Starting /dee2/code/volunteer_pipeline.sh SRR31291448
    current disk space = 384269328
    free memory = 129679404 
SRR31291448 SRAfilesize
019178bc1b2c537abe05f61c867a7d24  SRR31291448.sra
SRR31291448.sra file validated
SRR31291448 is single end
SRR31291448 is conventional basespace
SRR31291448 read1 length is 51 nt
##FastQC	0.11.5
>>Basic Statistics	pass
#Measure	Value
Filename	SRR31291448_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	34.18225	35.0	35.0	35.0	33.0	35.0
2	34.3065	35.0	35.0	35.0	33.0	35.0
3	34.38425	35.0	35.0	35.0	33.0	35.0
4	34.29925	35.0	35.0	35.0	32.0	35.0
5	34.4265	35.0	35.0	35.0	33.0	35.0
6	39.04025	40.0	40.0	40.0	37.0	40.0
7	38.8885	40.0	39.0	40.0	37.0	40.0
8	38.9025	40.0	39.0	40.0	36.0	40.0
9	38.9285	40.0	39.0	40.0	37.0	40.0
10	38.8725	40.0	39.0	40.0	37.0	40.0
11	38.941	40.0	39.0	40.0	36.0	40.0
12	38.95625	40.0	40.0	40.0	37.0	40.0
13	38.9475	40.0	39.0	40.0	37.0	40.0
14	38.91	40.0	39.0	40.0	37.0	40.0
15	38.74775	40.0	39.0	40.0	36.0	40.0
16	38.8095	40.0	39.0	40.0	36.0	40.0
17	38.9055	40.0	39.0	40.0	36.0	40.0
18	38.97575	40.0	39.0	40.0	37.0	40.0
19	38.96825	40.0	39.0	40.0	37.0	40.0
20	38.619	40.0	39.0	40.0	36.0	40.0
21	38.81325	40.0	39.0	40.0	36.0	40.0
22	38.848	40.0	39.0	40.0	37.0	40.0
23	38.75975	40.0	39.0	40.0	36.0	40.0
24	38.81225	40.0	39.0	40.0	36.0	40.0
25	38.76	40.0	39.0	40.0	36.0	40.0
26	38.663	40.0	39.0	40.0	36.0	40.0
27	38.777	40.0	39.0	40.0	36.0	40.0
28	38.82475	40.0	39.0	40.0	36.0	40.0
29	38.75775	40.0	39.0	40.0	36.0	40.0
30	38.79125	40.0	39.0	40.0	36.0	40.0
31	38.754	40.0	39.0	40.0	36.0	40.0
32	38.72225	40.0	39.0	40.0	36.0	40.0
33	38.49225	40.0	39.0	40.0	35.0	40.0
34	38.60525	40.0	39.0	40.0	36.0	40.0
35	38.683	40.0	39.0	40.0	36.0	40.0
36	38.59925	40.0	39.0	40.0	36.0	40.0
37	38.6425	40.0	39.0	40.0	36.0	40.0
38	38.708	40.0	39.0	40.0	36.0	40.0
39	38.702	40.0	39.0	40.0	36.0	40.0
40	38.638	40.0	39.0	40.0	36.0	40.0
41	38.7545	40.0	39.0	40.0	36.0	40.0
42	38.684	40.0	39.0	40.0	36.0	40.0
43	38.60175	40.0	39.0	40.0	36.0	40.0
44	38.565	40.0	39.0	40.0	36.0	40.0
45	38.62675	40.0	39.0	40.0	36.0	40.0
46	38.60825	40.0	39.0	40.0	36.0	40.0
47	38.60875	40.0	39.0	40.0	36.0	40.0
48	38.153	40.0	39.0	40.0	35.0	40.0
49	38.509	40.0	39.0	40.0	36.0	40.0
50	38.46025	40.0	39.0	40.0	36.0	40.0
51	37.7805	40.0	39.0	40.0	34.0	40.0
>>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
24	2.0
25	2.0
26	7.0
27	12.0
28	33.0
29	31.0
30	42.0
31	46.0
32	63.0
33	74.0
34	85.0
35	111.0
36	146.0
37	211.0
38	407.0
39	2728.0
>>END_MODULE
>>Per base sequence content	warn
#Base	G	A	T	C
1	35.78603716725264	24.91210447011552	17.9809141135108	21.320944249121045
2	34.10852713178294	23.680920230057513	16.65416354088522	25.55638909727432
3	34.175	19.675	18.55	27.6
