Starting /dee2/code/volunteer_pipeline.sh SRR5031003
    current disk space = 160560693248
    free memory = 73931740 
SRR5031003 SRAfilesize
cad80f84ff83f7df9559c262203d8f9c  SRR5031003.sra
SRR5031003.sra file validated
SRR5031003 is single end
SRR5031003 is conventional basespace
SRR5031003 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031003_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	32.29375	33.0	31.0	34.0	31.0	34.0
2	32.49475	34.0	31.0	34.0	31.0	34.0
3	32.53725	34.0	31.0	34.0	31.0	34.0
4	36.1715	37.0	35.0	37.0	35.0	37.0
5	36.13575	37.0	35.0	37.0	35.0	37.0
6	35.84375	37.0	35.0	37.0	33.0	37.0
7	35.84625	37.0	35.0	37.0	35.0	37.0
8	35.98375	37.0	35.0	37.0	35.0	37.0
9	37.5595	39.0	37.0	39.0	35.0	39.0
10	37.4715	39.0	37.0	39.0	34.0	39.0
11	37.08675	39.0	37.0	39.0	33.0	39.0
12	37.48725	39.0	37.0	39.0	34.0	39.0
13	37.48875	39.0	37.0	39.0	34.0	39.0
14	38.7625	40.0	38.0	41.0	34.0	41.0
15	38.81325	40.0	38.0	41.0	35.0	41.0
16	38.791	40.0	38.0	41.0	35.0	41.0
17	38.968	40.0	38.0	41.0	35.0	41.0
18	38.90725	40.0	38.0	41.0	35.0	41.0
19	38.7445	40.0	38.0	41.0	34.0	41.0
20	38.73575	40.0	38.0	41.0	34.0	41.0
21	38.79775	40.0	38.0	41.0	35.0	41.0
22	38.8365	40.0	39.0	41.0	34.0	41.0
23	38.457	40.0	38.0	41.0	34.0	41.0
24	38.88925	40.0	38.0	41.0	35.0	41.0
25	39.003	40.0	39.0	41.0	35.0	41.0
26	38.78025	40.0	38.0	41.0	34.0	41.0
27	38.862	40.0	38.0	41.0	35.0	41.0
28	38.582	40.0	38.0	41.0	34.0	41.0
29	38.309	40.0	38.0	41.0	33.0	41.0
30	38.2505	40.0	38.0	41.0	33.0	41.0
31	38.5115	40.0	38.0	41.0	34.0	41.0
32	38.58375	40.0	38.0	41.0	34.0	41.0
33	38.2775	40.0	38.0	41.0	33.0	41.0
34	38.26325	40.0	38.0	41.0	33.0	41.0
35	37.84575	40.0	37.0	41.0	33.0	41.0
36	37.76875	40.0	37.0	41.0	33.0	41.0
37	37.0105	39.0	36.0	41.0	31.0	41.0
38	37.21075	39.0	36.0	40.0	31.0	41.0
39	37.51175	39.0	37.0	41.0	33.0	41.0
40	37.638	40.0	37.0	41.0	33.0	41.0
41	37.6925	40.0	37.0	41.0	33.0	41.0
42	37.6175	40.0	37.0	41.0	32.0	41.0
43	37.43275	40.0	37.0	41.0	32.0	41.0
44	37.45375	40.0	37.0	41.0	32.0	41.0
45	37.53425	40.0	37.0	41.0	33.0	41.0
46	37.32775	40.0	37.0	41.0	32.0	41.0
47	36.80125	40.0	36.0	41.0	30.0	41.0
48	36.62475	39.0	35.0	41.0	30.0	41.0
49	36.83375	39.0	36.0	41.0	31.0	41.0
50	35.90075	38.0	35.0	40.0	30.0	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	1.0
15	2.0
16	1.0
17	0.0
18	1.0
19	2.0
20	0.0
21	5.0
22	3.0
23	8.0
24	9.0
25	13.0
26	15.0
27	17.0
28	30.0
29	52.0
30	46.0
31	50.0
32	93.0
33	110.0
34	162.0
35	200.0
36	272.0
37	464.0
38	842.0
39	1602.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	11.125	24.15	48.825	15.9
2	24.81203007518797	24.06015037593985	20.551378446115287	30.576441102756892
3	25.074999999999996	18.075	23.9	32.95
4	31.4	28.475	15.825	24.3
5	22.650000000000002	37.925	27.250000000000004	12.174999999999999
6	35.225	13.900000000000002	34.675	16.2
7	17.724999999999998	21.925	24.474999999999998	35.875
8	25.474999999999998	25.424999999999997	17.75	31.35
9	21.55	32.425	29.325000000000003	16.7
10	21.9	21.475	28.225	28.4
11	32.375	11.600000000000001	18.525	37.5
12	19.675	18.7	27.950000000000003	33.675
13	31.2	17.175	33.800000000000004	17.825
14	29.275000000000002	29.925	22.35	18.45
15	37.625	22.075	25.974999999999998	14.325
16	18.875	19.225	23.325000000000003	38.574999999999996
17	25.650000000000002	22.45	36.175000000000004	15.725
18	25.5	19.975	28.749999999999996	25.775
19	35.3	15.65	30.9	18.15
20	42.15	15.8	28.549999999999997	13.5
21	26.375	21.55	25.174999999999997	26.900000000000002
22	28.050000000000004	15.675	45.275	11.0
23	24.65	16.85	40.975	17.525
24	46.75	15.8	25.624999999999996	11.825
25	47.05	22.400000000000002	17.8	12.75
26	29.275000000000002	42.55	13.450000000000001	14.725
27	18.325	43.925	22.425	15.325
28	14.075	25.650000000000002	44.2	16.075
29	15.0	12.825000000000001	52.325	19.85
30	12.7	7.000000000000001	37.275000000000006	43.025000000000006
31	14.299999999999999	6.45	43.375	35.875
32	26.625	7.75	22.575	43.05
33	49.675000000000004	9.325	14.875	26.125
34	58.85	8.924999999999999	15.7	16.525000000000002
35	59.5	11.375	18.6	10.525
36	43.525000000000006	8.0	34.725	13.750000000000002
37	42.575	10.775	24.425	22.225
38	28.15	16.775000000000002	12.625	42.449999999999996
39	19.5	22.825	10.8	46.875
40	15.875	46.75	13.25	24.125
41	23.025000000000002	46.550000000000004	12.7	17.724999999999998
42	45.45	27.450000000000003	15.15	11.95
43	47.65	26.950000000000003	13.55	11.85
44	32.074999999999996	43.275000000000006	8.875	15.775
45	22.1	45.675	14.725	17.5
46	16.25	25.45	18.45	39.85
47	13.025	17.349999999999998	36.5	33.125
48	14.099999999999998	12.075	22.6	51.225
49	17.625	18.4	14.924999999999999	49.05
50	18.825	34.475	13.750000000000002	32.95
>>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	0.0
16	0.0
17	0.0
18	0.0
19	0.0
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	1.0
26	1.0
27	1.0
28	1.0
29	3.0
30	5.0
31	9.5
32	14.0
