Starting /dee2/code/volunteer_pipeline.sh SRR5031039
    current disk space = 160517111808
    free memory = 73935092 
SRR5031039 SRAfilesize
63164b7c80fc66bc5fa663e270e66105  SRR5031039.sra
SRR5031039.sra file validated
SRR5031039 is single end
SRR5031039 is conventional basespace
SRR5031039 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031039_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	50
%GC	51
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.34575	33.0	31.0	34.0	31.0	34.0
2	32.5775	34.0	31.0	34.0	31.0	34.0
3	32.547	34.0	31.0	34.0	31.0	34.0
4	36.188	37.0	35.0	37.0	35.0	37.0
5	36.0575	37.0	35.0	37.0	35.0	37.0
6	35.77675	37.0	35.0	37.0	33.0	37.0
7	35.96675	37.0	35.0	37.0	35.0	37.0
8	35.81825	37.0	35.0	37.0	35.0	37.0
9	37.56575	39.0	37.0	39.0	35.0	39.0
10	37.73725	39.0	37.0	39.0	35.0	39.0
11	37.6905	39.0	37.0	39.0	35.0	39.0
12	37.7265	39.0	37.0	39.0	35.0	39.0
13	37.66925	39.0	37.0	39.0	35.0	39.0
14	39.0845	41.0	39.0	41.0	36.0	41.0
15	39.08675	40.0	38.0	41.0	36.0	41.0
16	38.9035	40.0	38.0	41.0	35.0	41.0
17	38.93625	40.0	38.0	41.0	35.0	41.0
18	39.138	41.0	38.0	41.0	36.0	41.0
19	38.487	40.0	38.0	41.0	34.0	41.0
20	38.8455	40.0	38.0	41.0	35.0	41.0
21	38.69	40.0	38.0	41.0	34.0	41.0
22	38.9705	40.0	39.0	41.0	36.0	41.0
23	38.70075	40.0	38.0	41.0	35.0	41.0
24	38.77075	40.0	38.0	41.0	35.0	41.0
25	39.05325	41.0	39.0	41.0	36.0	41.0
26	38.7265	40.0	38.0	41.0	34.0	41.0
27	38.81625	40.0	38.0	41.0	35.0	41.0
28	38.8745	40.0	38.0	41.0	35.0	41.0
29	38.5445	40.0	38.0	41.0	34.0	41.0
30	38.51925	40.0	38.0	41.0	34.0	41.0
31	38.693	40.0	38.0	41.0	34.0	41.0
32	38.6875	40.0	38.0	41.0	34.0	41.0
33	38.78875	40.0	38.0	41.0	35.0	41.0
34	38.80275	40.0	38.0	41.0	35.0	41.0
35	38.665	40.0	38.0	41.0	35.0	41.0
36	38.2365	40.0	38.0	41.0	34.0	41.0
37	37.90725	40.0	38.0	41.0	33.0	41.0
38	37.04325	40.0	37.0	41.0	30.0	41.0
39	37.552	40.0	37.0	41.0	32.0	41.0
40	37.84825	40.0	38.0	41.0	33.0	41.0
41	38.1535	40.0	38.0	41.0	33.0	41.0
42	38.3735	40.0	38.0	41.0	34.0	41.0
43	38.58775	40.0	38.0	41.0	35.0	41.0
44	38.3215	40.0	38.0	41.0	34.0	41.0
45	38.23325	40.0	38.0	41.0	34.0	41.0
46	38.07225	40.0	38.0	41.0	33.0	41.0
47	37.58325	40.0	37.0	41.0	32.0	41.0
48	37.13125	40.0	37.0	41.0	31.0	41.0
49	37.45325	40.0	37.0	41.0	32.0	41.0
50	36.9915	40.0	36.0	41.0	31.0	41.0
>>END_MODULE
>>Per tile sequence quality	pass
#Tile	Base	Mean
1101	1	0.0
1101	2	0.0
1101	3	0.0
1101	4	0.0
1101	5	0.0
1101	6	0.0
1101	7	0.0
1101	8	0.0
1101	9	0.0
1101	10	0.0
1101	11	0.0
1101	12	0.0
1101	13	0.0
1101	14	0.0
1101	15	0.0
1101	16	0.0
1101	17	0.0
1101	18	0.0
1101	19	0.0
1101	20	0.0
1101	21	0.0
1101	22	0.0
1101	23	0.0
1101	24	0.0
1101	25	0.0
1101	26	0.0
1101	27	0.0
1101	28	0.0
1101	29	0.0
1101	30	0.0
1101	31	0.0
1101	32	0.0
1101	33	0.0
1101	34	0.0
1101	35	0.0
1101	36	0.0
1101	37	0.0
1101	38	0.0
1101	39	0.0
1101	40	0.0
1101	41	0.0
1101	42	0.0
1101	43	0.0
1101	44	0.0
1101	45	0.0
1101	46	0.0
1101	47	0.0
1101	48	0.0
1101	49	0.0
1101	50	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
2	1.0
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	2.0
16	0.0
17	1.0
18	2.0
19	0.0
20	1.0
21	8.0
22	4.0
23	1.0
24	3.0
25	10.0
26	10.0
27	26.0
28	20.0
29	36.0
30	51.0
31	48.0
32	92.0
33	94.0
34	121.0
35	207.0
36	249.0
37	403.0
38	626.0
39	1984.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	6.550000000000001	22.2	59.12500000000001	12.125
2	23.635453179769655	26.965448172258387	21.907861792689033	27.491236855282924
3	16.725	19.15	18.5	45.625
4	25.900000000000002	37.625	13.0	23.474999999999998
5	21.525	38.45	29.275000000000002	10.75
6	37.15	13.3	37.85	11.700000000000001
7	12.725	25.874999999999996	24.625	36.775000000000006
8	24.725	41.475	13.4	20.4
9	18.7	41.075	29.425	10.8
10	17.65	20.775	27.925	33.650000000000006
11	32.125	9.925	14.075	43.875
12	14.374999999999998	14.774999999999999	25.174999999999997	45.675
13	19.25	22.225	39.475	19.05
14	39.375	24.175	24.099999999999998	12.35
15	41.05	21.325	27.575	10.05
16	11.924999999999999	28.1	21.075	38.9
17	25.7	23.425	39.425	11.450000000000001
18	29.025000000000002	19.425	27.425	24.125
19	39.525	13.350000000000001	30.675	16.45
20	52.625	15.049999999999999	22.875	9.45
