Starting /dee2/code/volunteer_pipeline.sh SRR5031071
    current disk space = 284536639120
    free memory = 117675928 
SRR5031071 SRAfilesize
4c34ac1b60f6e5b89f5e802154c27133  SRR5031071.sra
SRR5031071.sra file validated
SRR5031071 is single end
SRR5031071 is conventional basespace
SRR5031071 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031071_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	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	32.383	33.0	31.0	34.0	31.0	34.0
2	32.58375	34.0	31.0	34.0	31.0	34.0
3	32.6925	34.0	31.0	34.0	31.0	34.0
4	36.20375	37.0	37.0	37.0	35.0	37.0
5	35.963	37.0	35.0	37.0	35.0	37.0
6	35.881	37.0	35.0	37.0	35.0	37.0
7	35.98	37.0	35.0	37.0	35.0	37.0
8	35.90325	37.0	35.0	37.0	35.0	37.0
9	37.588	39.0	37.0	39.0	35.0	39.0
10	37.795	39.0	37.0	39.0	35.0	39.0
11	37.7245	39.0	37.0	39.0	35.0	39.0
12	37.68525	39.0	37.0	39.0	35.0	39.0
13	37.64025	39.0	37.0	39.0	35.0	39.0
14	39.13425	41.0	38.0	41.0	36.0	41.0
15	39.07875	40.0	38.0	41.0	36.0	41.0
16	39.0335	40.0	38.0	41.0	36.0	41.0
17	38.93675	40.0	38.0	41.0	35.0	41.0
18	39.08925	40.0	38.0	41.0	36.0	41.0
19	38.8265	40.0	38.0	41.0	35.0	41.0
20	38.86475	40.0	38.0	41.0	35.0	41.0
21	38.7905	40.0	38.0	41.0	34.0	41.0
22	39.108	40.0	39.0	41.0	36.0	41.0
23	38.8155	40.0	38.0	41.0	35.0	41.0
24	38.8135	40.0	38.0	41.0	35.0	41.0
25	39.0725	41.0	39.0	41.0	35.0	41.0
26	38.7535	40.0	38.0	41.0	35.0	41.0
27	38.75875	40.0	38.0	41.0	35.0	41.0
28	38.683	40.0	38.0	41.0	35.0	41.0
29	38.271	40.0	38.0	41.0	33.0	41.0
30	38.0595	40.0	38.0	41.0	33.0	41.0
31	38.3525	40.0	38.0	41.0	34.0	41.0
32	38.3385	40.0	38.0	41.0	34.0	41.0
33	38.078	40.0	38.0	41.0	33.0	41.0
34	38.08025	40.0	38.0	41.0	33.0	41.0
35	38.1235	40.0	38.0	41.0	34.0	41.0
36	37.94275	40.0	38.0	41.0	34.0	41.0
37	37.45875	40.0	37.0	41.0	31.0	41.0
38	36.77675	39.0	36.0	41.0	30.0	41.0
39	37.20325	39.0	37.0	41.0	31.0	41.0
40	37.43375	39.0	37.0	41.0	32.0	41.0
41	37.746	40.0	37.0	41.0	33.0	41.0
42	37.988	40.0	38.0	41.0	33.0	41.0
43	38.24275	40.0	38.0	41.0	34.0	41.0
44	38.024	40.0	38.0	41.0	33.0	41.0
45	37.87425	40.0	37.0	41.0	33.0	41.0
46	37.64975	40.0	37.0	41.0	33.0	41.0
47	36.9865	40.0	36.0	41.0	31.0	41.0
48	36.6505	39.0	36.0	41.0	30.0	41.0
49	36.9015	40.0	36.0	41.0	31.0	41.0
50	36.391	39.0	35.0	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
14	2.0
15	1.0
16	1.0
17	1.0
18	1.0
19	4.0
20	3.0
21	5.0
22	6.0
23	4.0
24	11.0
25	6.0
26	12.0
27	16.0
28	25.0
29	40.0
30	43.0
31	57.0
32	90.0
33	99.0
34	152.0
35	203.0
36	262.0
37	442.0
38	787.0
39	1727.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	9.775	26.575	46.400000000000006	17.25
2	25.269221136989735	27.773603806661658	17.731029301277236	29.226145755071375
3	25.124999999999996	18.099999999999998	21.45	35.325
4	33.95	28.849999999999998	14.299999999999999	22.900000000000002
5	23.325000000000003	38.625	25.900000000000002	12.15
6	32.35	13.200000000000001	36.0	18.45
7	14.774999999999999	23.325000000000003	21.6	40.300000000000004
8	23.375	28.625	17.175	30.825000000000003
9	22.650000000000002	32.2	28.325	16.825000000000003
10	21.175	22.95	27.800000000000004	28.075
11	34.625	11.1	16.05	38.224999999999994
12	17.474999999999998	17.599999999999998	32.05	32.875
13	29.275000000000002	18.175	33.95	18.6
14	30.45	31.35	19.625	18.575
15	35.825	26.575	24.349999999999998	13.25
16	20.474999999999998	18.6	23.549999999999997	37.375
17	26.474999999999998	23.7	35.949999999999996	13.875000000000002
18	24.825	19.575	29.225	26.375
19	39.074999999999996	14.6	27.425	18.9
20	45.425	14.95	26.85	12.775