33	14.5
34	15.0
35	22.5
36	30.0
37	33.5
38	37.0
39	39.5
40	42.0
41	44.0
42	46.0
43	73.0
44	100.0
45	140.0
46	180.0
47	295.5
48	411.0
49	483.5
50	556.0
51	681.0
52	806.0
53	662.5
54	519.0
55	527.5
56	536.0
57	409.0
58	282.0
59	192.0
60	102.0
61	71.0
62	40.0
63	90.0
64	140.0
65	90.0
66	40.0
67	28.5
68	17.0
69	19.0
70	21.0
71	33.0
72	45.0
73	25.5
74	6.0
75	5.0
76	4.0
77	2.0
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	0.0
2	0.25
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	38.324999999999996
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.79908675799086	29.049999999999997
2	10.241356816699282	7.85
3	3.8486627527723414	4.425
4	1.82648401826484	2.8000000000000003
5	1.761252446183953	3.375
6	0.7827788649706457	1.7999999999999998
7	0.91324200913242	2.45
8	0.45662100456621	1.4000000000000001
9	0.5218525766470972	1.7999999999999998
>10	3.131115459882583	21.425
>50	0.5870841487279843	17.275
>100	0.1304631441617743	6.35
>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	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	122	3.05	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	96	2.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	90	2.25	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	89	2.225	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGC	82	2.0500000000000003	RNA PCR Primer, Index 23 (100% over 50bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	80	2.0	RNA PCR Primer, Index 1 (100% over 30bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	76	1.9	No Hit
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	68	1.7000000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	55	1.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	55	1.375	RNA PCR Primer, Index 1 (100% over 28bp)
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	44	1.0999999999999999	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	43	1.075	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	41	1.0250000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGA	40	1.0	RNA PCR Primer, Index 7 (97% over 35bp)
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	27	0.675	RNA PCR Primer, Index 1 (100% over 26bp)
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	27	0.675	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	25	0.625	RNA PCR Primer, Index 1 (100% over 27bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	21	0.525	RNA PCR Primer, Index 1 (100% over 33bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	21	0.525	No Hit
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	21	0.525	No Hit
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTC	20	0.5	RNA PCR Primer, Index 23 (100% over 44bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGACTGGAATTCTCGGGT	20	0.5	No Hit
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	19	0.475	No Hit
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	17	0.42500000000000004	RNA PCR Primer, Index 1 (100% over 26bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	16	0.4	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	16	0.4	RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCACTGGAATTCTCGGGT	15	0.375	No Hit
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	14	0.35000000000000003	No Hit
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	14	0.35000000000000003	No Hit
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13	0.325	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	12	0.3	RNA PCR Primer, Index 1 (100% over 30bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	12	0.3	No Hit
ATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTGCC	12	0.3	No Hit
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	11	0.27499999999999997	No Hit
CACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAAT	11	0.27499999999999997	No Hit
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	11	0.27499999999999997	No Hit
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	11	0.27499999999999997	No Hit
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCTGGAATTCTCGGGTG	10	0.25	No Hit
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	10	0.25	RNA PCR Primer, Index 1 (100% over 26bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTTGGAATTCTCGGGTG	10	0.25	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGTG	9	0.22499999999999998	No Hit
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCTTTTTGGAATTCTCGGGTGCCAAGGAACT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 25bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	9	0.22499999999999998	No Hit
TCCCTGAGACCCTTTAACCTGTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCCCTTTGTCATCCTATGCCTGTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
CTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG	8	0.2	RNA PCR Primer, Index 6 (100% over 34bp)