4	27.275	23.9	21.575	27.250000000000004
5	29.5	24.525	20.3	25.674999999999997
6	34.75	23.325000000000003	17.5	24.425
7	33.6	22.900000000000002	18.125	25.374999999999996
8	28.799999999999997	22.475	18.925	29.799999999999997
9	29.075	23.775	18.45	28.7
10	27.725	28.799999999999997	18.85	24.625
11	29.825000000000003	23.25	23.225	23.7
12	26.825	25.575	21.325	26.275
13	26.400000000000002	24.4	23.125	26.075
14	26.6	24.6	21.2	27.6
15	31.55	23.325000000000003	19.45	25.674999999999997
16	29.15	24.5	18.099999999999998	28.249999999999996
17	26.825	24.0	22.25	26.924999999999997
18	26.0	24.675	18.425	30.9
19	28.549999999999997	25.324999999999996	19.275000000000002	26.85
20	28.725	24.625	19.0	27.650000000000002
21	27.35	25.15	20.05	27.450000000000003
22	29.099999999999998	26.0	18.425	26.474999999999998
23	29.15	26.025	18.875	25.95
24	26.674999999999997	24.425	21.349999999999998	27.55
25	25.4	26.474999999999998	20.375	27.750000000000004
26	29.275000000000002	22.8	19.825	28.1
27	27.325	24.775	20.825	27.075
28	29.675	23.05	19.675	27.6
29	27.275	23.974999999999998	19.125	29.625
30	29.925	23.724999999999998	19.125	27.224999999999998
31	24.95	25.3	18.525	31.225
32	28.325	23.05	21.775	26.85
33	26.575	24.15	20.424999999999997	28.849999999999998
34	29.5	24.025	19.0	27.474999999999998
35	26.0	25.224999999999998	19.3	29.475
36	28.549999999999997	23.275000000000002	17.175	31.0
37	26.825	24.075	22.1	27.0
38	26.6	26.575	19.3	27.525
39	30.85	24.8	18.075	26.275
40	29.799999999999997	24.625	17.775	27.800000000000004
41	28.925	26.674999999999997	18.15	26.25
42	26.974999999999998	26.25	18.65	28.125
43	28.849999999999998	24.875	17.175	29.099999999999998
44	28.15	24.7	18.85	28.299999999999997
45	27.474999999999998	25.025	19.25	28.249999999999996
46	26.724999999999998	24.65	20.45	28.175
47	26.125	27.3	19.275000000000002	27.3
48	27.700000000000003	27.35	18.375	26.575
49	29.475	24.9	19.3	26.325
50	29.75	24.025	19.6	26.625
51	27.450000000000003	24.6	18.875	29.075
>>END_MODULE
>>Per sequence GC content	fail
#GC Content	Count
0	15.0
1	20.0
2	25.0
3	23.0
4	21.0
5	20.5
6	20.0
7	17.5
8	15.0
9	15.5
10	16.0
11	15.0
12	14.0
13	12.5
14	11.0
15	17.5
16	24.0
17	20.5
18	17.0
19	14.5
20	12.0
21	27.0
22	42.0
23	38.5
24	35.0
25	42.0
26	66.5
27	84.0
28	80.5
29	77.0
30	75.5
31	74.0
32	92.0
33	110.0
34	95.0
35	80.0
36	88.0
37	96.0
38	104.0
39	112.0
40	121.5
41	131.0
42	126.5
43	122.0
44	121.5
45	121.0
46	115.5
47	110.0
48	111.5
49	113.0
50	115.0
51	117.0
52	120.5
53	124.0
54	128.5
55	133.0
56	133.0
57	133.0
58	175.5
59	218.0
60	176.5
61	135.0
62	110.5
63	86.0
64	83.0
65	80.0
66	80.5
67	81.0
68	90.0
69	99.0
70	97.0
71	95.0
72	115.0
73	135.0
74	121.0
75	88.0
76	69.0
77	102.0
78	135.0
79	159.5
80	184.0
81	150.0
82	116.0
