Starting /dee2/code/volunteer_pipeline.sh SRR5031078
    current disk space = 160484163584
    free memory = 73933684 
SRR5031078 SRAfilesize
a314475c10c88b1f77daa143d4c4af4e  SRR5031078.sra
SRR5031078.sra file validated
SRR5031078 is single end
SRR5031078 is conventional basespace
SRR5031078 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031078_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	53
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.96325	31.0	31.0	34.0	30.0	34.0
2	32.4465	33.0	31.0	34.0	31.0	34.0
3	32.44925	34.0	31.0	34.0	31.0	34.0
4	36.129	37.0	35.0	37.0	35.0	37.0
5	36.1255	37.0	35.0	37.0	35.0	37.0
6	36.09625	37.0	35.0	37.0	35.0	37.0
7	35.86925	37.0	35.0	37.0	35.0	37.0
8	35.646	37.0	35.0	37.0	33.0	37.0
9	36.889	39.0	37.0	39.0	33.0	39.0
10	36.6165	39.0	37.0	39.0	32.0	39.0
11	37.4905	39.0	37.0	39.0	34.0	39.0
12	37.7225	39.0	37.0	39.0	35.0	39.0
13	37.48225	39.0	37.0	39.0	35.0	39.0
14	38.316	40.0	38.0	41.0	33.0	41.0
15	37.077	39.0	36.0	41.0	31.0	41.0
16	36.692	39.0	36.0	40.0	31.0	41.0
17	36.7675	39.0	36.0	40.0	31.0	41.0
18	38.16725	40.0	37.0	41.0	34.0	41.0
19	38.8075	40.0	38.0	41.0	36.0	41.0
20	38.36775	40.0	38.0	41.0	34.0	41.0
21	38.645	40.0	38.0	41.0	35.0	41.0
22	37.46725	39.0	37.0	41.0	32.0	41.0
23	37.883	39.0	37.0	40.0	33.0	41.0
24	37.167	39.0	37.0	40.0	31.0	41.0
25	38.114	40.0	37.0	41.0	33.0	41.0
26	37.9615	40.0	37.0	41.0	33.0	41.0
27	38.07475	40.0	38.0	41.0	34.0	41.0
28	38.327	40.0	38.0	41.0	34.0	41.0
29	38.32725	40.0	38.0	41.0	34.0	41.0
30	38.717	40.0	38.0	41.0	34.0	41.0
31	38.7795	40.0	38.0	41.0	35.0	41.0
32	38.867	40.0	38.0	41.0	35.0	41.0
33	38.85	40.0	39.0	41.0	35.0	41.0
34	38.22575	40.0	38.0	41.0	33.0	41.0
35	37.3935	40.0	37.0	41.0	30.0	41.0
36	32.9765	35.0	30.0	40.0	23.0	41.0
37	34.91175	37.0	33.0	39.0	30.0	40.0
38	36.2195	38.0	35.0	39.0	30.0	40.0
39	36.63075	38.0	36.0	40.0	31.0	40.0
40	36.975	39.0	37.0	40.0	32.0	41.0
41	37.4605	39.0	37.0	40.0	33.0	41.0
42	37.29425	40.0	37.0	40.0	32.0	41.0
43	37.429	40.0	37.0	40.0	33.0	41.0
44	36.471	39.0	36.0	40.0	30.0	41.0
45	36.71925	39.0	36.0	40.0	31.0	41.0
46	36.75775	39.0	36.0	40.0	31.0	41.0
47	35.812	38.0	34.0	40.0	28.0	41.0
48	36.78875	39.0	36.0	40.0	31.0	41.0
49	36.97275	39.0	37.0	41.0	32.0	41.0
50	35.159	38.0	34.0	40.0	28.0	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
14	2.0
15	1.0
16	2.0
17	0.0
18	3.0
19	1.0
20	3.0
21	7.0
22	6.0
23	14.0
24	4.0
25	11.0
26	11.0
27	17.0
28	21.0
29	32.0
30	39.0
31	72.0
32	91.0
33	129.0
34	177.0
35	284.0
36	482.0
37	772.0
38	1224.0
39	595.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	7.476869217304325	25.30632658164541	51.36284071017755	15.853963490872719
2	22.511255627813906	26.713356678339167	16.65832916458229	34.11705852926463
3	27.750000000000004	18.05	19.75	34.449999999999996
4	35.199999999999996	27.250000000000004	12.4	25.15
5	22.375	37.824999999999996	28.575	11.225
6	33.074999999999996	12.575	38.525	15.825
7	12.75	24.075	21.8	41.375
8	26.125	27.450000000000003	14.424999999999999	32.0
9	25.275	33.675	26.375	14.674999999999999
10	21.099999999999998	20.225	29.5	29.175
11	32.225	8.825	16.975	41.975
12	16.425	14.625	33.050000000000004	35.9
13	32.65	14.325	34.9	18.125
14	28.725	32.9	19.85	18.525
15	38.15	19.225	27.575	15.049999999999999
16	18.3	18.5	22.075	41.125
17	27.1	18.95	38.375	15.575
18	25.0	16.45	33.4	25.15
19	41.0	13.900000000000002	27.35	17.75
20	49.575	12.25	25.45	12.725
21	23.474999999999998	19.875	27.725	28.925
22	28.349999999999998	10.775	49.8	11.075
23	26.724999999999998	12.575	47.025	13.675
24	52.625	11.700000000000001	27.200000000000003	8.475000000000001
25	51.55	24.85	13.825000000000001	9.775
26	28.425	47.65	14.025000000000002	9.9
27	15.775	48.8	24.175	11.25
28	12.0	24.525	49.675000000000004	13.8
29	11.525	11.0	58.35	19.125
30	10.424999999999999	6.275	37.325	45.975
31	13.375	4.5	47.375	34.75
32	28.425	5.1499999999999995	21.575	44.85
33	55.574999999999996	8.875	11.75	23.799999999999997
34	64.3	7.475	14.2	14.025000000000002
35	67.30000000000001	7.049999999999999	17.675	7.9750000000000005
36	45.25	7.375	34.849999999999994	12.525
37	46.325	10.525	19.900000000000002	23.25
38	24.275	16.45	10.05	49.225
39	13.600000000000001	25.025	8.774999999999999	52.6
