Starting /dee2/code/volunteer_pipeline.sh SRR12060857
    current disk space = 344676900
    free memory = 65587544 
SRR12060857 SRAfilesize
6ca4bf3790540677505634d046e46dfb  SRR12060857.sra
SRR12060857.sra file validated
SRR12060857 is single end
SRR12060857 is conventional basespace
SRR12060857 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR12060857_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	48
>>END_MODULE
>>Per base sequence quality	pass
#Base	Mean	Median	Lower Quartile	Upper Quartile	10th Percentile	90th Percentile
1	31.13825	32.0	32.0	32.0	32.0	32.0
2	31.301	32.0	32.0	32.0	32.0	32.0
3	31.522	32.0	32.0	32.0	32.0	32.0
4	31.53275	32.0	32.0	32.0	32.0	32.0
5	31.47775	32.0	32.0	32.0	32.0	32.0
6	35.0215	36.0	36.0	36.0	36.0	36.0
7	35.054	36.0	36.0	36.0	36.0	36.0
8	35.034	36.0	36.0	36.0	36.0	36.0
9	34.99125	36.0	36.0	36.0	36.0	36.0
10	35.0775	36.0	36.0	36.0	36.0	36.0
11	35.014	36.0	36.0	36.0	36.0	36.0
12	34.954	36.0	36.0	36.0	32.0	36.0
13	35.0585	36.0	36.0	36.0	36.0	36.0
14	34.96425	36.0	36.0	36.0	36.0	36.0
15	34.843	36.0	36.0	36.0	36.0	36.0
16	34.998	36.0	36.0	36.0	36.0	36.0
17	34.96925	36.0	36.0	36.0	36.0	36.0
18	34.891	36.0	36.0	36.0	36.0	36.0
19	34.993	36.0	36.0	36.0	36.0	36.0
20	34.91125	36.0	36.0	36.0	36.0	36.0
21	35.03875	36.0	36.0	36.0	36.0	36.0
22	34.88125	36.0	36.0	36.0	36.0	36.0
23	35.0215	36.0	36.0	36.0	36.0	36.0
24	34.92	36.0	36.0	36.0	36.0	36.0
25	35.0255	36.0	36.0	36.0	36.0	36.0
26	34.8865	36.0	36.0	36.0	32.0	36.0
27	34.78175	36.0	36.0	36.0	32.0	36.0
28	34.97925	36.0	36.0	36.0	36.0	36.0
29	34.75125	36.0	36.0	36.0	32.0	36.0
30	34.7755	36.0	36.0	36.0	32.0	36.0
31	34.7695	36.0	36.0	36.0	36.0	36.0
32	34.7165	36.0	36.0	36.0	32.0	36.0
33	34.856	36.0	36.0	36.0	36.0	36.0
34	34.77925	36.0	36.0	36.0	32.0	36.0
35	34.54975	36.0	36.0	36.0	32.0	36.0
36	34.71425	36.0	36.0	36.0	32.0	36.0
37	34.52525	36.0	36.0	36.0	32.0	36.0
38	34.5745	36.0	36.0	36.0	32.0	36.0
39	34.41425	36.0	36.0	36.0	32.0	36.0
40	34.36025	36.0	36.0	36.0	32.0	36.0
41	34.46375	36.0	36.0	36.0	32.0	36.0
42	34.516	36.0	36.0	36.0	32.0	36.0
43	34.5775	36.0	36.0	36.0	32.0	36.0
44	34.44825	36.0	36.0	36.0	32.0	36.0
45	34.23025	36.0	36.0	36.0	32.0	36.0
46	34.27175	36.0	36.0	36.0	32.0	36.0
47	34.21175	36.0	36.0	36.0	32.0	36.0
48	34.23425	36.0	36.0	36.0	32.0	36.0
49	34.3235	36.0	36.0	36.0	32.0	36.0
50	33.5205	36.0	36.0	36.0	27.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
19	1.0
20	1.0
21	0.0
22	0.0
23	1.0
24	5.0
25	15.0
26	22.0
27	34.0
28	54.0
29	80.0
30	99.0
31	146.0
32	173.0
33	292.0
34	611.0
35	2466.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	25.8	31.374999999999996	31.95	10.875
2	26.424999999999997	19.0	28.625	25.95
3	34.375	19.0	22.45	24.175
4	34.9	26.55	22.55	16.0
5	20.724999999999998	37.55	23.75	17.974999999999998
6	23.625	23.05	34.699999999999996	18.625
7	36.275	25.85	25.3	12.575
8	18.725	28.625	39.574999999999996	13.075000000000001
9	22.275	36.725	20.775	20.225
10	40.675	17.5	27.825	14.000000000000002
11	20.150000000000002	21.7	39.050000000000004	19.1
12	21.875	20.175	29.725	28.225
13	28.275	23.95	19.575	28.199999999999996
14	21.478696741854638	42.18045112781955	22.656641604010026	13.684210526315791
15	27.35	35.325	23.45	13.875000000000002
16	17.9	38.725	24.975	18.4
17	25.474999999999998	34.150000000000006	28.000000000000004	12.375
18	41.375	20.45	18.275	19.900000000000002
19	25.374999999999996	30.0	27.575	17.05
20	24.65	26.674999999999997	34.300000000000004	14.374999999999998