21	19.725	25.275	25.624999999999996	29.375
22	32.5	10.6	50.4	6.5
23	24.45	12.025	52.175000000000004	11.35
24	53.025	13.05	28.775000000000002	5.1499999999999995
25	59.099999999999994	21.575	13.075000000000001	6.25
26	30.875000000000004	49.7	11.725	7.7
27	12.0	57.574999999999996	21.95	8.475000000000001
28	6.950000000000001	27.85	51.949999999999996	13.25
29	7.9	10.424999999999999	65.05	16.625
30	7.5	5.0	39.15	48.35
31	11.95	3.4250000000000003	48.525	36.1
32	24.05	3.5999999999999996	24.875	47.475
33	57.725	5.65	11.899999999999999	24.725
34	71.15	5.65	12.1	11.1
35	73.475	4.55	15.625	6.35
36	42.925000000000004	5.65	40.050000000000004	11.375
37	47.575	7.825	24.099999999999998	20.5
38	25.074999999999996	13.700000000000001	10.45	50.775000000000006
39	11.625	21.0	7.925	59.45
40	12.575	50.275000000000006	7.725	29.425
41	22.35	58.15	6.125	13.375
42	52.0	34.125	6.775	7.1
43	61.050000000000004	26.85	5.175	6.925000000000001
44	32.9	51.075	5.2749999999999995	10.75
45	15.15	58.3	10.65	15.9
46	9.125	28.825	15.299999999999999	46.75
47	6.550000000000001	11.875	41.225	40.35
48	7.425	10.45	23.474999999999998	58.650000000000006
49	11.675	16.25	10.8	61.275
50	16.575	40.325	10.25	32.85
>>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	0.5
22	1.0
23	0.5
24	0.0
25	0.0
26	0.0
27	1.0
28	2.0
29	1.0
30	0.0
31	5.5
32	11.0
33	7.5
34	4.0
35	10.5
36	17.0
37	23.5
38	30.0
39	25.5
40	21.0
41	28.5
42	36.0
43	83.5
44	131.0
45	187.5
46	244.0
47	461.0
48	678.0
49	614.5
50	551.0
51	796.5
52	1042.0
53	690.5
54	339.0
55	357.5
56	376.0
57	324.0
58	272.0
59	163.0
60	54.0
61	46.0
62	38.0
63	63.5
64	89.0
65	55.0
66	21.0
67	13.0
68	5.0
69	8.0
70	11.0
71	16.5
72	22.0
73	11.5
74	1.0
75	0.5
76	0.0
77	0.5
78	1.0
79	1.0
80	1.0
81	1.5
82	2.0
83	1.0
84	0.0
85	0.0
86	0.0
87	0.0
88	0.0
89	0.0
90	0.0
91	0.0
92	0.0
93	0.0
94	0.0
95	0.0
96	0.0
97	0.0
98	0.0
99	0.0
100	0.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
1	0.0
2	0.15
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	33.85
#Duplication Level	Percentage of deduplicated	Percentage of total
1	74.88921713441654	25.35
2	10.561299852289514	7.1499999999999995
3	3.766617429837518	3.8249999999999997
4	2.1418020679468244	2.9000000000000004
5	1.1078286558345642	1.875
6	1.329394387001477	2.7
7	0.8124076809453471	1.925
8	0.7385524372230428	2.0
9	0.29542097488921715	0.8999999999999999
>10	3.766617429837518	25.074999999999996
>50	0.29542097488921715	6.5
>100	0.29542097488921715	19.8
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	313	7.825	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	204	5.1	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	142	3.55	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	133	3.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	71	1.775	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	64	1.6	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	63	1.575	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	62	1.55	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	46	1.15	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	40	1.0	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	39	0.975	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	31	0.775	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	26	0.65	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	25	0.625	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	24	0.6	RNA PCR Primer, Index 1 (100% over 30bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	24	0.6	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCCTGTACTGAGCTGCCCCGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	23	0.575	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGG	22	0.5499999999999999	RNA PCR Primer, Index 2 (97% over 35bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	19	0.475	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	13	0.325	RNA PCR Primer, Index 1 (100% over 26bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	13	0.325	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	11	0.27499999999999997	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TCCTGTACTGAGCTGCCCCGATGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCCTGTACTGAGCTGCCCCGAGATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	10	0.25	RNA PCR Primer, Index 1 (100% over 33bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	10	0.25	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	9	0.22499999999999998	No Hit
