Starting /dee2/code/volunteer_pipeline.sh SRR12060859
    current disk space = 232199144
    free memory = 128987612 
SRR12060859 SRAfilesize
4d32f56ea1333d772c89dbcc3977a906  SRR12060859.sra
SRR12060859.sra file validated
SRR12060859 is single end
SRR12060859 is conventional basespace
SRR12060859 read1 length is 50 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR12060859_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	31.1175	32.0	32.0	32.0	32.0	32.0
2	31.44275	32.0	32.0	32.0	32.0	32.0
3	31.5085	32.0	32.0	32.0	32.0	32.0
4	31.55725	32.0	32.0	32.0	32.0	32.0
5	31.40725	32.0	32.0	32.0	32.0	32.0
6	34.9785	36.0	36.0	36.0	36.0	36.0
7	34.9975	36.0	36.0	36.0	36.0	36.0
8	34.97075	36.0	36.0	36.0	36.0	36.0
9	34.96775	36.0	36.0	36.0	36.0	36.0
10	34.95775	36.0	36.0	36.0	36.0	36.0
11	35.068	36.0	36.0	36.0	36.0	36.0
12	35.009	36.0	36.0	36.0	36.0	36.0
13	34.92175	36.0	36.0	36.0	36.0	36.0
14	34.99725	36.0	36.0	36.0	36.0	36.0
15	34.90275	36.0	36.0	36.0	36.0	36.0
16	35.02575	36.0	36.0	36.0	36.0	36.0
17	34.99625	36.0	36.0	36.0	36.0	36.0
18	34.999	36.0	36.0	36.0	36.0	36.0
19	35.025	36.0	36.0	36.0	36.0	36.0
20	35.09725	36.0	36.0	36.0	36.0	36.0
21	34.96975	36.0	36.0	36.0	36.0	36.0
22	34.90225	36.0	36.0	36.0	36.0	36.0
23	35.0875	36.0	36.0	36.0	36.0	36.0
24	34.9545	36.0	36.0	36.0	36.0	36.0
25	35.04425	36.0	36.0	36.0	36.0	36.0
26	34.8665	36.0	36.0	36.0	32.0	36.0
27	34.6885	36.0	36.0	36.0	32.0	36.0
28	34.8555	36.0	36.0	36.0	32.0	36.0
29	34.8485	36.0	36.0	36.0	32.0	36.0
30	34.81025	36.0	36.0	36.0	32.0	36.0
31	34.87375	36.0	36.0	36.0	36.0	36.0
32	34.73325	36.0	36.0	36.0	32.0	36.0
33	34.739	36.0	36.0	36.0	32.0	36.0
34	34.79275	36.0	36.0	36.0	36.0	36.0
35	34.48	36.0	36.0	36.0	32.0	36.0
36	34.6925	36.0	36.0	36.0	32.0	36.0
37	34.538	36.0	36.0	36.0	32.0	36.0
38	34.5585	36.0	36.0	36.0	32.0	36.0
39	34.433	36.0	36.0	36.0	32.0	36.0
40	34.4435	36.0	36.0	36.0	32.0	36.0
41	34.36525	36.0	36.0	36.0	32.0	36.0
42	34.49275	36.0	36.0	36.0	32.0	36.0
43	34.43225	36.0	36.0	36.0	32.0	36.0
44	34.30425	36.0	36.0	36.0	32.0	36.0
45	34.204	36.0	36.0	36.0	32.0	36.0
46	34.0815	36.0	36.0	36.0	32.0	36.0
47	34.125	36.0	36.0	36.0	32.0	36.0
48	33.971	36.0	36.0	36.0	32.0	36.0
49	33.9425	36.0	36.0	36.0	32.0	36.0
50	33.53975	36.0	36.0	36.0	27.0	36.0
>>END_MODULE
>>Per sequence quality scores	pass
#Quality	Count
22	1.0
23	3.0
24	6.0
25	12.0
26	30.0
27	41.0
28	42.0
29	82.0
30	85.0
31	124.0
32	212.0
33	296.0
34	665.0
35	2401.0
>>END_MODULE
>>Per base sequence content	fail
#Base	G	A	T	C
1	27.1	33.15	29.025000000000002	10.725
2	25.624999999999996	17.775	27.425	29.175
3	34.8	18.7	24.8	21.7
4	35.6	24.525	24.349999999999998	15.525
5	18.825	37.85	23.625	19.7
6	22.525000000000002	21.375	37.8	18.3
7	35.15	26.875	26.724999999999998	11.25
8	19.075	26.700000000000003	41.9	12.325
9	22.025	39.125	20.225	18.625
10	41.15	16.725	28.575	13.55
11	20.349999999999998	21.4	40.475	17.775
12	22.35	19.2	27.900000000000002	30.55
13	26.575	25.05	20.4	27.975
14	18.8141105829372	44.23317488116087	23.167375531648737	13.785339004253188
15	26.125	36.6	23.95	13.325000000000001
16	18.2	35.325	27.85	18.625
17	27.35	30.55	28.599999999999998	13.5
18	43.275000000000006	18.925	18.3	19.5
19	23.35	27.650000000000002	32.7	16.3
20	25.4	27.675	34.150000000000006	12.775
21	22.7	38.15	17.775	21.375
22	28.075	36.075	20.625	15.225
23	35.475	35.6	17.25	11.675
24	21.825	41.099999999999994	25.15	11.924999999999999
25	21.675	40.25	23.775	14.299999999999999
26	34.675	26.625	19.875	18.825