21	22.725	36.375	18.375	22.525000000000002
22	26.6	36.8	21.975	14.625
23	34.5	33.25	19.725	12.525
24	22.1	41.075	25.1	11.725
25	24.349999999999998	38.35	20.625	16.675
26	35.75	26.900000000000002	18.3	19.05
27	26.974999999999998	40.425	15.2	17.4
28	28.575	24.125	26.200000000000003	21.099999999999998
29	25.7	29.799999999999997	12.9	31.6
30	40.94665664913599	30.15276734284999	8.564988730277987	20.33558727773604
31	42.35	29.5	10.125	18.025
32	26.375	44.975	11.1	17.549999999999997
33	29.575000000000003	40.025	9.15	21.25
34	34.658664666166544	29.75743935983996	13.87846961740435	21.705426356589147
35	25.012506253126567	39.14457228614307	12.131065532766383	23.71185592796398
36	29.679679679679676	32.83283283283283	9.65965965965966	27.82782782782783
37	20.32032032032032	33.88388388388389	11.06106106106106	34.73473473473474
38	25.05	36.875	9.700000000000001	28.375
39	22.575	27.6	14.149999999999999	35.675000000000004
40	18.892508143322477	38.66198947632172	14.63292407917815	27.81257830117765
41	22.575	22.1	15.725	39.6
42	29.425	25.5	20.349999999999998	24.725
43	24.724724724724727	22.64764764764765	29.804804804804807	22.822822822822822
44	20.28514257128564	25.737868934467233	18.05902951475738	35.91795897948975
45	20.349999999999998	29.975	25.575	24.099999999999998
46	28.928928928928926	27.05205205205205	15.79079079079079	28.22822822822823
47	14.274999999999999	36.625	19.675	29.425
48	11.377844461115279	37.53438359589897	16.804201050262566	34.28357089272318
49	14.435826870152615	30.122591943957964	13.610207655741807	41.83137353014761
50	14.000000000000002	25.324999999999996	27.224999999999998	33.45
>>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	1.0
20	1.0
21	0.5
22	0.0
23	0.5
24	1.0
25	0.5
26	0.0
27	2.5
28	5.0
29	4.0
30	3.0
31	4.5
32	6.0
33	13.5
34	21.0
35	34.5
36	48.0
37	62.5
38	77.0
39	111.0
40	145.0
41	228.5
42	312.0
43	455.5
44	599.0
45	529.0
46	459.0
47	469.5
48	480.0
49	492.5
50	505.0
51	481.0
52	457.0
53	472.0
54	487.0
55	346.5
56	206.0
57	150.5
58	95.0
59	74.5
60	54.0
61	37.5
62	21.0
63	14.0
64	7.0
65	4.5
66	2.0
67	2.5
68	3.0
69	1.5
70	0.0
71	1.0
72	2.0
73	1.0
74	0.0
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	1.5
100	3.0
>>END_MODULE
>>Per base N content	pass
#Base	N-Count
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	0.25
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	0.17500000000000002
31	0.0
32	0.0
33	0.0
34	0.025
35	0.05
36	0.1
37	0.1
38	0.0
39	0.0
40	0.22499999999999998
41	0.0
42	0.0
43	0.1
44	0.05
45	0.0
46	0.1
47	0.0
48	0.025
49	0.075
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	warn
#Total Deduplicated Percentage	69.72500000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	90.96450340623879	63.425
2	3.979921118680531	5.55
3	1.6851918250268914	3.5249999999999995
4	0.9322337755467911	2.6
5	0.609537468626748	2.125
6	0.25098601649336677	1.05
7	0.2151308712800287	1.05
8	0.035855145213338116	0.2
9	0.14342058085335246	0.8999999999999999
>10	1.0756543564001435	13.25
>50	0.10756543564001435	6.325
>100	0.0	0.0
>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
TTCATGGACGTTGATAAGATCTTTCAGATCGGAAGAGCACACGTCTGAAC	96	2.4	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAAGA	79	1.975	No Hit
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	78	1.95	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAG	38	0.95	TruSeq Adapter, Index 7 (97% over 36bp)