21	25.124999999999996	21.15	25.275	28.449999999999996
22	30.075000000000003	12.7	46.550000000000004	10.674999999999999
23	25.75	12.425	43.675000000000004	18.15
24	53.125	13.55	25.025	8.3
25	48.575	25.5	15.375	10.549999999999999
26	26.825	46.300000000000004	14.025000000000002	12.85
27	15.174999999999999	46.25	23.175	15.4
28	11.375	24.55	47.625	16.45
29	14.6	13.475000000000001	54.6	17.325
30	10.85	7.35	35.025	46.775
31	13.5	6.125	48.525	31.85
32	28.299999999999997	6.5	21.3	43.9
33	52.849999999999994	11.4	13.8	21.95
34	58.5	8.125	17.525	15.85
35	64.1	7.249999999999999	18.375	10.274999999999999
36	41.925000000000004	7.5249999999999995	37.05	13.5
37	45.824999999999996	12.425	19.2	22.55
38	24.15	17.2	11.95	46.7
39	16.1	22.875	11.75	49.275000000000006
40	15.35	47.375	13.8	23.474999999999998
41	22.95	47.975	10.274999999999999	18.8
42	47.725	27.575	13.575000000000001	11.125
43	50.575	28.225	9.475	11.725
44	32.35	47.699999999999996	7.124999999999999	12.825000000000001
45	20.474999999999998	49.225	12.075	18.224999999999998
46	15.325	25.924999999999997	17.299999999999997	41.449999999999996
47	10.325	15.975	40.325	33.375
48	12.475	12.475	19.85	55.2
49	12.5	18.75	15.55	53.2
50	16.900000000000002	37.875	12.875	32.35
>>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	0.0
14	0.0
15	0.5
16	1.0
17	1.0
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.5
26	1.0
27	1.0
28	1.0
29	3.0
30	5.0
31	13.0
32	21.0
33	17.0
34	13.0
35	16.0
36	19.0
37	24.5
38	30.0
39	37.5
40	45.0
41	47.5
42	50.0
43	75.0
44	100.0
45	135.5
46	171.0
47	299.5
48	428.0
49	513.0
50	598.0
51	709.0
52	820.0
53	667.0
54	514.0
55	506.0
56	498.0
57	379.5
58	261.0
59	166.0
60	71.0
61	61.5
62	52.0
63	112.5
64	173.0
65	98.0
66	23.0
67	17.5
68	12.0
69	16.0
70	20.0
71	37.0
72	54.0
73	29.0
74	4.0
75	4.5
76	5.0
77	2.5
78	0.0
79	3.0
80	6.0
81	4.0
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	0.17500000000000002
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	37.375
#Duplication Level	Percentage of deduplicated	Percentage of total
1	76.18729096989966	28.475
2	9.364548494983277	7.000000000000001
3	5.016722408026756	5.625
4	1.7391304347826086	2.6
5	1.5384615384615385	2.875
6	0.5351170568561873	1.2
7	1.0702341137123745	2.8000000000000003
8	0.46822742474916385	1.4000000000000001
9	0.6020066889632106	2.025
>10	2.94314381270903	23.0
>50	0.13377926421404682	3.325
>100	0.4013377926421404	19.675
>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
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	164	4.1000000000000005	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	140	3.5000000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	135	3.375	No Hit
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	124	3.1	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	114	2.85	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	110	2.75	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	80	2.0	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	53	1.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	48	1.2	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	40	1.0	RNA PCR Primer, Index 1 (100% over 28bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	38	0.95	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	32	0.8	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTA	31	0.775	RNA PCR Primer, Index 7 (97% over 35bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	29	0.7250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	27	0.675	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26	0.65	RNA PCR Primer, Index 1 (100% over 26bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTC	25	0.625	RNA PCR Primer, Index 43 (100% over 44bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGC	25	0.625	RNA PCR Primer, Index 43 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	24	0.6	No Hit