83	157.0
84	198.0
85	147.0
86	96.0
87	79.0
88	62.0
89	47.5
90	33.0
91	25.0
92	17.0
93	9.0
94	1.0
95	0.5
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	0.44999999999999996
2	0.025
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	pass
#Total Deduplicated Percentage	75.97500000000001
#Duplication Level	Percentage of deduplicated	Percentage of total
1	87.59460348798947	66.55
2	6.811451135241856	10.35
3	2.4350115169463638	5.55
4	1.4149391247120764	4.3
5	0.723922342875946	2.75
6	0.09871668311944717	0.44999999999999996
7	0.361961171437973	1.925
8	0.09871668311944717	0.6
9	0.06581112207963145	0.44999999999999996
>10	0.361961171437973	5.125
>50	0.03290556103981573	1.95
>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
GGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCGCAAGGC	78	1.95	No Hit
GGGGGGGCCGGCGGCGGCGGCGACTCTGGACGCGAGCCGGGCCCTTCCCGT	41	1.0250000000000001	No Hit
CCGGGCGCGGTGGCGCACGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGAC	31	0.775	No Hit
TCTACGGCCATACCACCCTGAACGCGCCCGATCTCGTCTGATCTCGGAAGC	25	0.625	No Hit
GGGGGGCCGGCGGCGGCGGCGACTCTGGACGCGAGCCGGGCCCTTCCCGTG	22	0.5499999999999999	No Hit
GGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCGCAAGGCC	15	0.375	No Hit
GCCCCGGATAGCCGGGTCCCCGTCCGTCCCCGCTCGGCGGGGTCCCCGCGT	14	0.35000000000000003	No Hit
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	13	0.325	No Hit
GTTGGCCCCGGATAGCCGGGTCCCCGTCCGTCCCCGCTCGGCGGGGTCCCC	12	0.3	No Hit
CGGGGGGGCCGGCGGCGGCGGCGACTCTGGACGCGAGCCGGGCCCTTCCCG	12	0.3	No Hit
GGTTGGCCCCGGATAGCCGGGTCCCCGTCCGTCCCCGCTCGGCGGGGTCCC	10	0.25	No Hit
GACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCTA	10	0.25	No Hit
GATACGGCAGCGCCGAAGGAGCCTCGGTTGGCCCCGGATAGCCGGGTCCCC	9	0.22499999999999998	No Hit
ACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCTAG	9	0.22499999999999998	No Hit
GCCGGGTCCCCGTCCGTCCCCGCTCGGCGGGGTCCCCGCGTCGTCCCCGCG	8	0.2	No Hit
TTGGCCCCGGATAGCCGGGTCCCCGTCCGTCCCCGCTCGGCGGGGTCCCCG	8	0.2	No Hit
GGCCCCGGATAGCCGGGTCCCCGTCCGTCCCCGCTCGGCGGGGTCCCCGCG	8	0.2	No Hit
AGCGCCGAAGGAGCCTCGGTTGGCCCCGGATAGCCGGGTCCCCGTCCGTCC	7	0.17500000000000002	No Hit
GGGCGCGCGCCGCGGCTGGACGAGGCGCCGCCGCCCTCTCCCACGTCCGGG	7	0.17500000000000002	No Hit
GAACGATACGGCAGCGCCGAAGGAGCCTCGGTTGGCCCCGGATAGCCGGGT	7	0.17500000000000002	No Hit
AGGTGTAGAATAAGTGGGAGGCCCCCGGCGCCCGGCCCCGTCCTCGCGTCG	7	0.17500000000000002	No Hit
GGCGGATCTTTCCCGCTCCCCGTTCCTCCCGACCCCTCCACCCGCGCGTCG	7	0.17500000000000002	No Hit
GGTGCGGCCGGAAAGGGGGCCGCCCTCTCGCCCGTCACGTTGAACGCACGT	7	0.17500000000000002	No Hit
GTCCCCGCTCGGCGGGGTCCCCGCGTCGTCCCCGCGGCGGCGCGGGGTCTC	7	0.17500000000000002	No Hit
GGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCGCAAGGCCCTGGGT	7	0.17500000000000002	No Hit
