Starting /dee2/code/volunteer_pipeline.sh SRR32454948
    current disk space = 1177549168
    free memory = 201211184 
SRR32454948 SRAfilesize
c3e3d99245755a1851caaff29d6fcb90  SRR32454948.sra
SRR32454948.sra file validated
SRR32454948 is single end
SRR32454948 is conventional basespace
SRR32454948 read1 length is 51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR32454948_1.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	4000
Sequences flagged as poor quality	0
Sequence length	51
%GC	55
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	36.144	37.0	37.0	37.0	37.0	37.0
2	36.1075	37.0	37.0	37.0	37.0	37.0
3	36.205	37.0	37.0	37.0	37.0	37.0
4	36.3825	37.0	37.0	37.0	37.0	37.0
5	36.3305	37.0	37.0	37.0	37.0	37.0
6	36.4075	37.0	37.0	37.0	37.0	37.0
7	36.3165	37.0	37.0	37.0	37.0	37.0
8	36.549	37.0	37.0	37.0	37.0	37.0
9	35.9005	37.0	37.0	37.0	37.0	37.0
10	36.4635	37.0	37.0	37.0	37.0	37.0
11	36.5645	37.0	37.0	37.0	37.0	37.0
12	36.5255	37.0	37.0	37.0	37.0	37.0
13	36.4545	37.0	37.0	37.0	37.0	37.0
14	36.664	37.0	37.0	37.0	37.0	37.0
15	36.2705	37.0	37.0	37.0	37.0	37.0
16	36.355	37.0	37.0	37.0	37.0	37.0
17	36.409	37.0	37.0	37.0	37.0	37.0
18	36.167	37.0	37.0	37.0	37.0	37.0
19	36.3485	37.0	37.0	37.0	37.0	37.0
20	36.325	37.0	37.0	37.0	37.0	37.0
21	36.2765	37.0	37.0	37.0	37.0	37.0
22	36.443	37.0	37.0	37.0	37.0	37.0
23	36.357	37.0	37.0	37.0	37.0	37.0
24	36.363	37.0	37.0	37.0	37.0	37.0
25	36.317	37.0	37.0	37.0	37.0	37.0
26	36.054	37.0	37.0	37.0	37.0	37.0
27	36.1985	37.0	37.0	37.0	37.0	37.0
28	36.114	37.0	37.0	37.0	37.0	37.0
29	36.193	37.0	37.0	37.0	37.0	37.0
30	36.308	37.0	37.0	37.0	37.0	37.0
31	36.249	37.0	37.0	37.0	37.0	37.0
32	36.2555	37.0	37.0	37.0	37.0	37.0
33	36.306	37.0	37.0	37.0	37.0	37.0
34	36.255	37.0	37.0	37.0	37.0	37.0
35	36.1675	37.0	37.0	37.0	37.0	37.0
36	35.4105	37.0	37.0	37.0	25.0	37.0
37	36.259	37.0	37.0	37.0	37.0	37.0
38	36.087	37.0	37.0	37.0	37.0	37.0
39	35.984	37.0	37.0	37.0	37.0	37.0
40	36.1365	37.0	37.0	37.0	37.0	37.0
41	35.996	37.0	37.0	37.0	37.0	37.0
42	36.0755	37.0	37.0	37.0	37.0	37.0
43	36.143	37.0	37.0	37.0	37.0	37.0
44	36.305	37.0	37.0	37.0	37.0	37.0
45	36.277	37.0	37.0	37.0	37.0	37.0
46	36.2975	37.0	37.0	37.0	37.0	37.0
47	36.185	37.0	37.0	37.0	37.0	37.0
48	36.091	37.0	37.0	37.0	37.0	37.0
49	36.25	37.0	37.0	37.0	37.0	37.0
50	36.1965	37.0	37.0	37.0	37.0	37.0
51	35.8785	37.0	37.0	37.0	37.0	37.0
>>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
1101	51	0.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
25	7.0
26	13.0
27	15.0
28	19.0
29	44.0
30	35.0
31	39.0
32	49.0
33	66.0
34	108.0
35	236.0
36	1745.0
37	1624.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	54.75475475475476	17.067067067067068	16.616616616616618	11.561561561561561
2	22.325	7.025	12.950000000000001	57.699999999999996
3	20.200000000000003	47.875	7.95	23.974999999999998
4	22.400000000000002	8.9	48.225	20.474999999999998
5	37.25	9.775	34.275	18.7
6	62.64999999999999	6.775	14.85	15.725
7	65.2	9.8	11.95	13.05
8	18.5	9.8	61.375	10.325
9	60.95	12.65	11.125	15.275
10	67.4	10.100000000000001	11.025	11.475
11	23.175	5.55	51.975	19.3
12	18.75	10.875	54.725	15.65
13	14.099999999999998	9.575	21.975	54.35
14	21.125	56.974999999999994	11.5	10.4
15	68.125	11.05	12.0	8.825
16	18.875	12.049999999999999	58.3	10.775
17	62.125	10.325	18.099999999999998	9.45
18	65.825	10.825	15.675	7.675
19	20.175	12.75	59.12500000000001	7.95
20	16.525000000000002	52.7	23.200000000000003	7.575
21	54.574999999999996	21.475	15.5	8.450000000000001
22	22.25	51.0	19.275000000000002	7.475
