Starting /dee2/code/volunteer_pipeline.sh SRR5031052
    current disk space = 160520339456
    free memory = 73940728 
SRR5031052 SRAfilesize
4c739e38d92e2ecbfbc263b40719fc2f  SRR5031052.sra
SRR5031052.sra file validated
SRR5031052 is single end
SRR5031052 is conventional basespace
SRR5031052 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR5031052_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	32.2855	33.0	31.0	34.0	30.0	34.0
2	32.53	34.0	31.0	34.0	31.0	34.0
3	32.56875	34.0	31.0	34.0	31.0	34.0
4	36.151	37.0	35.0	37.0	35.0	37.0
5	35.873	37.0	35.0	37.0	35.0	37.0
6	35.75075	37.0	35.0	37.0	33.0	37.0
7	35.84075	37.0	35.0	37.0	35.0	37.0
8	35.696	37.0	35.0	37.0	33.0	37.0
9	37.43825	39.0	37.0	39.0	34.0	39.0
10	37.66325	39.0	37.0	39.0	35.0	39.0
11	37.51325	39.0	37.0	39.0	35.0	39.0
12	37.47375	39.0	37.0	39.0	34.0	39.0
13	37.594	39.0	37.0	39.0	35.0	39.0
14	38.86975	40.0	38.0	41.0	35.0	41.0
15	38.83825	40.0	38.0	41.0	35.0	41.0
16	38.831	40.0	38.0	41.0	35.0	41.0
17	38.81225	40.0	38.0	41.0	35.0	41.0
18	38.91425	40.0	38.0	41.0	35.0	41.0
19	38.5955	40.0	38.0	41.0	34.0	41.0
20	38.70525	40.0	38.0	41.0	34.0	41.0
21	38.64825	40.0	38.0	41.0	34.0	41.0
22	38.8585	40.0	38.0	41.0	35.0	41.0
23	38.562	40.0	38.0	41.0	34.0	41.0
24	38.73225	40.0	38.0	41.0	35.0	41.0
25	38.92525	40.0	38.0	41.0	35.0	41.0
26	38.418	40.0	38.0	41.0	34.0	41.0
27	38.3665	40.0	38.0	41.0	34.0	41.0
28	38.44875	40.0	38.0	41.0	34.0	41.0
29	37.9465	40.0	37.0	41.0	32.0	41.0
30	38.11675	40.0	38.0	41.0	33.0	41.0
31	38.2455	40.0	38.0	41.0	34.0	41.0
32	37.92775	40.0	38.0	41.0	33.0	41.0
33	37.4715	40.0	37.0	41.0	32.0	41.0
34	37.75275	40.0	37.0	41.0	33.0	41.0
35	37.72175	40.0	37.0	41.0	33.0	41.0
36	37.64275	40.0	37.0	41.0	33.0	41.0
37	36.94175	40.0	36.0	41.0	30.0	41.0
38	36.583	39.0	35.0	41.0	30.0	41.0
39	36.911	39.0	36.0	40.0	30.0	41.0
40	37.1825	39.0	37.0	41.0	31.0	41.0
41	37.42875	40.0	37.0	41.0	32.0	41.0
42	37.81225	40.0	37.0	41.0	33.0	41.0
43	38.11875	40.0	38.0	41.0	33.0	41.0
44	37.72675	40.0	37.0	41.0	33.0	41.0
45	37.691	40.0	37.0	41.0	33.0	41.0
46	37.52375	40.0	37.0	41.0	33.0	41.0
47	36.94775	40.0	36.0	41.0	30.0	41.0
48	36.48425	39.0	35.0	41.0	30.0	41.0
49	36.77125	39.0	35.0	41.0	31.0	41.0
50	36.348	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
12	1.0
13	0.0
14	0.0
15	2.0
16	3.0
17	0.0
18	2.0
19	3.0
20	5.0
21	10.0
22	2.0
23	4.0
24	6.0
25	11.0
26	11.0
27	30.0
28	24.0
29	43.0
30	49.0
31	79.0
32	92.0
33	124.0
34	175.0
35	219.0
36	270.0
37	412.0
38	773.0
39	1650.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	8.450000000000001	25.1	48.475	17.974999999999998
2	26.75175175175175	26.901901901901905	17.56756756756757	28.77877877877878
3	22.425	20.375	21.775	35.425000000000004
4	35.775	28.199999999999996	12.9	23.125
5	23.0	39.625	26.55	10.825
6	33.375	14.224999999999998	33.95	18.45
7	14.549999999999999	22.975	21.525	40.949999999999996
8	25.8	28.075	16.950000000000003	29.175
9	19.35	32.800000000000004	28.050000000000004	19.8
10	18.6	26.375	26.85	28.175
11	36.125	10.525	15.275	38.074999999999996
12	15.425	21.725	28.199999999999996	34.65
13	29.575000000000003	17.224999999999998	35.725	17.474999999999998
14	31.275	27.975	21.9	18.85
15	33.324999999999996	26.75	26.1	13.825000000000001
16	21.275	18.7	21.825	38.2
17	24.525	26.075	35.5	13.900000000000002
18	23.724999999999998	16.6	28.65	31.025000000000002
19	37.1	13.25	30.75	18.9
20	42.475	14.6	30.7	12.225
21	26.474999999999998	19.675	26.974999999999998	26.875
22	31.775	12.3	45.1	10.825
23	25.4	11.875	45.75	16.975
24	53.425	12.75	26.0	7.825
25	51.849999999999994	25.724999999999998	13.775	8.649999999999999
26	28.475	45.725	13.125	12.675
27	16.175	47.4	21.7	14.725
28	11.200000000000001	25.1	46.825	16.875
29	13.575000000000001	13.25	55.574999999999996	17.599999999999998
30	8.825	6.425	36.9	47.85
31	13.3	4.65	48.925000000000004	33.125