GACGGGAGCGGCCGCGGGTGCGCGTCTCTCGGGGTCGGGGGTGCGTGGCGG	7	0.17500000000000002	No Hit
AATCCCGCCCAGGCGGAACGATACGGCAGCGCCGAAGGAGCCTCGGTTGGC	7	0.17500000000000002	No Hit
GGACGGGAGCGGCCGCGGGTGCGCGTCTCTCGGGGTCGGGGGTGCGTGGCG	7	0.17500000000000002	No Hit
GGATTATGACTGAACGCCTCTAAGTCAGAATCCCGCCCAGGCGGAACGATA	6	0.15	No Hit
GTCGCCGCGCTCTCCCTCTCCCCCCGTCCGCCTCCCGGGCGGGCGTGGGGG	6	0.15	No Hit
CCCGGATAGCCGGGTCCCCGTCCGTCCCCGCTCGGCGGGGTCCCCGCGTCG	6	0.15	No Hit
CGGAACGATACGGCAGCGCCGAAGGAGCCTCGGTTGGCCCCGGATAGCCGG	5	0.125	No Hit
AACGGGACGGGAGCGGCCGCGGGTGCGCGTCTCTCGGGGTCGGGGGTGCGT	5	0.125	No Hit
GGAACGATACGGCAGCGCCGAAGGAGCCTCGGTTGGCCCCGGATAGCCGGG	5	0.125	No Hit
ATGACTGAACGCCTCTAAGTCAGAATCCCGCCCAGGCGGAACGATACGGCA	5	0.125	No Hit
ACCTCACCCCGAGTGTTACAGCCCTCCGGCCGCAGCTTTCGCCGAATCCCG	5	0.125	No Hit
GCCCAGGCGGAACGATACGGCAGCGCCGAAGGAGCCTCGGTTGGCCCCGGA	5	0.125	No Hit
CCCCGCCGGGCGTCGGGACCGGGGTCCGGTGCGGAGAGCCGTTCGTCTTGG	5	0.125	No Hit
AGCCGGGTCCCCGTCCGTCCCCGCTCGGCGGGGTCCCCGCGTCGTCCCCGC	5	0.125	No Hit
GCCCGGAGGATTCAACCCGGCGGCGCGCGTCCGGCCGTGCCGGTGGTCCCG	5	0.125	No Hit
AAGAGGGCGTGAAACCGTTAAGAGGTAAACGGGTGGGGTCCGCGCAGTCCG	5	0.125	No Hit
GGGGGGGCGGCGCGTCTCAGGGCGCGCCGAACCACCTCACCCCGAGTGTTA	5	0.125	No Hit
GGGGACCGCCCCCCGGCCGGCGACCGGCCGCCGCCGGGCGCACTTCCACCG	5	0.125	No Hit
AGTCGGAACGGAACGGGACGGGAGCGGCCGCGGGTGCGCGTCTCTCGGGGT	5	0.125	No Hit
GGCGCGCCGAACCACCTCACCCCGAGTGTTACAGCCCTCCGGCCGCAGCTT	5	0.125	No Hit
CCCCCGCCGGGCGTCGGGACCGGGGTCCGGTGCGGAGAGCCGTTCGTCTTG	5	0.125	No Hit
GAGCCTCGGTTGGCCCCGGATAGCCGGGTCCCCGTCCGTCCCCGCTCGGCG	5	0.125	No Hit
CGGTTGGCCCCGGATAGCCGGGTCCCCGTCCGTCCCCGCTCGGCGGGGTCC	5	0.125	No Hit
GGGGCGGCGGGTCCAACCCCGCGGGGGTTCCGGAGCGGGAGGAACCAGCGG	5	0.125	No Hit
GCCGCCGCCCTCTCCCACGTCCGGGGAGACCCCCCGTCCTTTCCGCCCGGG	5	0.125	No Hit
TCCCCGCTCGGCGGGGTCCCCGCGTCGTCCCCGCGGCGGCGCGGGGTCTCC	5	0.125	No Hit
GAGGATTCAACCCGGCGGCGCGCGTCCGGCCGTGCCGGTGGTCCCGGCGGA	5	0.125	No Hit
CCTCTCCCCCCGTCCGCCTCCCGGGCGGGCGTGGGGGTGGGGGCCGGGCCG	5	0.125	No Hit
>>END_MODULE
>>Adapter Content	pass
#Position	Illumina Universal Adapter	Illumina Small RNA 3' Adapter	Illumina Small RNA 5' Adapter	Nextera Transposase Sequence	SOLID Small RNA Adapter
1	0.0	0.0	0.0	0.0	0.0
2	0.0	0.0	0.0	0.0	0.0
3	0.0	0.0	0.0	0.0	0.0
4	0.0	0.0	0.0	0.0	0.0
5	0.0	0.0	0.0	0.0	0.0
6	0.0	0.0	0.0	0.0	0.0
7	0.0	0.0	0.0	0.0	0.0
8	0.0	0.0	0.0	0.0	0.0
9	0.0	0.0	0.0	0.0	0.0
10	0.0	0.0	0.0	0.0	0.0
11	0.0	0.0	0.0	0.0	0.0
12	0.0	0.0	0.0	0.0	0.0
13	0.0	0.0	0.0	0.0	0.0
14	0.0	0.0	0.0	0.0	0.0
15	0.025	0.0	0.0	0.0	0.0
16	0.025	0.0	0.0	0.0	0.0
17	0.05	0.0	0.0	0.0	0.0
18	0.075	0.0	0.0	0.0	0.0
19	0.075	0.0	0.0	0.0	0.0
20	0.1	0.0	0.0	0.0	0.0
21	0.1	0.0	0.0	0.0	0.0
22	0.125	0.0	0.0	0.0	0.0
23	0.125	0.0	0.0	0.0	0.0
24	0.175	0.0	0.0	0.0	0.0
25	0.25	0.0	0.0	0.0	0.0
26	0.25	0.0	0.0	0.0	0.0
27	0.25	0.0	0.0	0.0	0.0