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
CACCCGTAGAACCGACCTTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	8	0.2	No Hit
TGAGGTAGTAGGTTGTATGGTTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGC	8	0.2	RNA PCR Primer, Index 11 (100% over 50bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	6	0.15	No Hit
TCTTTGGTTATCTAGCTGTATGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
CTATACGACCTGCTGCCTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCAGAAGATTTCATGACCAATGAACACTCTGACCATGGAATTCTCGG	6	0.15	No Hit
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TAAGGCACGCGGTGAATGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
TGTAAACATCCCCGACTGGAAATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGTGGAATTCTCGGGTGC	6	0.15	No Hit
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTC	6	0.15	RNA PCR Primer, Index 11 (100% over 44bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
TGTAAACATCCCCGACTGGAAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	5	0.125	No Hit
TGAGGTAGTAGTTTGTGCTGTTATGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	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	0.2	0.0	0.0	0.0
2	0.0	0.2	0.0	0.0	0.0
3	0.0	0.25	0.0	0.0	0.0
4	0.0	0.25	0.0	0.0	0.0
5	0.0	0.275	0.0	0.0	0.0
6	0.0	0.325	0.0	0.0	0.0
7	0.0	0.575	0.0	0.0	0.0
8	0.0	0.7	0.0	0.0	0.0
9	0.0	0.725	0.0	0.0	0.0
10	0.0	0.875	0.0	0.0	0.0
11	0.0	0.975	0.0	0.0	0.0
12	0.0	1.25	0.0	0.0	0.0
13	0.0	1.55	0.0	0.0	0.0
14	0.0	1.675	0.0	0.0	0.0
15	0.0	2.1	0.0	0.0	0.0
16	0.0	2.95	0.0	0.0	0.0
17	0.0	3.325	0.0	0.0	0.0
18	0.0	3.875	0.0	0.0	0.0
19	0.0	4.225	0.0	0.0	0.0
20	0.0	5.175	0.0	0.0	0.0
21	0.0	10.775	0.0	0.0	0.0
22	0.0	21.45	0.0	0.0	0.0
23	0.0	56.8	0.0	0.0	0.0
24	0.0	75.55	0.0	0.0	0.0
25	0.0	81.425	0.0	0.0	0.0
26	0.0	82.375	0.0	0.0	0.0
27	0.0	82.85	0.0	0.0	0.0
28	0.0	83.225	0.0	0.0	0.0
29	0.0	83.6	0.0	0.0	0.0
30	0.0	83.95	0.0	0.0	0.0
31	0.0	84.9	0.0	0.0	0.0
32	0.0	85.85	0.0	0.0	0.0
33	0.0	87.025	0.0	0.0	0.0
34	0.0	89.175	0.0	0.0	0.0
35	0.0	90.175	0.0	0.0	0.0
36	0.0	90.7	0.0	0.0	0.0
37	0.0	91.225	0.0	0.0	0.0
38	0.0	91.625	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GAGGTAG	45	2.728484E-10	44.000004	2
GGTTGTA	20	6.952051E-4	44.000004	11
GGTGAGT	20	6.952051E-4	44.000004	17
AAGTAAT	45	2.728484E-10	44.000004	4
TCAAGTA	45	2.728484E-10	44.000004	2
AATCCAG	45	2.728484E-10	44.000004	8
ATCCAGG	45	2.728484E-10	44.000004	9
TTCAAGT	45	2.728484E-10	44.000004	1
AGGATAG	45	2.728484E-10	44.000004	13
TCCAGGA	45	2.728484E-10	44.000004	10
ACATCCT	20	6.952051E-4	44.000004	6
GGATAGG	45	2.728484E-10	44.000004	14
ATAGTTT	20	6.952051E-4	44.000004	17
AGTAATC	45	2.728484E-10	44.000004	5
CTGTGGA	20	6.952051E-4	44.000004	21
CGGTGAG	20	6.952051E-4	44.000004	16
TAATCCA	45	2.728484E-10	44.000004	7
GGTAGTA	45	2.728484E-10	44.000004	4
TGAGGTA	45	2.728484E-10	44.000004	1
AGGTAGT	45	2.728484E-10	44.000004	3
>>END_MODULE
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361677 spots for SRR5031039.sra
Written 361677 spots for SRR5031039.sra
Read 361685 spots for SRR5031039.sra
Written 361685 spots for SRR5031039.sra
SRR ids: ['SRR5031039.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_sdno9ohx
SRR5031039.sra spots: 4340132
blocks: [[1, 361677], [361678, 723354], [723355, 1085031], [1085032, 1446708], [1446709, 1808385], [1808386, 2170062], [2170063, 2531739], [2531740, 2893416], [2893417, 3255093], [3255094, 3616770], [3616771, 3978447], [3978448, 4340132]]
SRR5031039 file size 751181
SRR5031039 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031039 SRR5031039_1.fastq
Input file:	SRR5031039_1.fastq
trimmed:	SRR5031039-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- end quality threshold (-q):		10
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Sanger/Illumina 1.8+ FASTQ (auto detected)
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	12
Wed Mar  4 07:11:28 2020 >> started

