	6.647116324535679	6.800000000000001
3	3.176930596285435	4.875
4	1.3685239491691104	2.8000000000000003
5	1.0752688172043012	2.75
6	1.0263929618768328	3.15
7	0.39100684261974583	1.4000000000000001
8	0.635386119257087	2.6
9	0.3421309872922776	1.575
>10	2.4437927663734116	22.900000000000002
>50	0.09775171065493646	3.9
>100	0.04887585532746823	4.925
>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
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	197	4.925	RNA PCR Primer, Index 1 (100% over 27bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	80	2.0	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	76	1.9	RNA PCR Primer, Index 1 (96% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	42	1.05	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	34	0.8500000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	31	0.775	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	31	0.775	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (96% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	25	0.625	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (96% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (96% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	20	0.5	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (96% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
GTAAATGATGAGATTCCATTGGTCCGTGTTTCTGAACTACATGATTTTCC	17	0.42500000000000004	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCG	17	0.42500000000000004	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	15	0.375	RNA PCR Primer, Index 1 (96% over 27bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	15	0.375	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	15	0.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGCTGTGATGAGATGACTAAGTAGGAAGTGCCGTCAGAGTCGATAACTGA	14	0.35000000000000003	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGATGATGACACCTGGGTATGCTGCACACTCCCGACTGCGTCGTGGGG	13	0.325	No Hit
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAACTCCG	13	0.325	RNA PCR Primer, Index 1 (96% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	12	0.3	No Hit
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	12	0.3	No Hit
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC	12	0.3	RNA PCR Primer, Index 5 (100% over 35bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 33bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGC	11	0.27499999999999997	RNA PCR Primer, Index 8 (100% over 50bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	11	0.27499999999999997	RNA PCR Primer, Index 1 (96% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTAGATCGATGTGGTGCTCCGGAGTTCTCTTCGGGCCAGGGCCTAAGC	9	0.22499999999999998	No Hit
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAA	9	0.22499999999999998	No Hit
CACCCTGATGAACTGAATACCGCCCCAGTCTGATAGCTGTGGAGAAAGGT	9	0.22499999999999998	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCC	9	0.22499999999999998	No Hit
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAAT	9	0.22499999999999998	No Hit
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCA	8	0.2	RNA PCR Primer, Index 1 (95% over 23bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATTCCG	8	0.2	RNA PCR Primer, Index 1 (95% over 23bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	8	0.2	No Hit
TGAACTGATGATATCATTTCTTTCCCCGTCAGATCGACCCTGTTGATCTC	8	0.2	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCG	8	0.2	RNA PCR Primer, Index 1 (96% over 27bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGG	8	0.2	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	8	0.2	No Hit
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
CGACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	7	0.17500000000000002	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTC	7	0.17500000000000002	RNA PCR Primer, Index 8 (100% over 44bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCGGG	7	0.17500000000000002	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGGGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (96% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGGGCCAAGGAATTCCG	7	0.17500000000000002	RNA PCR Primer, Index 1 (95% over 23bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
AGTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATAC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CTGCAGTGATGACTATCTTAGGACACCTTTGGATTTACCGTGAAAAGAAG	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	6	0.15	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCAATGATGACTTATATATCTGTCAATCCCCTGAGAGATCACTGACGA	6	0.15	No Hit
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	6	0.15	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTCCTCCCG	6	0.15	No Hit
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ATTCATGATGAAATAGATCCTTGACTGAAGCTGATGATGCGTCTGTGTAA	6	0.15	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	6	0.15	No Hit
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAATTCCA	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	5	0.125	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGC	5	0.125	RNA PCR Primer, Index 1 (96% over 29bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	5	0.125	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAATCCCG	5	0.125	RNA PCR Primer, Index 1 (95% over 23bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCAG	5	0.125	RNA PCR Primer, Index 1 (96% over 26bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
GTCTATGATGATCCTATCCCGAACCTGAATTCCTGTTGAAAAACCATACT	5	0.125	No Hit
GTGAAATGATGGCAAATCATCTTTCGGGACTGACCTGAAATGAAGAGAAT	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	0.3	0.0	0.0	0.0
2	0.0	0.3	0.0	0.0	0.0
3	0.0	0.4	0.0	0.0	0.0
4	0.0	0.4	0.0	0.0	0.0
5	0.0	0.4	0.0	0.0	0.0
6	0.0	0.5	0.0	0.0	0.0
7	0.0	0.75	0.0	0.0	0.0
8	0.0	0.925	0.0	0.0	0.0
9	0.0	1.05	0.0	0.0	0.0
10	0.0	1.075	0.0	0.0	0.0
11	0.0	1.325	0.0	0.0	0.0
12	0.0	1.425	0.0	0.0	0.0
13	0.0	1.625	0.0	0.0	0.0
14	0.0	1.8	0.0	0.0	0.0
15	0.0	2.025	0.0	0.0	0.0
16	0.0	2.5	0.0	0.0	0.0
17	0.0	3.25	0.0	0.0	0.0
18	0.0	3.825	0.0	0.0	0.0
19	0.0	4.625	0.0	0.0	0.0
20	0.0	5.225	0.0	0.0	0.0
21	0.0	8.875	0.0	0.0	0.0
22	0.0	17.9	0.0	0.0	0.0
23	0.0	47.575	0.0	0.0	0.0
24	0.0	64.55	0.0	0.0	0.0
25	0.0	70.075	0.0	0.0	0.0
26	0.0	71.0	0.0	0.0	0.0
27	0.0	71.5	0.0	0.0	0.0
28	0.0	71.925	0.0	0.0	0.0
29	0.0	72.1	0.0	0.0	0.0
30	0.0	72.775	0.0	0.0	0.0
31	0.0	73.375	0.0	0.0	0.0
32	0.0	74.375	0.0	0.0	0.0
33	0.0	75.275	0.0	0.0	0.0
34	0.0	78.325	0.0	0.0	0.0
35	0.0	79.175	0.0	0.0	0.0
36	0.0	79.85	0.0	0.0	0.0
37	0.0	80.4	0.0	0.0	0.0
38	0.0	80.725	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AATCCAG	40	5.315087E-9	44.000004	8
CTGAGCT	20	6.952051E-4	44.000004	11
GAGCTTG	20	6.952051E-4	44.000004	13
GGATCCG	20	6.952051E-4	44.000004	3
CCGTCTG	20	6.952051E-4	44.000004	7
TCGGATC	20	6.952051E-4	44.000004	1
CGGATCC	20	6.952051E-4	44.000004	2
GATCCGT	20	6.952051E-4	44.000004	4
CTGGAAG	20	6.952051E-4	44.000004	16
TAATCCA	40	5.315087E-9	44.000004	7
GACTGGA	20	6.952051E-4	44.000004	14
GTGATGG	20	6.952051E-4	44.000004	18
TCCGTCT	20	6.952051E-4	44.000004	6
ATCCGTC	20	6.952051E-4	44.000004	5
ACTGGAA	20	6.952051E-4	44.000004	15
GTAATCC	40	5.315087E-9	44.000004	6
TGAGCTT	20	6.952051E-4	44.000004	12
CGTCTGA	20	6.952051E-4	44.000004	8
TCCCTGA	20	6.952051E-4	44.000004	1
AAGTAAT	35	1.02281774E-7	44.0	4
>>END_MODULE
Read 79281 spots for SRR5030924.sra
Written 79281 spots for SRR5030924.sra
Read 79281 spots for SRR5030924.sra
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Read 79281 spots for SRR5030924.sra
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Read 79281 spots for SRR5030924.sra
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Read 79281 spots for SRR5030924.sra
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Read 79281 spots for SRR5030924.sra
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Read 79281 spots for SRR5030924.sra
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Read 79281 spots for SRR5030924.sra
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Read 79281 spots for SRR5030924.sra
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Read 79281 spots for SRR5030924.sra
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Read 79302 spots for SRR5030924.sra
Written 79302 spots for SRR5030924.sra
SRR ids: ['SRR5030924.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_pktob3qr
SRR5030924.sra spots: 3805509
blocks: [[1, 79281], [79282, 158562], [158563, 237843], [237844, 317124], [317125, 396405], [396406, 475686], [475687, 554967], [554968, 634248], [634249, 713529], [713530, 792810], [792811, 872091], [872092, 951372], [951373, 1030653], [1030654, 1109934], [1109935, 1189215], [1189216, 1268496], [1268497, 1347777], [1347778, 1427058], [1427059, 1506339], [1506340, 1585620], [1585621, 1664901], [1664902, 1744182], [1744183, 1823463], [1823464, 1902744], [1902745, 1982025], [1982026, 2061306], [2061307, 2140587], [2140588, 2219868], [2219869, 2299149], [2299150, 2378430], [2378431, 2457711], [2457712, 2536992], [2536993, 2616273], [2616274, 2695554], [2695555, 2774835], [2774836, 2854116], [2854117, 2933397], [2933398, 3012678], [3012679, 3091959], [3091960, 3171240], [3171241, 3250521], [3250522, 3329802], [3329803, 3409083], [3409084, 3488364], [3488365, 3567645], [3567646, 3646926], [3646927, 3726207], [3726208, 3805509]]
SRR5030924 file size 658505
SRR5030924 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 48 -o SRR5030924 SRR5030924_1.fastq
Input file:	SRR5030924_1.fastq
trimmed:	SRR5030924-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):	32
Wed Mar  4 06:46:00 2020 >> started