40	13.775	50.275000000000006	9.625	26.325
41	24.474999999999998	50.849999999999994	7.35	17.325
42	49.6	30.575000000000003	9.35	10.475
43	52.075	30.7	6.9	10.325
44	30.425	50.324999999999996	5.55	13.700000000000001
45	16.55	51.625	13.200000000000001	18.625
46	11.3	25.775	18.475	44.45
47	7.875	14.75	39.300000000000004	38.074999999999996
48	8.799999999999999	12.325	20.625	58.25
49	12.025	19.875	11.175	56.925000000000004
50	19.5	37.375	11.975	31.15
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	0.0
1	0.0
2	0.0
3	0.0
4	0.0
5	0.0
6	0.0
7	0.0
8	0.0
9	0.0
10	0.0
11	0.0
12	0.0
13	0.0
14	0.0
15	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.0
24	0.0
25	0.0
26	0.0
27	0.0
28	0.0
29	1.0
30	2.0
31	4.5
32	7.0
33	8.5
34	10.0
35	11.0
36	12.0
37	16.0
38	20.0
39	24.0
40	28.0
41	29.0
42	30.0
43	46.0
44	62.0
45	94.5
46	127.0
47	248.5
48	370.0
49	439.0
50	508.0
51	706.0
52	904.0
53	723.5
54	543.0
55	566.5
56	590.0
57	499.0
58	408.0
59	267.0
60	126.0
61	88.0
62	50.0
63	69.0
64	88.0
65	67.5
66	47.0
67	32.5
68	18.0
69	15.5
70	13.0
71	21.0
72	29.0
73	16.5
74	4.0
75	3.0
76	2.0
77	1.0
78	0.0
79	1.0
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	0.025
2	0.05
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	40.949999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	77.47252747252747	31.724999999999998
2	10.317460317460316	8.450000000000001
3	3.5409035409035408	4.35
4	2.0757020757020754	3.4000000000000004
5	1.465201465201465	3.0
6	0.6715506715506716	1.6500000000000001
7	0.2442002442002442	0.7000000000000001
8	0.5494505494505495	1.7999999999999998
9	0.6715506715506716	2.475
>10	2.380952380952381	18.6
>50	0.3663003663003663	10.825
>100	0.2442002442002442	13.025
>500	0.0	0.0
>1k	0.0	0.0
>5k	0.0	0.0
>10k+	0.0	0.0
>>END_MODULE
>>Overrepresented sequences	fail
#Sequence	Count	Percentage	Possible Source
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	150	3.75	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	128	3.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	123	3.075	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	120	3.0	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	99	2.475	RNA PCR Primer, Index 1 (100% over 30bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	98	2.45	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	68	1.7000000000000002	RNA PCR Primer, Index 2 (100% over 35bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62	1.55	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	53	1.325	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	53	1.325	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	45	1.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	38	0.95	RNA PCR Primer, Index 1 (100% over 33bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	37	0.9249999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	36	0.8999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	30	0.75	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	27	0.675	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	24	0.6	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	21	0.525	RNA PCR Primer, Index 1 (100% over 28bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	19	0.475	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTC	18	0.44999999999999996	RNA PCR Primer, Index 2 (100% over 44bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 27bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (96% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGC	15	0.375	RNA PCR Primer, Index 2 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGTGGCATTCTCGGGTGCCAAGGAACTCCAGT	15	0.375	RNA PCR Primer, Index 1 (96% over 30bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGACGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	12	0.3	RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGTTGAAGCACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	10	0.25	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGGGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (96% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AAGCTGCCAGTTGAAGACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	8	0.2	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGCCGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	8	0.2	No Hit
TGTAAACATCCTCGCCTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	8	0.2	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 25bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCCGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	7	0.17500000000000002	No Hit
CTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
GTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGA	6	0.15	RNA PCR Primer, Index 2 (100% over 36bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTCGTCCCGGCCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTACCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTAT	6	0.15	RNA PCR Primer, Index 2 (100% over 48bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGGGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (96% over 28bp)
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	5	0.125	No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TCCCTGAGACCCTTTAACCTGTGCTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
ATCGGATCCGTCTGAGCTTGGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CAAAGAATTCTCCTTTTGGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCG	5	0.125	RNA PCR Primer, Index 2 (100% over 45bp)
AACCCGTAGATCCGATCTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGCAGCATTGTACAGGGCTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTCTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	5	0.125	No Hit
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGA	5	0.125	RNA PCR Primer, Index 2 (100% over 36bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATG	5	0.125	RNA PCR Primer, Index 2 (100% over 38bp)
>>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	0.525	0.0	0.0	0.0
2	0.0	0.525	0.0	0.0	0.0
3	0.0	0.725	0.0	0.0	0.0
4	0.0	0.825	0.0	0.0	0.0
5	0.0	0.975	0.0	0.0	0.0
6	0.0	1.15	0.0	0.0	0.0
7	0.0	1.925	0.0	0.0	0.0
8	0.0	2.275	0.0	0.0	0.0
9	0.0	2.35	0.0	0.0	0.0
10	0.0	2.65	0.0	0.0	0.0
11	0.0	2.875	0.0	0.0	0.0
12	0.0	3.15	0.0	0.0	0.0
13	0.0	3.55	0.0	0.0	0.0
14	0.0	3.75	0.0	0.0	0.0
15	0.0	4.275	0.0	0.0	0.0
16	0.0	6.425	0.0	0.0	0.0
17	0.0	7.45	0.0	0.0	0.0
18	0.0	9.1	0.0	0.0	0.0
19	0.0	9.65	0.0	0.0	0.0
20	0.0	10.475	0.0	0.0	0.0
21	0.0	15.25	0.0	0.0	0.0
22	0.0	27.575	0.0	0.0	0.0
23	0.0	58.75	0.0	0.0	0.0
24	0.0	72.875	0.0	0.0	0.0
25	0.0	78.175	0.0	0.0	0.0
26	0.0	79.925	0.0	0.0	0.0
27	0.0	80.675	0.0	0.0	0.0
28	0.0	81.15	0.0	0.0	0.0
29	0.0	81.75	0.0	0.0	0.0
30	0.0	82.125	0.0	0.0	0.0
31	0.0	82.725	0.0	0.0	0.0
32	0.0	83.575	0.0	0.0	0.0
33	0.0	84.3	0.0	0.0	0.0
34	0.0	86.85	0.0	0.0	0.0
35	0.0	87.75	0.0	0.0	0.0
36	0.0	88.3	0.0	0.0	0.0
37	0.0	89.125	0.0	0.0	0.0
38	0.0	89.5	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTGAGCT	80	0.0	44.000004	11
ACTTGTG	20	6.952051E-4	44.000004	15
AGGATAG	20	6.952051E-4	44.000004	13
CCTAACT	20	6.952051E-4	44.000004	11
ATAGGCT	20	6.952051E-4	44.000004	16
GAGCTTG	80	0.0	44.000004	13
CCGTCTG	80	0.0	44.000004	7
GGATAGG	20	6.952051E-4	44.000004	14
AACTTGT	20	6.952051E-4	44.000004	14
TAACTTG	20	6.952051E-4	44.000004	13
CTAACTT	20	6.952051E-4	44.000004	12
AGGCTTG	20	6.952051E-4	44.000004	18
GGCTTGG	40	5.315087E-9	44.000004	19
ACCCTAA	20	6.952051E-4	44.000004	9
CTTGTGA	20	6.952051E-4	44.000004	16
TCCGTCT	80	0.0	44.000004	6
ATCCGTC	80	0.0	44.000004	5
CAGGATA	20	6.952051E-4	44.000004	12
TGAGCTT	80	0.0	44.000004	12
CCCTAAC	20	6.952051E-4	44.000004	10
>>END_MODULE
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
Read 163994 spots for SRR5031078.sra
Written 163994 spots for SRR5031078.sra
Read 163992 spots for SRR5031078.sra
Written 163992 spots for SRR5031078.sra
SRR ids: ['SRR5031078.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_xnmreq78
SRR5031078.sra spots: 1967906
blocks: [[1, 163992], [163993, 327984], [327985, 491976], [491977, 655968], [655969, 819960], [819961, 983952], [983953, 1147944], [1147945, 1311936], [1311937, 1475928], [1475929, 1639920], [1639921, 1803912], [1803913, 1967906]]
SRR5031078 file size 340013
SRR5031078 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031078 SRR5031078_1.fastq
Input file:	SRR5031078_1.fastq
trimmed:	SRR5031078-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 07:19:39 2020 >> started