27	24.45	39.125	16.075	20.349999999999998
28	28.775000000000002	21.5	29.599999999999998	20.125
29	24.325	27.150000000000002	13.325000000000001	35.199999999999996
30	43.27163581790895	29.214607303651825	8.529264632316158	18.98449224612306
31	40.275	29.175	11.275	19.275000000000002
32	24.7	46.300000000000004	12.625	16.375
33	30.675	40.25	8.825	20.25
34	36.575	28.549999999999997	12.174999999999999	22.7
35	22.705676419104776	38.85971492873218	12.728182045511376	25.70642660665166
36	29.182295573893473	33.23330832708177	9.777444361090271	27.806951737934483
37	17.22930732683171	34.33358339584896	12.178044511127782	36.25906476619154
38	27.175	36.925000000000004	8.575000000000001	27.325
39	24.075	27.3	12.950000000000001	35.675000000000004
40	20.06504878658994	41.30597948461346	14.085564173129846	24.54340755566675
41	22.725	22.05	15.15	40.075
42	31.2	24.375	21.6	22.825
43	23.53088272068017	19.879969992498125	32.40810202550637	24.18104526131533
44	19.6	25.474999999999998	18.4	36.525
45	20.7	30.4	26.174999999999997	22.725
46	34.208552138034506	27.081770442610654	13.228307076769191	25.481370342585645
47	13.625000000000002	40.025	19.975	26.375
48	10.424999999999999	39.35	13.55	36.675000000000004
49	12.903225806451612	26.281570392598148	15.25381345336334	45.561390347586894
50	12.325	24.6	28.15	34.925
>>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	1.0
26	2.0
27	2.5
28	3.0
29	2.0
30	1.0
31	6.5
32	12.0
33	16.5
34	21.0
35	31.0
36	41.0
37	65.5
38	90.0
39	129.0
40	168.0
41	230.5
42	293.0
43	464.5
44	636.0
45	577.5
46	519.0
47	486.5
48	454.0
49	462.0
50	470.0
51	469.0
52	468.0
53	455.0
54	442.0
55	314.5
56	187.0
57	145.5
58	104.0
59	77.0
60	50.0
61	33.5
62	17.0
63	13.0
64	9.0
65	8.0
66	7.0
67	6.0
68	5.0
69	2.5
70	0.0
71	0.0
72	0.0
73	0.5
74	1.0
75	0.5
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	0.0
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	0.075
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	0.05
31	0.0
32	0.0
33	0.0
34	0.0
35	0.025
36	0.025
37	0.025
38	0.0
39	0.0
40	0.075
41	0.0
42	0.0
43	0.025
44	0.0
45	0.0
46	0.025
47	0.0
48	0.0
49	0.025
50	0.0
>>END_MODULE
>>Sequence Length Distribution	pass
#Length	Count
50	4000.0
>>END_MODULE
>>Sequence Duplication Levels	pass
#Total Deduplicated Percentage	70.19999999999999
#Duplication Level	Percentage of deduplicated	Percentage of total
1	91.95156695156696	64.55
2	3.7393162393162394	5.25
3	1.1396011396011396	2.4
4	0.9971509971509971	2.8000000000000003
5	0.39173789173789175	1.375
6	0.14245014245014245	0.6
7	0.14245014245014245	0.7000000000000001
8	0.17806267806267806	1.0
9	0.17806267806267806	1.125
>10	1.0327635327635327	12.675
>50	0.03561253561253561	1.8499999999999999
>100	0.07122507122507123	5.675
>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
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAAGA	121	3.025	No Hit
AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC	106	2.65	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTCATGGACGTTGATAAGATCTTTCAGATCGGAAGAGCACACGTCTGAAC	74	1.8499999999999999	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
TTGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAAT	32	0.8	TruSeq Adapter, Index 12 (100% over 41bp)
TCCCAAATGTAGACAAAGCAAGATCGGAAGAGCACACGTCTGAACTCCAG	31	0.775	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
GGGGATATGGCGGAATTGGTAGACGCTACGGACTTAGATCGGAAGAGCAC	29	0.7250000000000001	No Hit
TCCGCTGTAGCACATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	24	0.6	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA	23	0.575	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAAGATCGGAAG	22	0.5499999999999999	No Hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATG	21	0.525	TruSeq Adapter, Index 12 (100% over 49bp)
AGTTACTAATTCATGATCTGGTAGATCGGAAGAGCACACGTCTGAACTCC	20	0.5	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTAGGGAAGTACTTTAAGAAACATATGTATAAGATCGGAAGAGCACACGT	18	0.44999999999999996	No Hit
GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTCATGGACGTTGATAAGATCTTTCCAGATCGGAAGAGCACACGTCTGAA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC	18	0.44999999999999996	No Hit
CGGCTCTGATACCAATTGATGAGATCGGAAGAGCACACGTCTGAACTCCA	18	0.44999999999999996	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGTTACTAATTCATGATCTGGCATAGATCGGAAGAGCACACGTCTGAACT	17	0.42500000000000004	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTT	16	0.4	TruSeq Adapter, Index 12 (100% over 36bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCAGATCGGAAGAGCACACG	15	0.375	No Hit
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTAGATCGGAAGAGCACAC	15	0.375	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCAGATCGGAAGAGCACACGT	15	0.375	No Hit
TCCCAAATGTAGACAAAGCAGATCGGAAGAGCACACGTCTGAACTCCAGT	14	0.35000000000000003	Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGAAGATCGGAAGA	13	0.325	No Hit
CTTCGTGATTGATTTGCCATATTTTCTGATCAGATCGGAAGAGCACACGT	13	0.325	No Hit
TCCGCTGTAGCACACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	13	0.325	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TTTGGATTGAAGGGAGCTCTTAGATCGGAAGAGCACACGTCTGAACTCCA	12	0.3	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCAGATCGGAAGAGCACACG	11	0.27499999999999997	No Hit
GGGGATATAGCTCAGTTGGTAGAGCTCCGCTCTTGCAAAGATCGGAAGAG	11	0.27499999999999997	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCAGATCGGA	11	0.27499999999999997	No Hit
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTAGATCGGAAGAGCACAC	11	0.27499999999999997	No Hit
ATTCTTTGACGAGAAAAACGCTGGCTTACTGAGGTAAGATCGGAAGAGCA	10	0.25	No Hit
TCGGACCAGGCTTCATTCCCCAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TTTGGATTGAAGGGAGCTCTAAGATCGGAAGAGCACACGTCTGAACTCCA	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGATGTCGTCCAGCGGTTAGGATATCTGGCTTAGATCGGAAGAGCACA	9	0.22499999999999998	No Hit
ATTGTATCATTAACTATTTCTTTATAGATCGGAAGAGCACACGTCTGAAC	9	0.22499999999999998	Illumina Multiplexing PCR Primer 2.01 (100% over 25bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTCAGATCGGAAGAGCAC	9	0.22499999999999998	No Hit
GCGGCGACGTGGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTT	8	0.2	TruSeq Adapter, Index 12 (100% over 36bp)
TGACAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATC	8	0.2	TruSeq Adapter, Index 12 (100% over 42bp)
CGGAAAAATAGCTCGACGCCAGGATGAGATCGGAAGAGCACACGTCTGAA	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
TTCATGGACGTTGATAAGATCTTTAGATCGGAAGAGCACACGTCTGAACT	8	0.2	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
GCGTCTGTAGTCCAACGGTTAGGATAATTGCTAGATCGGAAGAGCACACG	8	0.2	No Hit
TTAAGTGTCACGGAAATCCCTAGATCGGAAGAGCACACGTCTGAACTCCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TCCGCTGTAGCACTTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGTGAGGGACGACGATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TCCGCTTTTATGTTAGTTCGTACTATAAGATCGGAAGAGCACACGTCTGA	7	0.17500000000000002	Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTT	6	0.15	TruSeq Adapter, Index 12 (100% over 36bp)