AGCCCATGATGGTATGAGAGTAGTGGACAGAAGGGATTTCTGAAAAACAC	8	0.2	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGT	8	0.2	No Hit
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCAATGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	7	0.17500000000000002	No Hit
CCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 24bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCCCTTACCCCAAAAAGCATTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTCTGGAATTCTCGGGT	7	0.17500000000000002	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
TGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTCT	7	0.17500000000000002	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
CTGGCCCTCTCTGCCCTTCCGTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGAACCATCACTCGACTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTAATGGAATTCTCGGGTGCCAAGGAACTC	6	0.15	RNA PCR Primer, Index 1 (100% over 26bp)
GCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTC	6	0.15	No Hit
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	6	0.15	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACAAATATAATTATACTATTATTGGAA	6	0.15	No Hit
CTCACGACTGTGAGATCAACCCATGCACCGCTCTGAGATGGAATTCTCGG	6	0.15	No Hit
TCTGGCTCCGTGTCTTCACTCCCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATGGTTTTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTCATCACGCTCGCCTGACTGGAATTCTCGGGT	5	0.125	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGCATTCTCGGGTGCC	5	0.125	No Hit
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AAGGGATTCTGATGTTGGTCACACTTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
CGCGACCTCAGATCAGACGTGGCGACCCGCTGCTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC	5	0.125	No Hit
TATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAATTCTCGGGTGCC	5	0.125	No Hit
CTGCGTTCGCGCTCTCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
ACTAATCCTAGCCCTAGCCCTACACTGGAATTCTCGGGTGCCAAGGAACT	5	0.125	RNA PCR Primer, Index 1 (100% over 25bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTAT	5	0.125	RNA PCR Primer, Index 23 (100% over 48bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	5	0.125	No Hit
CTGACTTGATGAAAGTACTTTTGAACCCTTTTCCATCTGATGTGGAATTC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	5	0.125	RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGCCATGGAATTCTCGGGTG	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	2.225	0.0	0.0	0.0
2	0.0	2.225	0.0	0.0	0.0
3	0.0	2.4	0.0	0.0	0.0
4	0.0	2.4	0.0	0.0	0.0
5	0.0	2.45	0.0	0.0	0.0
6	0.0	2.475	0.0	0.0	0.0
7	0.0	3.2	0.0	0.0	0.0
8	0.0	3.375	0.0	0.0	0.0
9	0.0	3.475	0.0	0.0	0.0
10	0.0	3.575	0.0	0.0	0.0
11	0.0	3.675	0.0	0.0	0.0
12	0.0	3.975	0.0	0.0	0.0
13	0.0	4.3	0.0	0.0	0.0
14	0.0	4.625	0.0	0.0	0.0
15	0.0	4.85	0.0	0.0	0.0
16	0.0	6.525	0.0	0.0	0.0
17	0.0	7.35	0.0	0.0	0.0
18	0.0	8.45	0.0	0.0	0.0
19	0.0	9.0	0.0	0.0	0.0
20	0.0	9.975	0.0	0.0	0.0
21	0.0	14.275	0.0	0.0	0.0
22	0.0	24.1	0.0	0.0	0.0
23	0.0	50.075	0.0	0.0	0.0
24	0.0	62.5	0.0	0.0	0.0
25	0.0	68.275	0.0	0.0	0.0
26	0.0	69.675	0.0	0.0	0.0
27	0.0	70.5	0.0	0.0	0.0
28	0.0	71.1	0.0	0.0	0.0
29	0.0	71.6	0.0	0.0	0.0
30	0.0	72.2	0.0	0.0	0.0
31	0.0	73.125	0.0	0.0	0.0
32	0.0	74.575	0.0	0.0	0.0
33	0.0	75.225	0.0	0.0	0.0
34	0.0	78.65	0.0	0.0	0.0
35	0.0	80.225	0.0	0.0	0.0
36	0.0	81.7	0.0	0.0	0.0
37	0.0	84.075	0.0	0.0	0.0
38	0.0	84.7	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
GGTGAGT	20	6.952051E-4	44.000004	17
TAAACAT	20	6.952051E-4	44.000004	3
AAACATC	20	6.952051E-4	44.000004	4
TGTAAAC	20	6.952051E-4	44.000004	1
GTAAACA	20	6.952051E-4	44.000004	2
AACATCC	20	6.952051E-4	44.000004	5
AACGCTG	30	1.9515464E-6	44.0	8
ACGCTGT	30	1.9515464E-6	44.0	9
TTCAACG	30	1.9515464E-6	44.0	5
TCGGTGA	30	1.9515464E-6	44.0	15
CATTCAA	30	1.9515464E-6	44.0	3
TCAACGC	30	1.9515464E-6	44.0	6
ACATTCA	30	1.9515464E-6	44.0	2
CTTGGCT	30	1.9515464E-6	44.0	16
GCTGTCG	30	1.9515464E-6	44.0	11
CGTATGC	25	3.6958358E-5	44.0	44
CGGTGAG	30	1.9515464E-6	44.0	16
GCTTGGC	30	1.9515464E-6	44.0	15
TCGTATG	25	3.6958358E-5	44.0	43
CTGTCGG	30	1.9515464E-6	44.0	12
>>END_MODULE
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263018 spots for SRR5031003.sra
Written 263018 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
Read 263012 spots for SRR5031003.sra
Written 263012 spots for SRR5031003.sra
SRR ids: ['SRR5031003.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_u6gkeps3
SRR5031003.sra spots: 3156150
blocks: [[1, 263012], [263013, 526024], [526025, 789036], [789037, 1052048], [1052049, 1315060], [1315061, 1578072], [1578073, 1841084], [1841085, 2104096], [2104097, 2367108], [2367109, 2630120], [2630121, 2893132], [2893133, 3156150]]
SRR5031003 file size 545965
SRR5031003 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031003 SRR5031003_1.fastq
Input file:	SRR5031003_1.fastq
trimmed:	SRR5031003-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 07:04:02 2020 >> started