23	18.9	52.37500000000001	18.75	9.975000000000001
24	18.2	14.6	55.925000000000004	11.275
25	15.675	8.075000000000001	60.0	16.25
26	18.5	9.425	19.75	52.325
27	18.425	6.875000000000001	54.05	20.65
28	24.099999999999998	6.4	17.724999999999998	51.775000000000006
29	60.875	6.825	13.925	18.375
30	22.8	6.9	13.850000000000001	56.45
31	23.674999999999997	9.375	25.05	41.9
32	35.699999999999996	10.424999999999999	37.2	16.675
33	60.525	12.475	13.950000000000001	13.05
34	51.949999999999996	28.4	8.5	11.15
35	22.5	56.10000000000001	9.875	11.525
36	18.125	46.35	23.7	11.825
37	16.400000000000002	19.825	48.5	15.275
38	12.925	17.925	40.35	28.799999999999997
39	11.525	18.3	25.424999999999997	44.75
40	13.700000000000001	16.7	36.125	33.475
41	26.950000000000003	16.55	12.775	43.725
42	56.35	14.625	9.025	20.0
43	56.99999999999999	14.075	10.775	18.15
44	43.725	14.85	23.225	18.2
45	28.825	14.374999999999998	35.625	21.175
46	38.175	12.425	12.575	36.825
47	12.625	15.525	8.9	62.949999999999996
48	9.85	30.125	7.1499999999999995	52.87500000000001
49	11.525	57.099999999999994	7.425	23.95
50	25.45	45.775	6.875000000000001	21.9
51	50.9	23.65	7.025	18.425
>>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	0.5
29	1.0
30	1.0
31	1.0
32	0.5
33	0.0
34	0.0
35	0.0
36	0.0
37	0.0
38	0.0
39	0.0
40	0.5
41	1.0
42	1.5
43	2.0
44	5.0
45	8.0
46	22.0
47	36.0
48	55.0
49	74.0
50	182.5
51	291.0
52	643.0
53	995.0
54	1008.5
55	1022.0
56	843.0
57	664.0
58	533.5
59	403.0
60	344.0
61	285.0
62	207.5
63	130.0
64	91.0
65	52.0
66	33.0
67	14.0
68	15.0
69	16.0
70	10.0
71	4.0
72	2.5
73	1.0
74	0.5
75	0.0
76	0.0
77	0.0
78	0.0
79	0.0
80	0.0
81	0.0
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	0.1
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	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
51	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
51	4000.0
>>END_MODULE
>>Sequence Duplication Levels	fail
#Total Deduplicated Percentage	34.25
#Duplication Level	Percentage of deduplicated	Percentage of total
1	75.76642335766424	25.95
2	12.116788321167883	8.3
3	3.64963503649635	3.75
4	1.532846715328467	2.1
5	1.2408759124087592	2.125
6	1.0218978102189782	2.1
7	0.8759124087591241	2.1
8	0.291970802919708	0.8
9	0.291970802919708	0.8999999999999999
>10	2.9197080291970803	18.3
>50	0.0	0.0
>100	0.291970802919708	33.575
>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
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAG	463	11.575000000000001	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAG	447	11.175	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCTGGAATTCTCGGGTGCCAAGG	229	5.7250000000000005	Illumina Small RNA Adapter 2 (100% over 21bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGCTGGAATTCTCGGGTGCCAAGG	204	5.1	Illumina Small RNA Adapter 2 (100% over 21bp)
CGCGACCTCAGATTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCA	49	1.225	RNA PCR Primer, Index 10 (97% over 37bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCAA	46	1.15	No Hit
CGCGACCTCAGATCAGACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	43	1.075	RNA PCR Primer, Index 1 (100% over 32bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGTGGAATTCTCGGGTGCCAAG	41	1.0250000000000001	No Hit
GCATTGGTTGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAG	31	0.775	No Hit
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAGG	29	0.7250000000000001	Illumina Small RNA Adapter 2 (100% over 21bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGTGGAATTCTCGGGTGCCAAGG	27	0.675	Illumina Small RNA Adapter 2 (100% over 21bp)
GCATGGGTTGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAG	26	0.65	No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCAAG	25	0.625	No Hit
GACTCTTAGCGGTGGATTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	23	0.575	RNA PCR Primer, Index 2 (100% over 34bp)
AGGGCTGGGTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCATA	23	0.575	RNA PCR Primer, Index 10 (97% over 37bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCTGGAATTCTCGGGTGCCAAGGA	23	0.575	RNA PCR Primer, Index 1 (100% over 22bp)
GGGCTGGAGAGATGGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	21	0.525	RNA PCR Primer, Index 2 (100% over 34bp)
AGGGCAAAAGCTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	20	0.5	RNA PCR Primer, Index 7 (100% over 35bp)
AGGGCAAAAGCTCGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG	18	0.44999999999999996	RNA PCR Primer, Index 7 (100% over 36bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTGGAATTCTCGGGTGCCAA	16	0.4	No Hit
AGGGCTGGGTCGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCAT	15	0.375	RNA PCR Primer, Index 10 (97% over 37bp)
TGGACGGCGGGGTTCTTGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	14	0.35000000000000003	RNA PCR Primer, Index 1 (100% over 32bp)
GCATTGGTTGTTCAGTGGTAGAATTCTCGCTGGAATTCTCGGGTGCCAAGG	14	0.35000000000000003	Illumina Small RNA Adapter 2 (100% over 21bp)
GCATGGGTTGTTCAGTGGTAGAATTCTCGCTGGAATTCTCGGGTGCCAAGG	14	0.35000000000000003	Illumina Small RNA Adapter 2 (100% over 21bp)
ATGGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAGGA	13	0.325	RNA PCR Primer, Index 1 (100% over 22bp)
GACTCTTAGCGGTGGATCACTTGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
CTATGGTTACGGCTGGCGGTATGGAATTCTCGGGTGCCAAGGAACTCCAGT	13	0.325	RNA PCR Primer, Index 1 (100% over 30bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGTGGAATTCTCGGGTGCCAAGGA	12	0.3	RNA PCR Primer, Index 1 (100% over 22bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTTGGAATTCTCGGGTGCCA	11	0.27499999999999997	No Hit
AGCAGGACGGTGGCCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	11	0.27499999999999997	RNA PCR Primer, Index 7 (100% over 35bp)
TGGGGGATCGTCTAACGGTAGGACCCCAGACTCTTGGAATTCTCGGGTGCC	11	0.27499999999999997	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCTGGAATTCTCGGGTGCCAAGG	10	0.25	Illumina Small RNA Adapter 2 (100% over 21bp)
TCATGAGAACGATCAAGTGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	10	0.25	RNA PCR Primer, Index 1 (100% over 30bp)
GGGGCTGTAGCTCAGATGGGAGAGCGCTGCAATCGTGGAATTCTCGGGTGC	10	0.25	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCAA	10	0.25	No Hit
TGGACGGCGGGGTTCTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
AGCGCCCGTCCGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCA	10	0.25	RNA PCR Primer, Index 10 (97% over 37bp)
GTGCTGTAGGCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGC	10	0.25	RNA PCR Primer, Index 10 (97% over 37bp)
CGCGACCTCAGATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCAT	10	0.25	RNA PCR Primer, Index 10 (97% over 37bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGTGGAATTCTCGGGTGCCAAGGA	10	0.25	RNA PCR Primer, Index 1 (100% over 22bp)
CGCGACCTCAGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGC	10	0.25	RNA PCR Primer, Index 10 (97% over 37bp)
GACTCTTAGCGGTGGATCACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	10	0.25	RNA PCR Primer, Index 1 (100% over 31bp)
GGGGCCATAGCTCAGTTGGGAGAGCGCTTGAATGGAATTCTCGGGTGCCAA	10	0.25	No Hit
GGGGCTGTAGCTCAGATGGGAGAGCGCTGCATGGAATTCTCGGGTGCCAAG	10	0.25	No Hit