Wed Mar  4 06:46:02 2020 >> done (2.407s)
3805509 reads processed; of these:
    155 ( 0.00%) short reads filtered out after trimming by size control
     12 ( 0.00%) empty reads filtered out after trimming by size control
3805342 (100.00%) reads available; of these:
 439771 (11.56%) trimmed reads available after processing
3365571 (88.44%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     61	  0.00%
 19	     60	  0.00%
 20	    130	  0.00%
 21	    178	  0.00%
 22	    347	  0.01%
 23	    425	  0.01%
 24	    411	  0.01%
 25	    575	  0.02%
 26	    488	  0.01%
 27	    578	  0.02%
 28	    901	  0.02%
 29	   1654	  0.04%
 30	   1009	  0.03%
 31	   1277	  0.03%
 32	   3388	  0.09%
 33	  10923	  0.29%
 34	  35192	  0.92%
 35	   7981	  0.21%
 36	   9485	  0.25%
 37	   4146	  0.11%
 38	   9387	  0.25%
 39	   7169	  0.19%
 40	  15366	  0.40%
 41	   8501	  0.22%
 42	  22151	  0.58%
 43	   9034	  0.24%
 44	  44989	  1.18%
 45	  27432	  0.72%
 46	  22476	  0.59%
 47	  23438	  0.62%
 48	  85649	  2.25%
 49	  84970	  2.23%
 50	3365571	 88.44%
3805342 reads passed initial QC