ATTGTATCATTAACTATTTCTTTATAAGATCGGAAGAGCACACGTCTGAA	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 24bp)
GAGGGACGACGATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCT	6	0.15	TruSeq Adapter, Index 1 (97% over 35bp)
TTTGGATTGAAGGGAGCTCTAGATCGGAAGAGCACACGTCTGAACTCCAG	6	0.15	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
AGTTACTAATTCATGATCTGGCAAGATCGGAAGAGCACACGTCTGAACTC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGAGATCGGAA	5	0.125	No Hit
GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTAGATCGGAAGAGCACAC	5	0.125	No Hit
TTCCACAGCTTTCTTGAACTTAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AGTTACTAATTCATGATCTGGCAAAGATCGGAAGAGCACACGTCTGAACT	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
AGTTACTAATTCATGATCTGGAAGATCGGAAGAGCACACGTCTGAACTCC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGAGATCGGAA	5	0.125	No Hit
GCTCGACGCCAGGATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
GGGTTGATATGAGAACACACGAGATCGGAAGAGCACACGTCTGAACTCCA	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
AAGGAAGCTATAAGTAATGAAGATCGGAAGAGCACACGTCTGAACTCCAG	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACCGGTAGACTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC	5	0.125	Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
>>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	0.6	0.0	0.0	0.0	0.0
2	0.6	0.0	0.0	0.0	0.0
3	0.6	0.0	0.0	0.0	0.0
4	0.6	0.0	0.0	0.0	0.0
5	0.6	0.0	0.0	0.0	0.0
6	0.625	0.0	0.0	0.0	0.0
7	0.675	0.0	0.0	0.0	0.0
8	1.025	0.0	0.0	0.0	0.0
9	2.175	0.0	0.0	0.0	0.0
10	2.4	0.0	0.0	0.0	0.0
11	2.725	0.0	0.0	0.0	0.0
12	3.225	0.0	0.0	0.0	0.0
13	3.8	0.0	0.0	0.0	0.0
14	5.725	0.0	0.0	0.0	0.0
15	7.275	0.0	0.0	0.0	0.0
16	8.975	0.0	0.0	0.0	0.0
17	13.675	0.0	0.0	0.0	0.0
18	15.75	0.0	0.0	0.0	0.0
19	17.625	0.0	0.0	0.0	0.0
20	19.675	0.0	0.0	0.0	0.0
21	23.625	0.0	0.0	0.0	0.0
22	31.225	0.0	0.0	0.0	0.0
23	38.6	0.0	0.0	0.0	0.0
24	44.7	0.0	0.0	0.0	0.0
25	61.325	0.0	0.0	0.0	0.0
26	65.575	0.0	0.0	0.0	0.0
27	68.45	0.0	0.0	0.0	0.0
28	69.55	0.0	0.0	0.0	0.0
29	70.85	0.0	0.0	0.0	0.0
30	71.825	0.0	0.0	0.0	0.0
31	73.275	0.0	0.0	0.0	0.0
32	76.0	0.0	0.0	0.0	0.0
33	78.625	0.0	0.0	0.0	0.0
34	81.775	0.0	0.0	0.0	0.0
35	83.95	0.0	0.0	0.0	0.0
36	86.3	0.0	0.0	0.0	0.0
37	87.575	0.0	0.0	0.0	0.0
38	88.35	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TGGCAGA	20	6.952051E-4	44.000004	19
TTGTAGT	20	6.952051E-4	44.000004	5
GGATTGT	20	6.952051E-4	44.000004	2
GATTGTA	20	6.952051E-4	44.000004	3
CTGGCAG	20	6.952051E-4	44.000004	18
ATTGTAG	20	6.952051E-4	44.000004	4
TGCCAAG	20	6.952051E-4	44.000004	32
GGGATTG	20	6.952051E-4	44.000004	1
ACTAATT	25	3.6958358E-5	44.0	5
CATGATC	25	3.6958358E-5	44.0	12
TTCATGA	25	3.6958358E-5	44.0	10
TTACTAA	25	3.6958358E-5	44.0	3
AATTCAT	25	3.6958358E-5	44.0	8
ATGATCT	25	3.6958358E-5	44.0	13
TCTGGCA	25	3.6958358E-5	44.0	17
TGATCTG	25	3.6958358E-5	44.0	14
CTAATTC	25	3.6958358E-5	44.0	6
GATCTGG	25	3.6958358E-5	44.0	15
TCATGAT	25	3.6958358E-5	44.0	11
TAATTCA	25	3.6958358E-5	44.0	7
>>END_MODULE
Rejected 4302781 READS because READLEN < 1
Read 4302781 spots for SRR12060859.sra
Written 4302781 spots for SRR12060859.sra
Rejected 4302781 READS because READLEN < 1
Read 4302781 spots for SRR12060859.sra
Written 4302781 spots for SRR12060859.sra
Rejected 4302781 READS because READLEN < 1
Read 4302781 spots for SRR12060859.sra
Written 4302781 spots for SRR12060859.sra
Rejected 4302781 READS because READLEN < 1
Read 4302781 spots for SRR12060859.sra
Written 4302781 spots for SRR12060859.sra