Wed Mar  4 07:04:04 2020 >> done (2.148s)
3156150 reads processed; of these:
    284 ( 0.01%) short reads filtered out after trimming by size control
      9 ( 0.00%) empty reads filtered out after trimming by size control
3155857 (99.99%) reads available; of these:
 203511 ( 6.45%) trimmed reads available after processing
2952346 (93.55%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     88	  0.00%
 19	     75	  0.00%
 20	    159	  0.01%
 21	    221	  0.01%
 22	    333	  0.01%
 23	    391	  0.01%
 24	    454	  0.01%
 25	    582	  0.02%
 26	    549	  0.02%
 27	    625	  0.02%
 28	    755	  0.02%
 29	   1000	  0.03%
 30	    780	  0.02%
 31	    863	  0.03%
 32	    945	  0.03%
 33	   1176	  0.04%
 34	   1701	  0.05%
 35	   2958	  0.09%
 36	   2728	  0.09%
 37	   3084	  0.10%
 38	   3407	  0.11%
 39	   3665	  0.12%
 40	   4596	  0.15%
 41	   4160	  0.13%
 42	   5448	  0.17%
 43	   7244	  0.23%
 44	  10334	  0.33%
 45	  13952	  0.44%
 46	  20305	  0.64%
 47	  23885	  0.76%
 48	  35805	  1.13%
 49	  51243	  1.62%
 50	2952346	 93.55%
3155857 reads passed initial QC