28	0.325	0.0	0.0	0.0	0.0
29	0.35	0.0	0.0	0.0	0.0
30	0.375	0.0	0.0	0.0	0.0
31	0.425	0.0	0.0	0.0	0.0
32	0.475	0.0	0.0	0.0	0.0
33	0.525	0.0	0.0	0.0	0.0
34	0.55	0.0	0.0	0.0	0.0
35	0.625	0.0	0.0	0.0	0.0
36	0.675	0.0	0.0	0.0	0.0
37	0.7	0.0	0.0	0.0	0.0
38	0.7	0.0	0.0	0.0	0.0
39	0.775	0.0	0.0	0.0	0.0
>>END_MODULE
>>Kmer Content	warn
#Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
AAGCGCA	25	0.0018715585	35.98	41
>>END_MODULE
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617148 spots for SRR31291448.sra
Written 1617148 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
Read 1617136 spots for SRR31291448.sra
Written 1617136 spots for SRR31291448.sra
SRR ids: ['SRR31291448.sra']
extra args: ['--split-files', '--defline-qual', '+']
tempdir: /tmp/pfd_f9hjy_od
SRR31291448.sra spots: 25874188
blocks: [[1, 1617136], [1617137, 3234272], [3234273, 4851408], [4851409, 6468544], [6468545, 8085680], [8085681, 9702816], [9702817, 11319952], [11319953, 12937088], [12937089, 14554224], [14554225, 16171360], [16171361, 17788496], [17788497, 19405632], [19405633, 21022768], [21022769, 22639904], [22639905, 24257040], [24257041, 25874188]]
SRR31291448 file size 4448804
SRR31291448 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 16 -o SRR31291448 SRR31291448_1.fastq
Input file:	SRR31291448_1.fastq
trimmed:	SRR31291448-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
Mon Nov 17 19:29:11 2025 >> started

Mon Nov 17 19:29:18 2025 >> done (6.062s)
25874188 reads processed; of these:
   18621 ( 0.07%) short reads filtered out after trimming by size control
     788 ( 0.00%) empty reads filtered out after trimming by size control
25854779 (99.92%) reads available; of these:
    7374 ( 0.03%) trimmed reads available after processing
25847405 (99.97%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	    3487	  0.01%
 19	    3648	  0.01%
 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	       0	  0.00%
 32	       0	  0.00%
 33	       0	  0.00%
 34	       0	  0.00%
 35	       0	  0.00%
 36	       0	  0.00%
 37	       0	  0.00%
 38	       0	  0.00%
 39	       0	  0.00%
 40	       0	  0.00%
 41	       0	  0.00%
 42	      14	  0.00%
 43	      11	  0.00%
 44	      13	  0.00%
 45	       2	  0.00%
 46	       5	  0.00%
 47	       7	  0.00%
 48	       0	  0.00%
 49	      28	  0.00%
 50	     159	  0.00%
 51	25847405	 99.97%
25854779 reads passed initial QC


criterion=sequence-density
sequence-density=2.23
sequence-density-rank=1
fanout-score=2.29
fanout-score-rank=24
prefix-density=3.05
prefix-fanout=1.7
sequence=GCGGCGGCGGCGACTCTGGACGCGAGCCGGGCCCTTCCCGTGGATCGCCTCAGCTGCGGCGGGCGTCGCGGCCGCTCCCGGGGAGCCCGGCGGGTGCCGGCGCGGGTCCCCTCCCCGCGGGG


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=34