32	30.275000000000002	4.875	22.575	42.275
33	52.275000000000006	10.875	12.925	23.925
34	61.7	6.15	17.775	14.374999999999998
35	67.7	6.4	17.424999999999997	8.475000000000001
36	45.800000000000004	6.825	35.725	11.65
37	43.95	12.5	21.8	21.75
38	25.3	17.25	12.475	44.975
39	15.425	21.15	12.775	50.64999999999999
40	15.775	45.5	12.75	25.974999999999998
41	23.325000000000003	48.875	7.875	19.925
42	47.05	30.0	13.725000000000001	9.225
43	52.775000000000006	27.675	6.75	12.8
44	36.375	45.75	6.425	11.450000000000001
45	20.9	49.875	11.825	17.4
46	16.425	27.0	16.275000000000002	40.300000000000004
47	9.1	13.925	40.575	36.4
48	12.875	11.625	20.599999999999998	54.900000000000006
49	12.075	18.275	13.775	55.875
50	17.549999999999997	35.949999999999996	11.774999999999999	34.725
>>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	0.5
18	1.0
19	0.5
20	0.0
21	0.0
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	0.0
28	0.0
29	0.5
30	1.0
31	4.5
32	8.0
33	8.0
34	8.0
35	14.5
36	21.0
37	19.0
38	17.0
39	27.5
40	38.0
41	48.0
42	58.0
43	84.0
44	110.0
45	158.0
46	206.0
47	302.0
48	398.0
49	506.5
50	615.0
51	751.5
52	888.0
53	660.5
54	433.0
55	432.5
56	432.0
57	321.5
58	211.0
59	149.0
60	87.0
61	65.5
62	44.0
63	151.5
64	259.0
65	151.0
66	43.0
67	31.5
68	20.0
69	27.0
70	34.0
71	48.0
72	62.0
73	32.5
74	3.0
75	1.5
76	0.0
77	0.0
78	0.0
79	0.5
80	1.0
81	1.0
82	1.0
83	0.5
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	0.1
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	35.175
#Duplication Level	Percentage of deduplicated	Percentage of total
1	73.98720682302772	26.025
2	10.376687988628287	7.3
3	4.690831556503198	4.95
4	2.4875621890547266	3.5000000000000004
5	1.279317697228145	2.25
6	0.42643923240938164	0.8999999999999999
7	1.2082444918265813	2.9749999999999996
8	0.7818052594171997	2.1999999999999997
9	0.4975124378109453	1.575
>10	3.553660270078181	23.575
>50	0.42643923240938164	10.8
>100	0.28429282160625446	13.950000000000001
>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
CGCGACCTCAGATCAGACGTGGCGACCCGCTGATGGAATTCTCGGGTGCC	184	4.6	No Hit
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	132	3.3000000000000003	RNA PCR Primer, Index 1 (100% over 27bp)
AAGCTGCCAGTTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	124	3.1	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	118	2.9499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	93	2.325	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	87	2.175	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	76	1.9	RNA PCR Primer, Index 1 (100% over 30bp)
TTTGAACCATCACTCGACTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA	65	1.625	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	56	1.4000000000000001	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	55	1.375	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGATTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	50	1.25	RNA PCR Primer, Index 1 (100% over 28bp)
GGGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAA	36	0.8999999999999999	No Hit
TCTTTGGTTATCTAGCTGTATGATGGAATTCTCGGGTGCCAAGGAACTCC	35	0.8750000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
CTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTG	34	0.8500000000000001	No Hit
CAACGGAATCCCAAAAGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	33	0.8250000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
ACTAATCCTAGCCCTAGCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG	32	0.8	RNA PCR Primer, Index 1 (100% over 29bp)
AGCTGGTGTTGTGAATCAGGCCGTGGAATTCTCGGGTGCCAAGGAACTCC	28	0.7000000000000001	RNA PCR Primer, Index 1 (100% over 27bp)
TCGGATCCGTCTGAGCTTGGCTATTGGAATTCTCGGGTGCCAAGGAACTC	25	0.625	RNA PCR Primer, Index 1 (100% over 26bp)
ACTTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTT	25	0.625	No Hit
TCGGATCCGTCTGAGCTTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	23	0.575	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTTGGAATTCTCGGGTGCCAAGGAACTCCA	23	0.575	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	23	0.575	RNA PCR Primer, Index 1 (100% over 26bp)
TGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGG	23	0.575	RNA PCR Primer, Index 2 (97% over 35bp)
TATTGCACTCGTCCCGGCCTCCTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	22	0.5499999999999999	RNA PCR Primer, Index 1 (100% over 28bp)
AATATAACACAGATGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	21	0.525	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCTCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	20	0.5	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	20	0.5	RNA PCR Primer, Index 1 (100% over 27bp)
GTTAGTACTTGGATGGGAGACCGCCTGGGAATACCGGGTGCTGTAGGCTT	19	0.475	No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	19	0.475	RNA PCR Primer, Index 1 (100% over 26bp)
TGAGGTAGTAGATTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	19	0.475	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	18	0.44999999999999996	RNA PCR Primer, Index 1 (100% over 28bp)
GTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTC	17	0.42500000000000004	RNA PCR Primer, Index 24 (100% over 44bp)
CCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	16	0.4	RNA PCR Primer, Index 1 (100% over 33bp)
AGCAGCATTGTACAGGGCTATGATGGAATTCTCGGGTGCCAAGGAACTCC	16	0.4	RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGAGACCCTTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	16	0.4	RNA PCR Primer, Index 1 (100% over 26bp)
TCCCTGAGACCCTAACTTGTGATGGAATTCTCGGGTGCCAAGGAACTCCA	15	0.375	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGAA	15	0.375	No Hit
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
TAACAGTCTACAGCCATGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTC	13	0.325	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGC	13	0.325	RNA PCR Primer, Index 24 (100% over 50bp)
TAGCAGCACGTAAATATTGGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	13	0.325	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTAACTTGTGAATGGAATTCTCGGGTGCCAAGGAACTCC	13	0.325	RNA PCR Primer, Index 1 (100% over 27bp)
TGTAAACATCCCCGACTGGAAGCTGGAATTCTCGGGTGCCAAGGAACTCC	12	0.3	RNA PCR Primer, Index 1 (100% over 27bp)
CACCCGTAGAACCGACCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA	12	0.3	RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGAGACCCTTTAACCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12	0.3	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 28bp)
TCGGATCCGTCTGAGCTTGGCTATGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
ACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTCC	11	0.27499999999999997	RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGTTTGTACAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TTCAAGTAATCCAGGATAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCC	10	0.25	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
TAGCACCATCTGAAATCGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	10	0.25	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA	10	0.25	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTGGTGTTGTGAATCAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTAACTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 30bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 26bp)
TCGGATCCGTCTGAGCTTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 27bp)
TCACAGTGAACCGGTCTCTTTATGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
ATAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
TCACAGTGAACCGGTCTCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	8	0.2	RNA PCR Primer, Index 1 (100% over 30bp)
TGAGGTAGTAGATTGTATAGTTATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGATGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
TGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGCGTCGCTTGGA	8	0.2	No Hit
TATACAAGGGCAAGCTCTCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
TCAGTGCACTACAGAACTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	8	0.2	RNA PCR Primer, Index 1 (100% over 28bp)
ATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATTCT	8	0.2	No Hit
TAACAGTCTACAGCCATGGTCGTTGGAATTCTCGGGTGCCAAGGAACTCC	8	0.2	RNA PCR Primer, Index 1 (100% over 27bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCA	8	0.2	No Hit
TAGTAGACCGTATAGCGTACGTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CACCCGTAGAACCGACCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCTATTGAAAGTCAGCCCTCGACACAAGGGTTTGTTGGAA	7	0.17500000000000002	No Hit
TGAGGTAGTAGGTTGTATGGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTCGTCCCGGCCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTGTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CGCCTGTCTGAGCGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
CGCACGGGGTCGGCGGCGATGTCGGCTGGAATTCTCGGGTGCCAAGGAAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 24bp)
TCGAGGAGCTCACAGTCTAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 29bp)
CAGGATCACAGAAAAAGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 33bp)
TTGCTGTGATGACTATCTTAGGACACCTTTGGATTAACCGTGGAATTCTC	7	0.17500000000000002	No Hit
TCGGATCCGTCTGAGCTTGGCTTTTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AGAGGTAGTAGGTTGCATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 28bp)
CATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTCT	7	0.17500000000000002	No Hit
AAGGGATTCTGATGTTGGTCACACTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
GAGACCGCCTGGGAATACCGGGTGCTGTAGGCTTTGGAATTCTCGGGTGC	7	0.17500000000000002	No Hit
AACCATTCGTAGACGACCTGCTTCTGGAATTCTCGGGTGCCAAGGAACTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 26bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC	6	0.15	RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATTCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGGAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
TTTGGCAATGGTAGAACTCACATGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTTGGAATT	6	0.15	No Hit
GGGGGGCCCAAGTCCTTCTGATCGAGGCCCTGGAATTCTCGGGTGCCAAG	6	0.15	No Hit
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TCTTTGGTTATCTAGCTGTATTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TGTAAACATCCCCGACTGGATGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
ATCCCGGACGAGCCCCCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	5	0.125	RNA PCR Primer, Index 1 (100% over 32bp)
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGTTTGTACAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
AGAAATGCGGATATGGGACTGAGATGGAATTCTCGGGTGCCAAGGAACTC	5	0.125	RNA PCR Primer, Index 1 (100% over 26bp)
TGCGGGGCTAGGGCTAACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	5	0.125	No Hit
TCTTTGGTTATCTAGCTGTATGTGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
ACATTGATCATCGACACTTCGAACGCACTTGCGGCCCCGGGTTGGAATTC	5	0.125	No Hit
CGCGACCTCAGATCAGACGTGGCGACCCGCTGAATGGAATTCTCGGGTGC	5	0.125	No Hit
TCGGATCCGTCTGAGCTTGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCGGATCCGTCTGAGCTTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA	5	0.125	RNA PCR Primer, Index 1 (100% over 28bp)
AAGAAAGATTGCAAGAACTGCTAATTCTGGAATTCTCGGGTGCCAAGGAA	5	0.125	RNA PCR Primer, Index 1 (100% over 23bp)
CTAGACTGAGGCTCCTTGAGGTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
>>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	0.325	0.0	0.0	0.0
2	0.0	0.35	0.0	0.0	0.0
3	0.0	0.4	0.0	0.0	0.0
4	0.0	0.45	0.0	0.0	0.0
5	0.0	0.475	0.0	0.0	0.0
6	0.0	0.5	0.0	0.0	0.0
7	0.0	1.05	0.0	0.0	0.0
8	0.0	1.1	0.0	0.0	0.0
9	0.0	1.15	0.0	0.0	0.0
10	0.0	1.225	0.0	0.0	0.0
11	0.0	1.35	0.0	0.0	0.0