TAGCTTATCAGACTGATGTTGACTGGAATTCTCGGGTGCCAAGGAACTCCA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 28bp)
GCGGGTGTAGCTCAGGGGTAGAGCACAACTGGAATTCTCGGGTGCCAAGGA	9	0.22499999999999998	RNA PCR Primer, Index 1 (100% over 22bp)
GGGCTGGAGAGATGGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	9	0.22499999999999998	RNA PCR Primer, Index 7 (100% over 35bp)
TGGGGGATCGTCTAACGGTAGGACCCCAGACTTGGAATTCTCGGGTGCCAA	9	0.22499999999999998	No Hit
AGAAGCCCGGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCA	8	0.2	RNA PCR Primer, Index 10 (97% over 37bp)
GCCCGGATAGCTCAGTCGGTAGAGCATCAGATGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
GCATTTGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAAG	8	0.2	No Hit
TAGCTTATCAGACTGATGTTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	8	0.2	RNA PCR Primer, Index 1 (100% over 29bp)
GGGGCTGTAGCTCAGATGGGAGAGCGCTGCAATCGCTGGAATTCTCGGGTG	7	0.17500000000000002	No Hit
ATTCCGGAGAGGGAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	7	0.17500000000000002	RNA PCR Primer, Index 7 (100% over 35bp)
AGAAGCCCGGCTCGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGC	7	0.17500000000000002	RNA PCR Primer, Index 10 (97% over 37bp)
GTGCTGTAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCA	7	0.17500000000000002	RNA PCR Primer, Index 10 (97% over 37bp)
GGCTGGTCCGAAGGTAGTGAGTTATCTCAATTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCTGGAATTCTCGGGTGCCAAG	7	0.17500000000000002	No Hit
GCATGGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCAA	7	0.17500000000000002	No Hit
CGGAGTGTGGCTCAGCCTGGTAGAGCACCTTGGAATTCTCGGGTGCCAAGG	7	0.17500000000000002	Illumina Small RNA Adapter 2 (100% over 21bp)
ACTCTTAGCGGTGGATCACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 31bp)
AGCGCCCGTCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCATA	7	0.17500000000000002	RNA PCR Primer, Index 10 (97% over 37bp)
TGGACGGCGGGGTTCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT	7	0.17500000000000002	RNA PCR Primer, Index 1 (100% over 30bp)
GGGGCTGTAGCTCAGATGGGAGAGCGCTGCAATTGGAATTCTCGGGTGCCA	7	0.17500000000000002	No Hit
ACAGTAGTCTGCACATTGGTTATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GTTTCCGTAGTGTAGTGGTTATCACGCTCGCCTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
CGGCGCGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCATATC	6	0.15	RNA PCR Primer, Index 10 (97% over 37bp)
GCTCCCTTCGTCTAGCGGTCTAGGACGTCGCCCTCTTGGAATTCTCGGGTG	6	0.15	No Hit
ACTCTTAGCGGTGGATCACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	6	0.15	RNA PCR Primer, Index 1 (100% over 32bp)
CGCGACCTCAGATCAGACGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	6	0.15	RNA PCR Primer, Index 1 (100% over 31bp)
TGGACGGCGGGGTTCTTGCGGATGGAATTCTCGGGTGCCAAGGAACTCCAG	6	0.15	RNA PCR Primer, Index 1 (100% over 29bp)
GGGAGCCTGAGAAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGC	6	0.15	RNA PCR Primer, Index 10 (97% over 37bp)
CCCAGTGTTCAGACTACCTGTTCTGGAATTCTCGGGTGCCAAGGAACTCCA	6	0.15	RNA PCR Primer, Index 1 (100% over 28bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
TTCCGGAGAGGGAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG	6	0.15	RNA PCR Primer, Index 7 (100% over 36bp)
GGTGCTGTAGGCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGC	6	0.15	RNA PCR Primer, Index 10 (97% over 37bp)
GGTGCTGTAGGCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG	6	0.15	RNA PCR Primer, Index 7 (100% over 36bp)
GCCCGGATAGCTCAGTCGGTAGAGCATCAGACTGGAATTCTCGGGTGCCAA	6	0.15	No Hit
GCATTTGTGGTTCAGTGGTAGAATTCTCGCTGGAATTCTCGGGTGCCAAGG	5	0.125	Illumina Small RNA Adapter 2 (100% over 21bp)
TCATGAGAACGATCAAGTGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC	5	0.125	RNA PCR Primer, Index 1 (100% over 31bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCTGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
ACTCTTAGCGGTGGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	5	0.125	RNA PCR Primer, Index 2 (100% over 34bp)
TCCCTGGTCTAGTGGTTAGGATTCGGCGCTGGAATTCTCGGGTGCCAAGGA	5	0.125	RNA PCR Primer, Index 1 (100% over 22bp)
GACTCTTAGCGGTGGATCACTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	5	0.125	RNA PCR Primer, Index 1 (100% over 29bp)
CGCGACCTCAGATCAGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
GACTCTTAGCGGTGGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (100% over 33bp)
AGAAGCCCGGCTCGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG	5	0.125	RNA PCR Primer, Index 7 (100% over 36bp)
ACTCTTAGCGGTGGATCACTCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	5	0.125	RNA PCR Primer, Index 1 (100% over 30bp)
AGAAGCCGGCGGGAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	5	0.125	RNA PCR Primer, Index 7 (100% over 35bp)
GCATGGGTGGTTCAGTGGTAGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	5	0.125	RNA PCR Primer, Index 1 (96% over 33bp)
ACTCTTAGCGGTGGATTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	5	0.125	RNA PCR Primer, Index 7 (100% over 35bp)
GGGTGCTGTAGGCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA	5	0.125	RNA PCR Primer, Index 7 (100% over 35bp)
CGCGGCGCCTCGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG	5	0.125	RNA PCR Primer, Index 7 (100% over 36bp)
ATGGGTGGTTCAGTGGTAGAATTCTCGCTGGAATTCTCGGGTGCCAAGGAA	5	0.125	RNA PCR Primer, Index 1 (100% over 23bp)
>>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	0.05	0.0	0.0	0.0
2	0.0	0.05	0.0	0.0	0.0
3	0.0	0.05	0.0	0.0	0.0
4	0.0	0.05	0.0	0.0	0.0
5	0.0	0.1	0.0	0.0	0.0
6	0.0	0.1	0.0	0.0	0.0
7	0.0	0.1	0.0	0.0	0.0
8	0.0	0.225	0.0	0.0	0.0
9	0.0	0.425	0.0	0.0	0.0
10	0.0	1.025	0.0	0.0	0.0
11	0.0	1.825	0.0	0.0	0.0
12	0.0	3.4	0.0	0.0	0.0
13	0.0	5.0	0.0	0.0	0.0
14	0.0	8.025	0.0	0.0	0.0
15	0.0	11.025	0.0	0.0	0.0
16	0.0	14.475	0.0	0.0	0.0
17	0.0	18.35	0.0	0.0	0.0
18	0.0	22.15	0.0	0.0	0.0
19	0.0	24.725	0.0	0.0	0.0
20	0.0	28.725	0.0	0.0	0.0
21	0.0	31.5	0.0	0.0	0.0
22	0.0	34.85	0.0	0.0	0.0
23	0.0	37.95	0.0	0.0	0.0
24	0.0	39.95	0.0	0.0	0.0
25	0.0	41.2	0.0	0.0	0.0
26	0.0	42.225	0.0	0.0	0.0
27	0.0	42.85	0.0	0.0	0.0
28	0.0	43.35	0.0	0.0	0.0
29	0.0	44.05	0.0	0.0	0.0
30	0.0	46.525	0.0	0.0	0.0
31	0.0	61.175	0.0	0.0	0.0
32	0.0	89.35	0.0	0.0	0.0
33	0.0	93.65	0.0	0.0	0.0
34	0.0	94.9	0.0	0.0	0.0
35	0.0	96.225	0.0	0.0	0.0
36	0.0	97.05	0.0	0.0	0.0
37	0.0	97.675	0.0	0.0	0.0
38	0.0	97.925	0.0	0.0	0.0
39	0.0	98.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	fail
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CATTGGT	90	0.0	45.000004	2
TCTCGCT	65	0.0	45.000004	25
TCTCGCC	95	0.0	45.000004	25
TGGTGGT	90	0.0	45.000004	5
GCATTGG	90	0.0	45.000004	1
CTCGCCT	95	0.0	45.000004	26
ATGGGTG	70	0.0	45.0	3
GTAGAAT	160	0.0	45.0	18
TGGTTCA	150	0.0	45.0	8
AGCTCAG	20	6.222983E-4	45.0	9
TGGTAGA	160	0.0	45.0	16
ATTGGTG	80	0.0	45.0	3
AGTGGTA	160	0.0	45.0	14
TAGCTCA	20	6.222983E-4	45.0	8
GGTTCAG	150	0.0	45.0	9
GTTCAGT	160	0.0	45.0	10
AGAATTC	160	0.0	45.0	20
TTCTCGC	160	0.0	45.0	24
GGTAGAA	160	0.0	45.0	17
TTGGTGG	80	0.0	45.0	4
>>END_MODULE
Read 4088434 spots for SRR32454948.sra
Written 4088434 spots for SRR32454948.sra
Read 4088434 spots for SRR32454948.sra
Written 4088434 spots for SRR32454948.sra