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	24	0.6	RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	21	0.525	No Hit
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	19	0.475	No Hit
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	16	0.4	No Hit
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	10	0.25	No Hit
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
ACAAATGATGAACCTTTTGACGGGCGGACAGAAACTCTGTGCTGAATGTC	9	0.22499999999999998	No Hit
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	9	0.22499999999999998	No Hit
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACT	9	0.22499999999999998	RNA PCR Primer, Index 3 (100% over 34bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	9	0.22499999999999998	No Hit
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	8	0.2	No Hit
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGG	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
TCCTGTACTGAGCTGCCCCGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
TATTGCACTCGTCCCGGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	6	0.15	RNA PCR Primer, Index 1 (100% over 30bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CAACGGAATCCCAAAAGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TATGCAAGGGCAAGCTCTCTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAAT	5	0.125	No Hit
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGAAATCAAA	5	0.125	No Hit
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	5	0.125	No Hit
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGTGGAATTCTCGGGTGCC	5	0.125	No Hit
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	5	0.125	No Hit
TTACTTGATGATAGTAAAAGATCTGATGTGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	5	0.125	No Hit
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	5	0.125	No Hit
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTACATTGTCTGCTGGGTTTCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAAGGCACGCGGTGAATGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGGTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCAACCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
>>END_MODULE
>>Adapter Content	fail
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.7	0.0	0.0	0.0
2	0.0	0.7	0.0	0.0	0.0
3	0.0	0.775	0.0	0.0	0.0
4	0.0	0.825	0.0	0.0	0.0
5	0.0	0.875	0.0	0.0	0.0
6	0.0	0.925	0.0	0.0	0.0
7	0.0	1.7	0.0	0.0	0.0
8	0.0	1.975	0.0	0.0	0.0
9	0.0	2.0	0.0	0.0	0.0
10	0.0	2.15	0.0	0.0	0.0
11	0.0	2.375	0.0	0.0	0.0
12	0.0	2.675	0.0	0.0	0.0
13	0.0	2.825	0.0	0.0	0.0
14	0.0	3.075	0.0	0.0	0.0
15	0.0	3.4	0.0	0.0	0.0
16	0.0	4.575	0.0	0.0	0.0
17	0.0	5.175	0.0	0.0	0.0
18	0.0	6.25	0.0	0.0	0.0
19	0.0	6.725	0.0	0.0	0.0
20	0.0	7.4	0.0	0.0	0.0
21	0.0	12.225	0.0	0.0	0.0
22	0.0	22.825	0.0	0.0	0.0
23	0.0	52.45	0.0	0.0	0.0
24	0.0	64.35	0.0	0.0	0.0
25	0.0	70.575	0.0	0.0	0.0
26	0.0	72.025	0.0	0.0	0.0
27	0.0	73.0	0.0	0.0	0.0
28	0.0	73.6	0.0	0.0	0.0
29	0.0	74.55	0.0	0.0	0.0
30	0.0	75.075	0.0	0.0	0.0
31	0.0	75.725	0.0	0.0	0.0
32	0.0	76.7	0.0	0.0	0.0
33	0.0	77.775	0.0	0.0	0.0
34	0.0	82.1	0.0	0.0	0.0
35	0.0	83.275	0.0	0.0	0.0
36	0.0	84.175	0.0	0.0	0.0
37	0.0	85.1	0.0	0.0	0.0