fanout-score=105.18
fanout-score-rank=1
prefix-density=0.95
prefix-fanout=1.0
sequence=GGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGT
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 16 -x GCGGCGGCGGCGACTCTGGACGCGAGCCGGGCCCTTCCCGTGGATCGCCTCAGCTGCGGCGGGCGTCGCGGCCGCTCCCGGGGAGCCCGGCGGGTGCCGGCGCGGGTCCCCTCCCCGCGGGG -o SRR31291448 -
Input file:	STDIN
trimmed:	SRR31291448-trimmed.fastq

Parameters used:
-- 3' end adapter sequence (-x):	GCGGCGGCGGCGACTCTGGACGCGAGCCGGGCCCTTCCCGTGGATCGCCTCAGCTGCGGCGGGC
-- 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
Mon Nov 17 19:29:37 2025 >> started

Mon Nov 17 19:29:41 2025 >> done (3.557s)
8618260 reads processed; of these:
 193024 ( 2.24%) short reads filtered out after trimming by size control
    531 ( 0.01%) empty reads filtered out after trimming by size control
8424705 (97.75%) reads available; of these:
 336821 ( 4.00%) trimmed reads available after processing
8087884 (96.00%) untrimmed reads available after processing

Length distribution of reads after trimming:
length	count	percentage
 18	   1217	  0.01%
 19	   1231	  0.01%
 20	     17	  0.00%
 21	     11	  0.00%
 22	     30	  0.00%
 23	     54	  0.00%
 24	     84	  0.00%
 25	    205	  0.00%
 26	    250	  0.00%
 27	    167	  0.00%
 28	    119	  0.00%
 29	    226	  0.00%
 30	   1269	  0.02%
 31	   1353	  0.02%
 32	    346	  0.00%
 33	    103	  0.00%
 34	     63	  0.00%
 35	     96	  0.00%
 36	     19	  0.00%
 37	     29	  0.00%
 38	     66	  0.00%
 39	     67	  0.00%
 40	     90	  0.00%
 41	    239	  0.00%
 42	   3390	  0.04%
 43	   4213	  0.05%
 44	   9484	  0.11%
 45	  10396	  0.12%
 46	  27540	  0.33%
 47	  87228	  1.04%
 48	 189599	  2.25%
 49	      7	  0.00%
 50	     53	  0.00%
 51	8085444	 95.97%


criterion=sequence-density
sequence-density=0.71
sequence-density-rank=1
fanout-score=3.35
fanout-score-rank=20
prefix-density=1.26
prefix-fanout=1.9
sequence=GCCCGGTGGGGAAGGTGGCTCGGGGGGGGCGGCGCGTCTCAGGGCGCGCCGAACCACCTCACCCCGAGTGTTACAGCCCTCCGGCCGCAGCTTTCGCCGAATCCCGGGGCCGAGGAAGCCAGATACCCGTCGCCGCGCTCTCCCTCTCCCCCCGTCCGCCTCCCGGGCGGGCGTGGGGGTGGGGGCCGGGCCGCCCCTCCCACGGCGCGACCGCTCTCCCACCCCCCTCCGTCGCCTCTCTCGGGGCCCGGTGGG


criterion=fanout-score
sequence-density=0.01
sequence-density-rank=29
fanout-score=83.02
fanout-score-rank=1
prefix-density=0.94
prefix-fanout=1.0
sequence=GGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAAATTCTTGGACCGGCGCAAGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGTTCCGACCATAAACGATGCCGACTGGCGATGCGGCGGCGTTATTCCCATGACCCGCCGGGCAGCTTCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGAAACCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCTCGATTCCGTGGGTGGTGGTGCATGGCCGTT