Wed Mar  4 07:19:40 2020 >> done (1.422s)
1967906 reads processed; of these:
    122 ( 0.01%) short reads filtered out after trimming by size control
      4 ( 0.00%) empty reads filtered out after trimming by size control
1967780 (99.99%) reads available; of these:
 159930 ( 8.13%) trimmed reads available after processing
1807850 (91.87%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     47	  0.00%
 19	     78	  0.00%
 20	    108	  0.01%
 21	    161	  0.01%
 22	    325	  0.02%
 23	    324	  0.02%
 24	    349	  0.02%
 25	    497	  0.03%
 26	    354	  0.02%
 27	    431	  0.02%
 28	    509	  0.03%
 29	    777	  0.04%
 30	    537	  0.03%
 31	    603	  0.03%
 32	    828	  0.04%
 33	   1676	  0.09%
 34	   2121	  0.11%
 35	   6117	  0.31%
 36	   3323	  0.17%
 37	   3175	  0.16%
 38	   3035	  0.15%
 39	   3188	  0.16%
 40	   3482	  0.18%
 41	   4140	  0.21%
 42	   4789	  0.24%
 43	   7228	  0.37%
 44	   8102	  0.41%
 45	  10888	  0.55%
 46	  14818	  0.75%
 47	  12271	  0.62%
 48	  34072	  1.73%
 49	  31577	  1.60%
 50	1807850	 91.87%
1967780 reads passed initial QC