TCCCAAATGTAGACAAAGCAAGATCGGAAGAGCACACGTCTGAACTCCAG	36	0.8999999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TTGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTAT	30	0.75	TruSeq Adapter, Index 10 (100% over 41bp)
TTCATGGACGTTGATAAGATCTTTCCAGATCGGAAGAGCACACGTCTGAA	29	0.7250000000000001	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TCCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTTGGATTGAAGGGAGCTCTTAGATCGGAAGAGCACACGTCTGAACTCCA	22	0.5499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAG	21	0.525	TruSeq Adapter, Index 7 (97% over 36bp)
AGTTACTAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCC	21	0.525	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTAGGGAAGTACTTTAAGAAACATATGTATAAGATCGGAAGAGCACACGT	19	0.475	No Hit
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	19	0.475	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCAGATCGGA	19	0.475	No Hit
AGTTACTAATTCATGATCTGGCATAGATCGGAAGAGCACACGTCTGAACT	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
CGGCTCTGATACCAATTGATGAGATCGGAAGAGCACACGTCTGAACTCCA	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGCTGTAGCACACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	16	0.4	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	15	0.375	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	15	0.375	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	14	0.35000000000000003	No Hit
GGGGATATGGCGGAATTGGTAGACGCTACGGACTTAGATCGGAAGAGCAC	14	0.35000000000000003	No Hit
TTTGGATTGAAGGGAGCTCTAAGATCGGAAGAGCACACGTCTGAACTCCA	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTCATGGACGTTGATAAGATCTTTAGATCGGAAGAGCACACGTCTGAACT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAAGATCGGAAG	12	0.3	No Hit
TCGGACCAGGCTTCATTCCCCAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTAGATCGGAAGAGCACAC	12	0.3	No Hit
GAGGGACGACGATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTA	12	0.3	TruSeq Adapter, Index 7 (97% over 35bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTAGATCGGAAGAGCACAC	12	0.3	No Hit
CTTCGTGATTGATTTGCCATATTTTCTGATCAGATCGGAAGAGCACACGT	11	0.27499999999999997	No Hit
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTTAGATCGGAAGAGCACA	11	0.27499999999999997	No Hit
GCGGACTGCTCGAGCTGCAGATCGGAAGAGCACACGTCTGAACTCCAGTC	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AAGGAAGCTATAAGTAATGAAGATCGGAAGAGCACACGTCTGAACTCCAG	10	0.25	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCCCAAATGTAGACAAAGCAGATCGGAAGAGCACACGTCTGAACTCCAGT	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGTTGTAGTCTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TCCCAAATGTAGACAAAGCTAGATCGGAAGAGCACACGTCTGAACTCCAG	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	9	0.22499999999999998	No Hit
GGGTTGATATGAGAACACACGAGATCGGAAGAGCACACGTCTGAACTCCA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTAAGTGTCACGGAAATCCCTAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCAGATCGGAAGAGCACACG	7	0.17500000000000002	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATG	7	0.17500000000000002	TruSeq Adapter, Index 10 (100% over 49bp)
ATGATATTTGTAGTAATGGCGAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGCTTTTATGTTAGTTCGTACTATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
TTTGGATTGAAGGGAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCAG	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TTAGGGAAGTACTTTAAGAAACATATGTAAGATCGGAAGAGCACACGTCT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 21bp)
TTCATGGACGTTGATAAGATCTTTCTAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGAAGATCGGAAGA	6	0.15	No Hit