12	0.0	1.5	0.0	0.0	0.0
13	0.0	1.7	0.0	0.0	0.0
14	0.0	1.9	0.0	0.0	0.0
15	0.0	2.1	0.0	0.0	0.0
16	0.0	3.1	0.0	0.0	0.0
17	0.0	3.675	0.0	0.0	0.0
18	0.0	4.825	0.0	0.0	0.0
19	0.0	5.325	0.0	0.0	0.0
20	0.0	6.15	0.0	0.0	0.0
21	0.0	11.05	0.0	0.0	0.0
22	0.0	21.975	0.0	0.0	0.0
23	0.0	50.875	0.0	0.0	0.0
24	0.0	65.5	0.0	0.0	0.0
25	0.0	71.85	0.0	0.0	0.0
26	0.0	73.55	0.0	0.0	0.0
27	0.0	74.4	0.0	0.0	0.0
28	0.0	74.95	0.0	0.0	0.0
29	0.0	75.6	0.0	0.0	0.0
30	0.0	76.15	0.0	0.0	0.0
31	0.0	77.0	0.0	0.0	0.0
32	0.0	78.425	0.0	0.0	0.0
33	0.0	79.525	0.0	0.0	0.0
34	0.0	85.35	0.0	0.0	0.0
35	0.0	86.25	0.0	0.0	0.0
36	0.0	86.775	0.0	0.0	0.0
37	0.0	87.55	0.0	0.0	0.0
38	0.0	88.0	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
GTTGAAG	20	6.952051E-4	44.000004	10
AAGTAAT	20	6.952051E-4	44.000004	4
TCAAGTA	20	6.952051E-4	44.000004	2
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
AGGATAG	20	6.952051E-4	44.000004	13
ATAGGCT	20	6.952051E-4	44.000004	16
GAAGAAC	20	6.952051E-4	44.000004	13
GTGAGTT	20	6.952051E-4	44.000004	18
ACATCCT	20	6.952051E-4	44.000004	6
ACATTCA	40	5.315087E-9	44.000004	2
GAGTTGG	20	6.952051E-4	44.000004	20
GGATAGG	20	6.952051E-4	44.000004	14
GCTGCCA	20	6.952051E-4	44.000004	3
GCTGTCG	40	5.315087E-9	44.000004	11
>>END_MODULE
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201307 spots for SRR5031052.sra
Written 201307 spots for SRR5031052.sra
Read 201312 spots for SRR5031052.sra
Written 201312 spots for SRR5031052.sra
SRR ids: ['SRR5031052.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_m5oj15sy
SRR5031052.sra spots: 2415689
blocks: [[1, 201307], [201308, 402614], [402615, 603921], [603922, 805228], [805229, 1006535], [1006536, 1207842], [1207843, 1409149], [1409150, 1610456], [1610457, 1811763], [1811764, 2013070], [2013071, 2214377], [2214378, 2415689]]
SRR5031052 file size 417625
SRR5031052 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -l 18 -q 10 -k inf -t 12 -o SRR5031052 SRR5031052_1.fastq
Input file:	SRR5031052_1.fastq
trimmed:	SRR5031052-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 07:14:08 2020 >> started

Wed Mar  4 07:14:10 2020 >> done (1.666s)
2415689 reads processed; of these:
    263 ( 0.01%) short reads filtered out after trimming by size control
     21 ( 0.00%) empty reads filtered out after trimming by size control
2415405 (99.99%) reads available; of these:
 124975 ( 5.17%) trimmed reads available after processing
2290430 (94.83%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	     71	  0.00%
 19	     77	  0.00%
 20	    157	  0.01%
 21	    169	  0.01%
 22	    300	  0.01%
 23	    386	  0.02%
 24	    453	  0.02%
 25	    671	  0.03%
 26	    450	  0.02%
 27	    527	  0.02%
 28	    685	  0.03%
 29	    847	  0.04%
 30	    744	  0.03%
 31	    797	  0.03%
 32	    898	  0.04%
 33	    930	  0.04%
 34	   1122	  0.05%
 35	   2101	  0.09%
 36	   2038	  0.08%
 37	   2105	  0.09%
 38	   2136	  0.09%
 39	   2394	  0.10%
 40	   2661	  0.11%
 41	   2777	  0.11%
 42	   3629	  0.15%
 43	   5793	  0.24%
 44	   7554	  0.31%
 45	   9690	  0.40%
 46	  13909	  0.58%
 47	  15653	  0.65%
 48	  21651	  0.90%
 49	  21600	  0.89%
 50	2290430	 94.83%
2415405 reads passed initial QC


criterion=sequence-density
sequence-density=87.04
sequence-density-rank=1
fanout-score=21.02
fanout-score-rank=1
prefix-density=89.10
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC


criterion=fanout-score
sequence-density=87.04
sequence-density-rank=1
fanout-score=21.02
fanout-score-rank=1
prefix-density=89.10
prefix-fanout=20.5
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC
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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC -o SRR5031052 -
Input file:	STDIN
trimmed:	SRR5031052-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCC
-- 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 07:14:23 2020 >> started

Wed Mar  4 07:14:27 2020 >> done (3.748s)
2360510 reads processed; of these:
 113404 ( 4.80%) short reads filtered out after trimming by size control
   9990 ( 0.42%) empty reads filtered out after trimming by size control
2237116 (94.77%) reads available; of these:
2127725 (95.11%) trimmed reads available after processing
 109391 ( 4.89%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  12415	  0.55%
 19	  23784	  1.06%
 20	 118647	  5.30%
 21	 273494	 12.23%
 22	 694708	 31.05%
 23	 330218	 14.76%
 24	 143346	  6.41%
 25	  38952	  1.74%
 26	  19119	  0.85%
 27	  15772	  0.71%
 28	  15998	  0.72%
 29	  13398	  0.60%
 30	  22587	  1.01%
 31	  34893	  1.56%
 32	  25209	  1.13%
 33	 138077	  6.17%
 34	  23310	  1.04%
 35	  15526	  0.69%
 36	  18536	  0.83%
 37	  10261	  0.46%
 38	  12381	  0.55%
 39	  10409	  0.47%
 40	  16348	  0.73%
 41	  20561	  0.92%
 42	  23885	  1.07%
 43	  16052	  0.72%
 44	  12288	  0.55%
 45	  17772	  0.79%
 46	  12521	  0.56%
 47	  10781	  0.48%
 48	    913	  0.04%
 49	   1167	  0.05%
 50	  93788	  4.19%


criterion=sequence-density
sequence-density=3.92
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=18
prefix-density=0.00
prefix-fanout=1.0
sequence=AAGCTGCCAGTTGAAGAACTGT


criterion=fanout-score
sequence-density=0.02
sequence-density-rank=38
fanout-score=134.45
fanout-score-rank=1
prefix-density=2.51
prefix-fanout=1.0
sequence=ATTGTATAGTTTAACAGTCTACAGCCATGGTCGT
                                 Started job on |	Mar 04 07:14:49
                             Started mapping on |	Mar 04 07:14:49
                                    Finished on |	Mar 04 07:15:15
       Mapping speed, Million of reads per hour |	317.36

                          Number of input reads |	2292011
                      Average input read length |	26
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1150374
                        Uniquely mapped reads % |	50.19%
                          Average mapped length |	24.18
                       Number of splices: Total |	1558
            Number of splices: Annotated (sjdb) |	317
                       Number of splices: GT/AG |	1479
                       Number of splices: GC/AG |	20
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	59
                      Mismatch rate per base, % |	0.21%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.67
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.03
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	763001
             % of reads mapped to multiple loci |	33.29%
        Number of reads mapped to too many loci |	50652
             % of reads mapped to too many loci |	2.21%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	13.77%
                     % of reads unmapped: other |	0.54%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	378636	378636	378636
N_multimapping	763001	763001	763001
N_noFeature	68549	80552	799666
N_ambiguous	630324	323516	10627
UnstrandedReadsAssigned:451501 PositiveStrandReadsAssigned:746306 NegativeStrandReadsAssigned:340081
Dataset is classified unstranded
MeadianReadLen=22 20thPercentileLength=22 echo kmer=19
SRR5031052 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: SRR5031052-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 2,292,011 reads, 553,597 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,080 rounds

 109283 SRR5031052.ke.tsv
  52636 SRR5031052.se.tsv
 161919 total
==> SRR5031052.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

==> SRR5031052.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	0
ENSMUSG00000102851	0
ENSMUSG00000103377	0
ENSMUSG00000104017	0
ENSMUSG00000103025	0
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	0
SRR5031052 completed mapping pipeline successfully