Read 4088434 spots for SRR32454948.sra
Written 4088434 spots for SRR32454948.sra
Read 4088434 spots for SRR32454948.sra
Written 4088434 spots for SRR32454948.sra
Read 4088434 spots for SRR32454948.sra
Written 4088434 spots for SRR32454948.sra
Read 4088434 spots for SRR32454948.sra
Written 4088434 spots for SRR32454948.sra
Read 4088437 spots for SRR32454948.sra
Read 4088434 spots for SRR32454948.sra
Written 4088437 spots for SRR32454948.sra
Written 4088434 spots for SRR32454948.sra
SRR ids: ['SRR32454948.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_zljvk41_
SRR32454948.sra spots: 32707475
blocks: [[1, 4088434], [4088435, 8176868], [8176869, 12265302], [12265303, 16353736], [16353737, 20442170], [20442171, 24530604], [24530605, 28619038], [28619039, 32707475]]
SRR32454948 file size 5625708
SRR32454948 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	/usr/local/bin/skewer -f sanger -l 18 -q 10 -k inf -t 8 -o SRR32454948 SRR32454948_1.fastq
Input file:	SRR32454948_1.fastq
trimmed:	SRR32454948-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 
-- minimum overlap length for adapter detection (-k):	inf
-- number of concurrent threads (-t):	8
Sat Nov  1 18:09:22 2025 >> started

Sat Nov  1 18:10:09 2025 >> done (47.192s)
32707475 reads processed; of these:
     434 ( 0.00%) short reads filtered out after trimming by size control
       4 ( 0.00%) empty reads filtered out after trimming by size control
32707037 (100.00%) reads available; of these:
     321 ( 0.00%) trimmed reads available after processing
32706716 (100.00%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 50	     321	  0.00%
 51	32706716	100.00%
32707037 reads passed initial QC


criterion=sequence-density
sequence-density=97.82
sequence-density-rank=1
fanout-score=9.09
fanout-score-rank=1
prefix-density=98.60
prefix-fanout=9.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCATATC


criterion=fanout-score
sequence-density=97.82
sequence-density-rank=1
fanout-score=9.09
fanout-score-rank=1
prefix-density=98.60
prefix-fanout=9.0
sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCATATC
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:	/usr/local/bin/skewer -f sanger -l 18 -t 8 -x TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCATATC -o SRR32454948 -
Input file:	STDIN
trimmed:	SRR32454948-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGCATATC
-- 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):		Sanger/Illumina 1.8+ FASTQ 
-- minimum overlap length for adapter detection (-k):	3
-- number of concurrent threads (-t):	8
Sat Nov  1 18:12:19 2025 >> started

Sat Nov  1 18:12:38 2025 >> done (19.608s)
32039547 reads processed; of these:
 7499702 (23.41%) short reads filtered out after trimming by size control
    8972 ( 0.03%) empty reads filtered out after trimming by size control
24530873 (76.56%) reads available; of these:
24451162 (99.68%) trimmed reads available after processing
   79711 ( 0.32%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  914495	  3.73%
 19	 1356209	  5.53%
 20	 1012009	  4.13%
 21	 1104618	  4.50%
 22	 1000653	  4.08%
 23	  682928	  2.78%
 24	  424304	  1.73%
 25	  301207	  1.23%
 26	  202590	  0.83%
 27	  167430	  0.68%
 28	  331648	  1.35%
 29	  833182	  3.40%
 30	 4715012	 19.22%
 31	 8606884	 35.09%
 32	 1242299	  5.06%
 33	  462450	  1.89%
 34	  484528	  1.98%
 35	  248929	  1.01%
 36	  127611	  0.52%
 37	   48507	  0.20%
 38	   33575	  0.14%
 39	   39173	  0.16%
 40	   30286	  0.12%
 41	   56845	  0.23%
 42	   11959	  0.05%