criterion=sequence-density
sequence-density=89.37
sequence-density-rank=1
fanout-score=18.91
fanout-score-rank=2
prefix-density=90.46
prefix-fanout=18.7
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC


criterion=fanout-score
sequence-density=3.73
sequence-density-rank=3
fanout-score=72.06
fanout-score-rank=1
prefix-density=90.35
prefix-fanout=3.0
sequence=GAATTCTCGGGGGCCAAGGAACT
Potential 3prime adapter identified. Now checking if in reference sequence
Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192.
1 reads; of these:
  1 (100.00%) were unpaired; of these:
    1 (100.00%) aligned 0 times
    0 (0.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
0.00% overall alignment rate
Adapter seq not found in reference. Now shuffling file before clipping
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -t 12 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC -o SRR5031078 -
Input file:	STDIN
trimmed:	SRR5031078-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC
-- 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 07:19:54 2020 >> started

Wed Mar  4 07:19:57 2020 >> done (3.159s)
1924052 reads processed; of these:
 138766 ( 7.21%) short reads filtered out after trimming by size control
  13713 ( 0.71%) empty reads filtered out after trimming by size control
1771573 (92.08%) reads available; of these:
1709521 (96.50%) trimmed reads available after processing
  62052 ( 3.50%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  11641	  0.66%
 19	  23100	  1.30%
 20	 114888	  6.49%
 21	 224613	 12.68%
 22	 624036	 35.22%
 23	 279357	 15.77%
 24	 122297	  6.90%
 25	  33657	  1.90%
 26	  16486	  0.93%
 27	  12392	  0.70%
 28	  13414	  0.76%
 29	   9993	  0.56%
 30	  13862	  0.78%
 31	  15249	  0.86%
 32	  16688	  0.94%
 33	  54571	  3.08%
 34	  16562	  0.93%
 35	  12446	  0.70%
 36	  14067	  0.79%
 37	   7487	  0.42%
 38	   7294	  0.41%
 39	   6791	  0.38%
 40	  10081	  0.57%
 41	  12072	  0.68%
 42	  12798	  0.72%
 43	   8705	  0.49%
 44	   6302	  0.36%
 45	   8280	  0.47%
 46	   5934	  0.33%
 47	   3997	  0.23%
 48	    735	  0.04%
 49	   1213	  0.07%
 50	  50565	  2.85%


criterion=sequence-density
sequence-density=8.53
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=14
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTT


criterion=fanout-score
sequence-density=0.48
sequence-density-rank=28
fanout-score=29.68
fanout-score-rank=1
prefix-density=13.99
prefix-fanout=1.0
sequence=CTGAGCTTGGCA
                                 Started job on |	Mar 04 07:20:18
                             Started mapping on |	Mar 04 07:20:18
                                    Finished on |	Mar 04 07:20:44
       Mapping speed, Million of reads per hour |	251.35

                          Number of input reads |	1815301
                      Average input read length |	25
                                    UNIQUE READS:
                   Uniquely mapped reads number |	980230
                        Uniquely mapped reads % |	54.00%
                          Average mapped length |	23.83
                       Number of splices: Total |	4394
            Number of splices: Annotated (sjdb) |	1541
                       Number of splices: GT/AG |	4329
                       Number of splices: GC/AG |	37
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	28
                      Mismatch rate per base, % |	0.35%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.78
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.10
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	644330
             % of reads mapped to multiple loci |	35.49%
        Number of reads mapped to too many loci |	27875
             % of reads mapped to too many loci |	1.54%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	8.43%
                     % of reads unmapped: other |	0.54%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	190741	190741	190741
N_multimapping	644330	644330	644330
N_noFeature	50952	60690	627062
N_ambiguous	579905	269321	6831
UnstrandedReadsAssigned:349373 PositiveStrandReadsAssigned:650219 NegativeStrandReadsAssigned:346337
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=21 echo kmer=19
SRR5031078 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: SRR5031078-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 1,815,301 reads, 491,049 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,080 rounds

 109283 SRR5031078.ke.tsv
  52636 SRR5031078.se.tsv
 161919 total
==> SRR5031078.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

==> SRR5031078.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031078 completed mapping pipeline successfully