38	0.0	85.675	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
ACTGTTG	20	6.952051E-4	44.000004	18
ACAGTGA	20	6.952051E-4	44.000004	3
ACCGGTC	20	6.952051E-4	44.000004	10
GAGGTAG	20	6.952051E-4	44.000004	2
GTTGAAG	20	6.952051E-4	44.000004	10
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
AACCGGT	20	6.952051E-4	44.000004	9
AATCCAG	20	6.952051E-4	44.000004	8
CAGTTGA	20	6.952051E-4	44.000004	8
ATCCAGG	20	6.952051E-4	44.000004	9
CCAGTTG	20	6.952051E-4	44.000004	7
AACTGTT	20	6.952051E-4	44.000004	17
TTCAAGT	20	6.952051E-4	44.000004	1
TTCAACG	40	5.315087E-9	44.000004	5
AGGATAG	20	6.952051E-4	44.000004	13
TCGGTGA	40	5.315087E-9	44.000004	15
ATAGGCT	20	6.952051E-4	44.000004	16
CATTCAA	40	5.315087E-9	44.000004	3
GAAGAAC	20	6.952051E-4	44.000004	13
>>END_MODULE
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153854 spots for SRR5031071.sra
Written 153854 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
Read 153853 spots for SRR5031071.sra
Written 153853 spots for SRR5031071.sra
SRR ids: ['SRR5031071.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_olp4jcsu
SRR5031071.sra spots: 3692473
blocks: [[1, 153853], [153854, 307706], [307707, 461559], [461560, 615412], [615413, 769265], [769266, 923118], [923119, 1076971], [1076972, 1230824], [1230825, 1384677], [1384678, 1538530], [1538531, 1692383], [1692384, 1846236], [1846237, 2000089], [2000090, 2153942], [2153943, 2307795], [2307796, 2461648], [2461649, 2615501], [2615502, 2769354], [2769355, 2923207], [2923208, 3077060], [3077061, 3230913], [3230914, 3384766], [3384767, 3538619], [3538620, 3692473]]
SRR5031071 file size 634884
SRR5031071 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 24 -o SRR5031071 SRR5031071_1.fastq
Input file:	SRR5031071_1.fastq
trimmed:	SRR5031071-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):	24
Fri Jan 10 00:55:02 2020 >> started

Fri Jan 10 00:55:04 2020 >> done (1.714s)
3692473 reads processed; of these:
    259 ( 0.01%) short reads filtered out after trimming by size control
      5 ( 0.00%) empty reads filtered out after trimming by size control
3692209 (99.99%) reads available; of these:
 183242 ( 4.96%) trimmed reads available after processing
3508967 (95.04%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     79	  0.00%
 19	    112	  0.00%
 20	    232	  0.01%
 21	    272	  0.01%
 22	    528	  0.01%
 23	    614	  0.02%
 24	    640	  0.02%
 25	    887	  0.02%
 26	    678	  0.02%
 27	    838	  0.02%
 28	    981	  0.03%
 29	   1736	  0.05%
 30	   1013	  0.03%
 31	   1166	  0.03%
 32	   1343	  0.04%
 33	   1496	  0.04%
 34	   1528	  0.04%
 35	   3214	  0.09%
 36	   2913	  0.08%
 37	   3120	  0.08%
 38	   3160	  0.09%
 39	   3326	  0.09%
 40	   3759	  0.10%
 41	   3638	  0.10%
 42	   5116	  0.14%
 43	   8034	  0.22%
 44	  11198	  0.30%
 45	  13967	  0.38%
 46	  18978	  0.51%
 47	  22799	  0.62%
 48	  31770	  0.86%
 49	  34107	  0.92%
 50	3508967	 95.04%
3692209 reads passed initial QC


criterion=sequence-density
sequence-density=85.78
sequence-density-rank=1
fanout-score=20.20
fanout-score-rank=1
prefix-density=87.95
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=85.78
sequence-density-rank=1
fanout-score=20.20
fanout-score-rank=1
prefix-density=87.95
prefix-fanout=19.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC
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 24 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC -o SRR5031071 -
Input file:	STDIN
trimmed:	SRR5031071-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTACAGCATCTCGTATGCC
-- 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):	24
Fri Jan 10 00:55:22 2020 >> started

Fri Jan 10 00:55:25 2020 >> done (3.029s)
3606344 reads processed; of these:
 211000 ( 5.85%) short reads filtered out after trimming by size control
  19949 ( 0.55%) empty reads filtered out after trimming by size control
3375395 (93.60%) reads available; of these:
3207200 (95.02%) trimmed reads available after processing
 168195 ( 4.98%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  18111	  0.54%
 19	  35277	  1.05%
 20	 177538	  5.26%
 21	 378594	 11.22%
 22	1064590	 31.54%
 23	 478025	 14.16%
 24	 207847	  6.16%
 25	  58416	  1.73%
 26	  29857	  0.88%
 27	  25053	  0.74%
 28	  27575	  0.82%
 29	  21150	  0.63%
 30	  32947	  0.98%
 31	  36801	  1.09%
 32	  43008	  1.27%
 33	 165255	  4.90%
 34	  45527	  1.35%
 35	  33563	  0.99%
 36	  38261	  1.13%
 37	  20329	  0.60%
 38	  21454	  0.64%
 39	  21066	  0.62%
 40	  31776	  0.94%
 41	  40435	  1.20%
 42	  45357	  1.34%
 43	  30996	  0.92%
 44	  23767	  0.70%
 45	  32039	  0.95%
 46	  24240	  0.72%
 47	  18873	  0.56%
 48	   1514	  0.04%
 49	   2284	  0.07%
 50	 143870	  4.26%


criterion=sequence-density
sequence-density=7.41
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=16
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.64
sequence-density-rank=20
fanout-score=13.13
fanout-score-rank=1
prefix-density=8.36
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Jan 10 00:55:47
                             Started mapping on |	Jan 10 00:55:48
                                    Finished on |	Jan 10 00:56:12
       Mapping speed, Million of reads per hour |	519.19

                          Number of input reads |	3461260
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1786426
                        Uniquely mapped reads % |	51.61%
                          Average mapped length |	24.87
                       Number of splices: Total |	2186
            Number of splices: Annotated (sjdb) |	311
                       Number of splices: GT/AG |	2071
                       Number of splices: GC/AG |	29
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	86
                      Mismatch rate per base, % |	0.20%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.84
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1154946
             % of reads mapped to multiple loci |	33.37%
        Number of reads mapped to too many loci |	84086
             % of reads mapped to too many loci |	2.43%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	11.96%
                     % of reads unmapped: other |	0.63%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	519888	519888	519888
N_multimapping	1154946	1154946	1154946
N_noFeature	83921	107370	1212659
N_ambiguous	1012843	522696	17833
UnstrandedReadsAssigned:689662 PositiveStrandReadsAssigned:1156360 NegativeStrandReadsAssigned:555934
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031071 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: SRR5031071-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 3,461,260 reads, 887,051 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 873 rounds

 109283 SRR5031071.ke.tsv
  52636 SRR5031071.se.tsv
 161919 total
==> SRR5031071.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

==> SRR5031071.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	3
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031071 completed mapping pipeline successfully