Wed Mar  4 07:11:30 2020 >> done (2.295s)
4340132 reads processed; of these:
    211 ( 0.00%) short reads filtered out after trimming by size control
     14 ( 0.00%) empty reads filtered out after trimming by size control
4339907 (99.99%) reads available; of these:
 201044 ( 4.63%) trimmed reads available after processing
4138863 (95.37%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     83	  0.00%
 19	    104	  0.00%
 20	    174	  0.00%
 21	    265	  0.01%
 22	    459	  0.01%
 23	    510	  0.01%
 24	    478	  0.01%
 25	    691	  0.02%
 26	    510	  0.01%
 27	    829	  0.02%
 28	    879	  0.02%
 29	   1775	  0.04%
 30	    930	  0.02%
 31	   1006	  0.02%
 32	    995	  0.02%
 33	   1430	  0.03%
 34	   1811	  0.04%
 35	   3821	  0.09%
 36	   3278	  0.08%
 37	   3537	  0.08%
 38	   3119	  0.07%
 39	   3564	  0.08%
 40	   4074	  0.09%
 41	   3956	  0.09%
 42	   5391	  0.12%
 43	   7838	  0.18%
 44	  11366	  0.26%
 45	  15461	  0.36%
 46	  19804	  0.46%
 47	  26012	  0.60%
 48	  39680	  0.91%
 49	  37214	  0.86%
 50	4138863	 95.37%
4339907 reads passed initial QC