AGTTACTAATTCATGATCTGGCAAAGATCGGAAGAGCACACGTCTGAACT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATATAGCTCAGTTGGTAGAGCTCCGCTCTTGCAAAGATCGGAAGAG	6	0.15	No Hit
TAAAACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
AACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TCCGCTGTAGCACTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGGATGTAGCTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
GGTGAGGGACGACGATTTAGATCGGAAGAGCACACGTCTGAACTCCAGTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
AGGGCTATAGCTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAG	5	0.125	TruSeq Adapter, Index 7 (97% over 36bp)
TCCGTTATCGTCCAGCGGTTAGGATATCTGGCAGATCGGAAGAGCACACG	5	0.125	No Hit
TGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATC	5	0.125	TruSeq Adapter, Index 10 (100% over 42bp)
TCCGCTTTTATGTTAGTTCGTACTATAGATCGGAAGAGCACACGTCTGAA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GGTGAGGGACGACGATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TGTCGAGTAGACCTTGTTGTTTTGTTTTATTGCAAGATCGGAAGAGCACA	5	0.125	No Hit
GGGGATGTAGCTCAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTCCATTGTCTAATGGATAGGACATAGGTCTTCTAAACAGATCGGAAG	5	0.125	No Hit
ATTGTATCATTAACTATTTCTTTATAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTCAGATCGGAAGAGCAC	5	0.125	No Hit
TTCATGGACGTTGATAAGATCTTTTAGATCGGAAGAGCACACGTCTGAAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
AAAACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
ATTTATTTCTACATCTAGGATCCGATTTGTATCAGATCGGAAGAGCACAC	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	0.2	0.0	0.0	0.0	0.0
2	0.2	0.0	0.0	0.0	0.0
3	0.2	0.0	0.0	0.0	0.0
4	0.225	0.0	0.0	0.0	0.0
5	0.225	0.0	0.0	0.0	0.0
6	0.25	0.0	0.0	0.0	0.0
7	0.25	0.0	0.0	0.0	0.0
8	0.55	0.0	0.0	0.0	0.0
9	1.675	0.0	0.0	0.0	0.0
10	1.7	0.0	0.0	0.0	0.0
11	1.95	0.0	0.0	0.0	0.0
12	2.15	0.0	0.0	0.0	0.0
13	2.7	0.0	0.0	0.0	0.0
14	5.95	0.0	0.0	0.0	0.0
15	7.575	0.0	0.0	0.0	0.0
16	9.8	0.0	0.0	0.0	0.0
17	14.35	0.0	0.0	0.0	0.0
18	16.55	0.0	0.0	0.0	0.0
19	18.525	0.0	0.0	0.0	0.0
20	21.925	0.0	0.0	0.0	0.0
21	26.4	0.0	0.0	0.0	0.0
22	33.725	0.0	0.0	0.0	0.0
23	40.3	0.0	0.0	0.0	0.0
24	46.225	0.0	0.0	0.0	0.0
25	61.675	0.0	0.0	0.0	0.0
26	66.65	0.0	0.0	0.0	0.0
27	70.275	0.0	0.0	0.0	0.0
28	71.8	0.0	0.0	0.0	0.0
29	72.825	0.0	0.0	0.0	0.0
30	74.225	0.0	0.0	0.0	0.0
31	75.725	0.0	0.0	0.0	0.0
32	78.525	0.0	0.0	0.0	0.0
33	80.775	0.0	0.0	0.0	0.0
34	83.575	0.0	0.0	0.0	0.0
35	85.7	0.0	0.0	0.0	0.0
36	87.675	0.0	0.0	0.0	0.0
37	88.575	0.0	0.0	0.0	0.0
38	89.7	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
CTTTCAG	20	6.952051E-4	44.000004	21
GTTGATA	20	6.952051E-4	44.000004	10
TTCATGG	20	6.952051E-4	44.000004	1
ATCTTTC	20	6.952051E-4	44.000004	19
AGCTCAG	20	6.952051E-4	44.000004	9
CTCCTTG	20	6.952051E-4	44.000004	27
ACGTTGA	20	6.952051E-4	44.000004	8
TAGCTCA	20	6.952051E-4	44.000004	8
TGATAAG	20	6.952051E-4	44.000004	12
ATGGACG	20	6.952051E-4	44.000004	4
GACGTTG	20	6.952051E-4	44.000004	7
AAGATCT	20	6.952051E-4	44.000004	16
TTCTCCT	20	6.952051E-4	44.000004	25
TCATGGA	20	6.952051E-4	44.000004	2
TTGATAA	20	6.952051E-4	44.000004	11
TCTCCTT	20	6.952051E-4	44.000004	26
CATGGAC	20	6.952051E-4	44.000004	3
CGTTGAT	20	6.952051E-4	44.000004	9
AGATCTT	20	6.952051E-4	44.000004	17
TCTTTCA	20	6.952051E-4	44.000004	20
>>END_MODULE
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
Rejected 2108972 READS because READLEN < 1
Read 2108972 spots for SRR12060857.sra
Written 2108972 spots for SRR12060857.sra
Rejected 2108964 READS because READLEN < 1