criterion=sequence-density
sequence-density=80.00
sequence-density-rank=1
fanout-score=19.22
fanout-score-rank=2
prefix-density=82.58
prefix-fanout=18.6
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC


criterion=fanout-score
sequence-density=4.44
sequence-density-rank=2
fanout-score=54.76
fanout-score-rank=1
prefix-density=82.61
prefix-fanout=2.9
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 48 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC -o SRR5030924 -
Input file:	STDIN
trimmed:	SRR5030924-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTTGAATCTCGTATGCC
-- 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):	32
Wed Mar  4 06:46:20 2020 >> started

Wed Mar  4 06:46:25 2020 >> done (5.580s)
3710209 reads processed; of these:
 129097 ( 3.48%) short reads filtered out after trimming by size control
  18397 ( 0.50%) empty reads filtered out after trimming by size control
3562715 (96.02%) reads available; of these:
3103236 (87.10%) trimmed reads available after processing
 459479 (12.90%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  17929	  0.50%
 19	  35255	  0.99%
 20	 132650	  3.72%
 21	 370475	 10.40%
 22	1090729	 30.62%
 23	 628588	 17.64%
 24	 211441	  5.93%
 25	  36228	  1.02%
 26	  18135	  0.51%
 27	  18839	  0.53%
 28	  21296	  0.60%
 29	  18631	  0.52%
 30	  27774	  0.78%
 31	  34372	  0.96%
 32	  37422	  1.05%
 33	 115810	  3.25%
 34	  36135	  1.01%
 35	  23361	  0.66%
 36	  33300	  0.93%
 37	  15103	  0.42%
 38	  20209	  0.57%
 39	  17347	  0.49%
 40	  26619	  0.75%
 41	  28584	  0.80%
 42	  34842	  0.98%
 43	  23977	  0.67%
 44	  25636	  0.72%
 45	  26445	  0.74%
 46	  20965	  0.59%
 47	  17562	  0.49%
 48	   7394	  0.21%
 49	  12725	  0.36%
 50	 376937	 10.58%


criterion=sequence-density
sequence-density=5.46
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=15
prefix-density=0.00
prefix-fanout=1.0
sequence=TCCCTGAGACCCTTTAACCTGTGAA


criterion=fanout-score
sequence-density=0.41
sequence-density-rank=33
fanout-score=9.78
fanout-score-rank=1
prefix-density=0.72
prefix-fanout=5.5
sequence=GGAATTCTCGGGGCCCAGGAA
                                 Started job on |	Mar 04 06:47:07
                             Started mapping on |	Mar 04 06:47:07
                                    Finished on |	Mar 04 06:47:36
       Mapping speed, Million of reads per hour |	454.08

                          Number of input reads |	3657848
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1702492
                        Uniquely mapped reads % |	46.54%
                          Average mapped length |	27.44
                       Number of splices: Total |	2102
            Number of splices: Annotated (sjdb) |	223
                       Number of splices: GT/AG |	1903
                       Number of splices: GC/AG |	20
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	179
                      Mismatch rate per base, % |	0.17%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.35
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.13
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1455608
             % of reads mapped to multiple loci |	39.79%
        Number of reads mapped to too many loci |	90814
             % of reads mapped to too many loci |	2.48%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.62%
                     % of reads unmapped: other |	0.56%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	499748	499748	499748
N_multimapping	1455608	1455608	1455608
N_noFeature	75348	91713	1367238
N_ambiguous	900413	615111	13562
UnstrandedReadsAssigned:726731 PositiveStrandReadsAssigned:995668 NegativeStrandReadsAssigned:321692
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5030924 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: SRR5030924-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,657,848 reads, 698,891 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,122 rounds

 109283 SRR5030924.ke.tsv
  52636 SRR5030924.se.tsv
 161919 total
==> SRR5030924.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

==> SRR5030924.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5030924 completed mapping pipeline successfully