criterion=sequence-density
sequence-density=91.18
sequence-density-rank=1
fanout-score=18.19
fanout-score-rank=1
prefix-density=92.73
prefix-fanout=17.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC


criterion=fanout-score
sequence-density=91.18
sequence-density-rank=1
fanout-score=18.19
fanout-score-rank=1
prefix-density=92.73
prefix-fanout=17.9
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC -o SRR5031039 -
Input file:	STDIN
trimmed:	SRR5031039-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGCTACATCTCGTATGCC
-- maximum error ratio allowed (-r):	0.100
-- maximum indel error ratio allowed (-d):	0.030
-- minimum read length allowed after trimming (-l):	18
-- file format (-f):		Unknown format (auto detected)
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	12
Wed Mar  4 07:11:48 2020 >> started

Wed Mar  4 07:11:55 2020 >> done (6.558s)
4245561 reads processed; of these:
 147234 ( 3.47%) short reads filtered out after trimming by size control
  11539 ( 0.27%) empty reads filtered out after trimming by size control
4086788 (96.26%) reads available; of these:
3972193 (97.20%) trimmed reads available after processing
 114595 ( 2.80%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18735	  0.46%
 19	  43481	  1.06%
 20	 199322	  4.88%
 21	 492335	 12.05%
 22	1521090	 37.22%
 23	 762849	 18.67%
 24	 264537	  6.47%
 25	  43650	  1.07%
 26	  20827	  0.51%
 27	  21450	  0.52%
 28	  25014	  0.61%
 29	  19913	  0.49%
 30	  34317	  0.84%
 31	  45271	  1.11%
 32	  49604	  1.21%
 33	 109873	  2.69%
 34	  41765	  1.02%
 35	  25457	  0.62%
 36	  27600	  0.68%
 37	  15922	  0.39%
 38	  18833	  0.46%
 39	  15980	  0.39%
 40	  22121	  0.54%
 41	  29127	  0.71%
 42	  30126	  0.74%
 43	  21987	  0.54%
 44	  17897	  0.44%
 45	  21467	  0.53%
 46	  15246	  0.37%
 47	  12001	  0.29%
 48	   1109	  0.03%
 49	   1603	  0.04%
 50	  96279	  2.36%


criterion=sequence-density
sequence-density=3.99
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=TGTAAACATCCT


criterion=fanout-score
sequence-density=0.37
sequence-density-rank=33
fanout-score=16.29
fanout-score-rank=1
prefix-density=6.02
prefix-fanout=1.0
sequence=CTGAGCTTGGCATT
                                 Started job on |	Mar 04 07:12:17
                             Started mapping on |	Mar 04 07:12:18
                                    Finished on |	Mar 04 07:12:44
       Mapping speed, Million of reads per hour |	578.93

                          Number of input reads |	4181134
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1972363
                        Uniquely mapped reads % |	47.17%
                          Average mapped length |	23.81
                       Number of splices: Total |	2330
            Number of splices: Annotated (sjdb) |	233
                       Number of splices: GT/AG |	2155
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	1
               Number of splices: Non-canonical |	158
                      Mismatch rate per base, % |	0.14%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.67
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1805567
             % of reads mapped to multiple loci |	43.18%
        Number of reads mapped to too many loci |	78968
             % of reads mapped to too many loci |	1.89%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	7.23%
                     % of reads unmapped: other |	0.53%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	403204	403204	403204
N_multimapping	1805567	1805567	1805567
N_noFeature	75059	91888	1521439
N_ambiguous	1078935	695001	11714
UnstrandedReadsAssigned:818369 PositiveStrandReadsAssigned:1185474 NegativeStrandReadsAssigned:439210
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031039 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: SRR5031039-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 4,181,134 reads, 841,829 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,147 rounds

 109283 SRR5031039.ke.tsv
  52636 SRR5031039.se.tsv
 161919 total
==> SRR5031039.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

==> SRR5031039.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031039 completed mapping pipeline successfully