 43	    3201	  0.01%
 44	    2385	  0.01%
 45	    1589	  0.01%
 46	    1327	  0.01%
 47	    2076	  0.01%
 48	    1253	  0.01%
 49	       0	  0.00%
 50	       8	  0.00%
 51	   79703	  0.32%


criterion=sequence-density
sequence-density=46.72
sequence-density-rank=1
fanout-score=2.00
fanout-score-rank=8
prefix-density=46.63
prefix-fanout=2.0
sequence=GGTGGTTCAGTGGTAGAATTCTCGCCT


criterion=fanout-score
sequence-density=0.96
sequence-density-rank=10
fanout-score=11.47
fanout-score-rank=1
prefix-density=2.45
prefix-fanout=4.5
sequence=TAGCTCAGTTGG
                                 Started job on |	Nov 01 18:13:22
                             Started mapping on |	Nov 01 18:13:22
                                    Finished on |	Nov 01 18:14:40
       Mapping speed, Million of reads per hour |	1163.00

                          Number of input reads |	25198363
                      Average input read length |	28
                                    UNIQUE READS:
                   Uniquely mapped reads number |	1692899
                        Uniquely mapped reads % |	6.72%
                          Average mapped length |	20.27
                       Number of splices: Total |	65683
            Number of splices: Annotated (sjdb) |	6054
                       Number of splices: GT/AG |	61904
                       Number of splices: GC/AG |	1211
                       Number of splices: AT/AC |	0
               Number of splices: Non-canonical |	2568
                      Mismatch rate per base, % |	1.97%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.75
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.12
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	12561098
             % of reads mapped to multiple loci |	49.85%
        Number of reads mapped to too many loci |	8502188
             % of reads mapped to too many loci |	33.74%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	9.59%
                     % of reads unmapped: other |	0.10%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	10944366	10944366	10944366
N_multimapping	12561098	12561098	12561098
N_noFeature	958443	1117793	1530009
N_ambiguous	46523	42545	462
UnstrandedReadsAssigned:687933 PositiveStrandReadsAssigned:532561 NegativeStrandReadsAssigned:162428
Dataset is classified unstranded
MeadianReadLen=30 20thPercentileLength=22 echo kmer=19
SRR32454948 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: 31,715
[index] number of k-mers: 49,362,984
[index] number of equivalence classes: 166,181
[quant] running in single-end mode
[quant] will process file 1: SRR32454948-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 25,198,363 reads, 315,071 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 701 rounds

  31716 SRR32454948.ke.tsv
  32883 SRR32454948.se.tsv
  64599 total
==> SRR32454948.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
ENSRNOT00000047550.4	955	856	3	7.14683
ENSRNOT00000040993.4	1039	940	0	0
ENSRNOT00000050156.3	1545	1446	46	64.8717
ENSRNOT00000043693.3	684	585	3	10.4576
ENSRNOT00000046201.3	204	105	0	0
ENSRNOT00000046108.3	681	582	1	3.50383
ENSRNOT00000049683.3	784	685	7	20.8388
ENSRNOT00000041241.3	348	249	2	16.3793
ENSRNOT00000044582.3	297	198	0	0

==> SRR32454948.se.tsv <==
ENSRNOG00000046319	0
ENSRNOG00000047964	0
ENSRNOG00000050370	0
ENSRNOG00000032365	0
ENSRNOG00000040300	0
ENSRNOG00000058808	0
ENSRNOG00000061316	1
ENSRNOG00000050129	0
ENSRNOG00000040316	0
ENSRNOG00000023659	0
SRR32454948 completed mapping pipeline successfully