Read 2108964 spots for SRR12060857.sra
Written 2108964 spots for SRR12060857.sra
SRR ids: ['SRR12060857.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_8bbp7wq8
SRR12060857.sra spots: 33743432
blocks: [[1, 2108964], [2108965, 4217928], [4217929, 6326892], [6326893, 8435856], [8435857, 10544820], [10544821, 12653784], [12653785, 14762748], [14762749, 16871712], [16871713, 18980676], [18980677, 21089640], [21089641, 23198604], [23198605, 25307568], [25307569, 27416532], [27416533, 29525496], [29525497, 31634460], [31634461, 33743432]]
SRR12060857 file size 4756428
SRR12060857 completed basic pipeline successfully
skewer v0.2.2 [April 4, 2016]
COMMAND LINE:	skewer -f sanger -l 18 -q 10 -k inf -t 16 -o SRR12060857 SRR12060857_1.fastq
Input file:	SRR12060857_1.fastq
trimmed:	SRR12060857-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):	16
Fri Apr 26 13:22:42 2024 >> started

Fri Apr 26 13:23:04 2024 >> done (22.082s)
33743432 reads processed; of these:
 6226240 (18.45%) short reads filtered out after trimming by size control
   79665 ( 0.24%) empty reads filtered out after trimming by size control
27437527 (81.31%) reads available; of these:
  838758 ( 3.06%) trimmed reads available after processing
26598769 (96.94%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  835343	  3.04%
 19	       0	  0.00%
 20	       0	  0.00%
 21	       0	  0.00%
 22	       0	  0.00%
 23	       0	  0.00%
 24	       0	  0.00%
 25	       0	  0.00%
 26	       0	  0.00%
 27	       0	  0.00%
 28	       0	  0.00%
 29	       0	  0.00%
 30	       0	  0.00%
 31	       1	  0.00%
 32	       0	  0.00%
 33	       0	  0.00%
 34	       0	  0.00%
 35	      15	  0.00%
 36	      12	  0.00%
 37	       6	  0.00%
 38	      35	  0.00%
 39	       4	  0.00%
 40	      31	  0.00%
 41	       1	  0.00%
 42	       3	  0.00%
 43	       4	  0.00%
 44	       0	  0.00%
 45	       0	  0.00%
 46	     273	  0.00%
 47	     211	  0.00%
 48	    1255	  0.00%
 49	    1564	  0.01%
 50	26598769	 96.94%
27437527 reads passed initial QC


criterion=sequence-density
sequence-density=84.73
sequence-density-rank=1
fanout-score=49.44
fanout-score-rank=1
prefix-density=91.31
prefix-fanout=45.9
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCT


criterion=fanout-score
sequence-density=84.73
sequence-density-rank=1
fanout-score=49.44
fanout-score-rank=1
prefix-density=91.31
prefix-fanout=45.9
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCT
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 -f sanger -l 18 -t 16 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCT -o SRR12060857 -
Input file:	STDIN
trimmed:	SRR12060857-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCT
-- 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):	16
Fri Apr 26 13:23:49 2024 >> started

Fri Apr 26 13:24:18 2024 >> done (28.690s)
26791938 reads processed; of these:
   19529 ( 0.07%) short reads filtered out after trimming by size control
      84 ( 0.00%) empty reads filtered out after trimming by size control
26772325 (99.93%) reads available; of these:
25694993 (95.98%) trimmed reads available after processing
 1077332 ( 4.02%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  832781	  3.11%
 19	 1019477	  3.81%
 20	 1447057	  5.41%
 21	 2585512	  9.66%
 22	 2296110	  8.58%
 23	 1966058	  7.34%
 24	 4918993	 18.37%
 25	 1707554	  6.38%
 26	  944223	  3.53%
 27	  484683	  1.81%
 28	  392948	  1.47%
 29	  428953	  1.60%
 30	  487861	  1.82%
 31	  886408	  3.31%