Rejected 4302781 READS because READLEN < 1
Read 4302781 spots for SRR12060859.sra
Written 4302781 spots for SRR12060859.sra
Rejected 4302781 READS because READLEN < 1
Read 4302781 spots for SRR12060859.sra
Written 4302781 spots for SRR12060859.sra
Rejected 4302781 READS because READLEN < 1
Read 4302781 spots for SRR12060859.sra
Written 4302781 spots for SRR12060859.sra
Rejected 4302781 READS because READLEN < 1
Read 4302781 spots for SRR12060859.sra
Written 4302781 spots for SRR12060859.sra
SRR ids: ['SRR12060859.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_vyi731g8
SRR12060859.sra spots: 34422248
blocks: [[1, 4302781], [4302782, 8605562], [8605563, 12908343], [12908344, 17211124], [17211125, 21513905], [21513906, 25816686], [25816687, 30119467], [30119468, 34422248]]
SRR12060859 file size 4852548
SRR12060859 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 SRR12060859 SRR12060859_1.fastq
Input file:	SRR12060859_1.fastq
trimmed:	SRR12060859-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
Sun Jan 11 18:57:28 2026 >> started

Sun Jan 11 18:57:41 2026 >> done (12.423s)
34422248 reads processed; of these:
 5921657 (17.20%) short reads filtered out after trimming by size control
  238072 ( 0.69%) empty reads filtered out after trimming by size control
28262519 (82.11%) reads available; of these:
  755130 ( 2.67%) trimmed reads available after processing
27507389 (97.33%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  751379	  2.66%
 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	      10	  0.00%
 36	      10	  0.00%
 37	       5	  0.00%
 38	      31	  0.00%
 39	       3	  0.00%
 40	      38	  0.00%
 41	       5	  0.00%
 42	       8	  0.00%
 43	       5	  0.00%
 44	       1	  0.00%
 45	       0	  0.00%
 46	     261	  0.00%
 47	     230	  0.00%
 48	    1372	  0.00%
 49	    1771	  0.01%
 50	27507389	 97.33%
28262519 reads passed initial QC


criterion=sequence-density
sequence-density=84.26
sequence-density-rank=1
fanout-score=48.62
fanout-score-rank=1
prefix-density=91.67
prefix-fanout=44.7
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAA


criterion=fanout-score
sequence-density=84.26
sequence-density-rank=1
fanout-score=48.62
fanout-score-rank=1
prefix-density=91.67
prefix-fanout=44.7
sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAA
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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAA -o SRR12060859 -
Input file:	STDIN
trimmed:	SRR12060859-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAA
-- 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
Sun Jan 11 18:58:43 2026 >> started

Sun Jan 11 18:58:58 2026 >> done (14.979s)
27597519 reads processed; of these:
   19882 ( 0.07%) short reads filtered out after trimming by size control
     219 ( 0.00%) empty reads filtered out after trimming by size control
27577418 (99.93%) reads available; of these:
26564802 (96.33%) trimmed reads available after processing
 1012616 ( 3.67%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	  747515	  2.71%
 19	  926929	  3.36%
 20	 1286985	  4.67%
 21	 2646652	  9.60%
 22	 2683370	  9.73%
 23	 2150649	  7.80%
 24	 5359397	 19.43%
 25	 1466843	  5.32%
 26	  924343	  3.35%
 27	  379335	  1.38%
 28	  320236	  1.16%
 29	  392650	  1.42%
 30	  451975	  1.64%
 31	  895039	  3.25%
 32	  805571	  2.92%
 33	 1063742	  3.86%
 34	  644301	  2.34%
 35	  733697	  2.66%
 36	  358496	  1.30%
 37	  233781	  0.85%