criterion=sequence-density
sequence-density=85.22
sequence-density-rank=1
fanout-score=21.52
fanout-score-rank=1
prefix-density=85.47
prefix-fanout=21.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC


criterion=fanout-score
sequence-density=85.22
sequence-density-rank=1
fanout-score=21.52
fanout-score-rank=1
prefix-density=85.47
prefix-fanout=21.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC -o SRR5031003 -
Input file:	STDIN
trimmed:	SRR5031003-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGAGTGGATCTCGTATGCC
-- 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 07:04:20 2020 >> started

Wed Mar  4 07:04:25 2020 >> done (4.739s)
3082465 reads processed; of these:
 208676 ( 6.77%) short reads filtered out after trimming by size control
  75644 ( 2.45%) empty reads filtered out after trimming by size control
2798145 (90.78%) reads available; of these:
2651877 (94.77%) trimmed reads available after processing
 146268 ( 5.23%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  16146	  0.58%
 19	  29517	  1.05%
 20	 133192	  4.76%
 21	 307668	 11.00%
 22	 813297	 29.07%
 23	 382718	 13.68%
 24	 172753	  6.17%
 25	  48268	  1.72%
 26	  25832	  0.92%
 27	  20529	  0.73%
 28	  22834	  0.82%
 29	  17927	  0.64%
 30	  26649	  0.95%
 31	  46785	  1.67%
 32	  36293	  1.30%
 33	 107079	  3.83%
 34	  52540	  1.88%
 35	  49287	  1.76%
 36	  69901	  2.50%
 37	  19307	  0.69%
 38	  20644	  0.74%
 39	  19083	  0.68%
 40	  27695	  0.99%
 41	  38031	  1.36%
 42	  45817	  1.64%
 43	  32347	  1.16%
 44	  22283	  0.80%
 45	  26781	  0.96%
 46	  22225	  0.79%
 47	  15322	  0.55%
 48	   1527	  0.05%
 49	   3093	  0.11%
 50	 124775	  4.46%


criterion=sequence-density
sequence-density=6.30
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=AACATTCAACGCTGTCGGTGAGTTTT


criterion=fanout-score
sequence-density=0.64
sequence-density-rank=22
fanout-score=11.83
fanout-score-rank=1
prefix-density=7.53
prefix-fanout=1.0
sequence=TGAGCTTGGCTTTT
                                 Started job on |	Mar 04 07:05:26
                             Started mapping on |	Mar 04 07:05:26
                                    Finished on |	Mar 04 07:05:51
       Mapping speed, Million of reads per hour |	413.50

                          Number of input reads |	2871537
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1452838
                        Uniquely mapped reads % |	50.59%
                          Average mapped length |	25.32
                       Number of splices: Total |	1362
            Number of splices: Annotated (sjdb) |	244
                       Number of splices: GT/AG |	1267
                       Number of splices: GC/AG |	16
                       Number of splices: AT/AC |	2
               Number of splices: Non-canonical |	77
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.70
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	1011142
             % of reads mapped to multiple loci |	35.21%
        Number of reads mapped to too many loci |	82165
             % of reads mapped to too many loci |	2.86%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	10.58%
                     % of reads unmapped: other |	0.75%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	407557	407557	407557
N_multimapping	1011142	1011142	1011142
N_noFeature	96109	116469	1008841
N_ambiguous	797325	419499	15014
UnstrandedReadsAssigned:559404 PositiveStrandReadsAssigned:916870 NegativeStrandReadsAssigned:428983
Dataset is classified unstranded
MeadianReadLen=23 20thPercentileLength=22 echo kmer=19
SRR5031003 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: SRR5031003-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,871,537 reads, 706,010 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,196 rounds

 109283 SRR5031003.ke.tsv
  52636 SRR5031003.se.tsv
 161919 total
==> SRR5031003.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

==> SRR5031003.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	1
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031003 completed mapping pipeline successfully