 32	  695039	  2.60%
 33	  852115	  3.18%
 34	  678468	  2.53%
 35	  697521	  2.61%
 36	  368003	  1.37%
 37	  266915	  1.00%
 38	  277369	  1.04%
 39	 1031530	  3.85%
 40	  321291	  1.20%
 41	  232646	  0.87%
 42	  350968	  1.31%
 43	  121306	  0.45%
 44	   78572	  0.29%
 45	   57721	  0.22%
 46	   33269	  0.12%
 47	   35579	  0.13%
 48	     684	  0.00%
 49	     251	  0.00%
 50	  274460	  1.03%


criterion=sequence-density
sequence-density=4.42
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=8
prefix-density=0.00
prefix-fanout=1.0
sequence=GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAA


criterion=fanout-score
sequence-density=0.25
sequence-density-rank=18
fanout-score=12.26
fanout-score-rank=1
prefix-density=2.96
prefix-fanout=1.0
sequence=GTAGACAAAGCTTTTT
                                 Started job on |	Apr 26 13:24:56
                             Started mapping on |	Apr 26 13:24:56
                                    Finished on |	Apr 26 13:27:26
       Mapping speed, Million of reads per hour |	658.03

                          Number of input reads |	27417914
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	11611284
                        Uniquely mapped reads % |	42.35%
                          Average mapped length |	26.69
                       Number of splices: Total |	111757
            Number of splices: Annotated (sjdb) |	30815
                       Number of splices: GT/AG |	100283
                       Number of splices: GC/AG |	1032
                       Number of splices: AT/AC |	218
               Number of splices: Non-canonical |	10224
                      Mismatch rate per base, % |	0.29%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.17
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	13081742
             % of reads mapped to multiple loci |	47.71%
        Number of reads mapped to too many loci |	1382308
             % of reads mapped to too many loci |	5.04%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	4.52%
                     % of reads unmapped: other |	0.38%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2724888	2724888	2724888
N_multimapping	13081742	13081742	13081742
N_noFeature	5299995	5809944	10752412
N_ambiguous	566078	213165	7772
UnstrandedReadsAssigned:5745211 PositiveStrandReadsAssigned:5588175 NegativeStrandReadsAssigned:851100
Dataset is classified positive stranded
MeadianReadLen=24 20thPercentileLength=21 echo kmer=19
SRR12060857 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: 48,359
[index] number of k-mers: 44,957,248
[index] number of equivalence classes: 195,259
[quant] running in single-end mode
[quant] will process file 1: SRR12060857-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 27,417,914 reads, 1,366,545 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 964 rounds

  48360 SRR12060857.ke.tsv
  32833 SRR12060857.se.tsv
  81193 total
==> SRR12060857.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	311	53.1874
AT1G18320.1	699	600	0	0
AT5G11100.1	1709	1610	2	0.511999
AT4G35335.1	1280	1181	5	1.74496
AT1G60930.1	3876	3777	3	0.327371
AT1G17000.1	2351	2252	0	0
AT3G55270.1	3130	3031	15	2.03972
AT4G16150.1	3181	3082	24.2793	3.2469
AT3G18150.1	1370	1271	9	2.91852

==> SRR12060857.se.tsv <==
AT1G01010	1
AT1G01020	15
AT1G03987	0
AT1G01030	2
AT1G01040	110
AT1G03993	2
AT1G01046	78
AT1G01050	17
AT1G03997	0
AT1G01060	21
SRR12060857 completed mapping pipeline successfully