 38	  242081	  0.88%
 39	 1315592	  4.77%
 40	  337813	  1.22%
 41	  233995	  0.85%
 42	  319935	  1.16%
 43	  126887	  0.46%
 44	   90536	  0.33%
 45	   70706	  0.26%
 46	   35547	  0.13%
 47	   39422	  0.14%
 48	     715	  0.00%
 49	     305	  0.00%
 50	  292378	  1.06%


criterion=sequence-density
sequence-density=5.58
sequence-density-rank=1
fanout-score=0.00
fanout-score-rank=9
prefix-density=0.00
prefix-fanout=1.0
sequence=GCGGATATAGTCGAATGGTAAAATTTCTCCTTGCCAAGGAGATCGGAA


criterion=fanout-score
sequence-density=0.26
sequence-density-rank=17
fanout-score=14.29
fanout-score-rank=1
prefix-density=3.67
prefix-fanout=1.0
sequence=AGTCCAACGGTAGGATAATTG
                                 Started job on |	Jan 11 18:59:43
                             Started mapping on |	Jan 11 18:59:44
                                    Finished on |	Jan 11 19:01:36
       Mapping speed, Million of reads per hour |	907.79

                          Number of input reads |	28242418
                      Average input read length |	27
                                    UNIQUE READS:
                   Uniquely mapped reads number |	12839563
                        Uniquely mapped reads % |	45.46%
                          Average mapped length |	26.98
                       Number of splices: Total |	101428
            Number of splices: Annotated (sjdb) |	28071
                       Number of splices: GT/AG |	86619
                       Number of splices: GC/AG |	1060
                       Number of splices: AT/AC |	197
               Number of splices: Non-canonical |	13552
                      Mismatch rate per base, % |	0.29%
                         Deletion rate per base |	0.00%
                        Deletion average length |	1.15
                        Insertion rate per base |	0.00%
                       Insertion average length |	1.05
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	12437630
             % of reads mapped to multiple loci |	44.04%
        Number of reads mapped to too many loci |	1807128
             % of reads mapped to too many loci |	6.40%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	3.70%
                     % of reads unmapped: other |	0.40%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	2965225	2965225	2965225
N_multimapping	12437630	12437630	12437630
N_noFeature	6019963	6579909	11916729
N_ambiguous	602237	235710	7894
UnstrandedReadsAssigned:6217363 PositiveStrandReadsAssigned:6023944 NegativeStrandReadsAssigned:914940
Dataset is classified positive stranded
MeadianReadLen=24 20thPercentileLength=21 echo kmer=19
SRR12060859 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: SRR12060859-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 28,242,418 reads, 1,321,084 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 964 rounds

  48360 SRR12060859.ke.tsv
  32833 SRR12060859.se.tsv
  81193 total
==> SRR12060859.ke.tsv <==
target_id	length	eff_length	est_counts	tpm
AT1G19090.1	2509	2410	383	68.6404
AT1G18320.1	699	600	0	0
AT5G11100.1	1709	1610	0	0
AT4G35335.1	1280	1181	6	2.19432
AT1G60930.1	3876	3777	3	0.343062
AT1G17000.1	2351	2252	1	0.191792
AT3G55270.1	3130	3031	21	2.99248
AT4G16150.1	3181	3082	18	2.52254
AT3G18150.1	1370	1271	6	2.03894

==> SRR12060859.se.tsv <==
AT1G01010	3
AT1G01020	11
AT1G03987	0
AT1G01030	0
AT1G01040	128
AT1G03993	3
AT1G01046	78
AT1G01050	20
AT1G03997	0
AT1G01060	16
SRR12060859 completed mapping pipeline successfully