                                 Started job on |	Nov 17 19:30:06
                             Started mapping on |	Nov 17 19:30:07
                                    Finished on |	Nov 17 19:30:51
       Mapping speed, Million of reads per hour |	2099.55

                          Number of input reads |	25661224
                      Average input read length |	50
                                    UNIQUE READS:
                   Uniquely mapped reads number |	14936777
                        Uniquely mapped reads % |	58.21%
                          Average mapped length |	50.21
                       Number of splices: Total |	856013
            Number of splices: Annotated (sjdb) |	831394
                       Number of splices: GT/AG |	837069
                       Number of splices: GC/AG |	6289
                       Number of splices: AT/AC |	895
               Number of splices: Non-canonical |	11760
                      Mismatch rate per base, % |	1.09%
                         Deletion rate per base |	0.01%
                        Deletion average length |	1.50
                        Insertion rate per base |	0.03%
                       Insertion average length |	1.22
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |	5556772
             % of reads mapped to multiple loci |	21.65%
        Number of reads mapped to too many loci |	1252386
             % of reads mapped to too many loci |	4.88%
                                  UNMAPPED READS:
       % of reads unmapped: too many mismatches |	0.00%
                 % of reads unmapped: too short |	14.08%
                     % of reads unmapped: other |	1.17%
                                  CHIMERIC READS:
                       Number of chimeric reads |	0
                            % of chimeric reads |	0.00%
N_unmapped	5167675	5167675	5167675
N_multimapping	5556772	5556772	5556772
N_noFeature	4949198	5059937	14501957
N_ambiguous	417553	92907	95796
UnstrandedReadsAssigned:9570026 PositiveStrandReadsAssigned:9783933 NegativeStrandReadsAssigned:339024
Dataset is classified positive stranded
MeadianReadLen=51 20thPercentileLength=51 echo kmer=47
SRR31291448 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31

[quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20
[index] k-mer length: 31
[index] number of targets: 109,282
[index] number of k-mers: 95,711,799
[index] number of equivalence classes: 391,900
[quant] running in single-end mode
[quant] will process file 1: SRR31291448-trimmed.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 25,661,224 reads, 7,820,106 reads pseudoaligned
[   em] quantifying the abundances ... done
[   em] the Expectation-Maximization algorithm ran for 1,159 rounds

 109283 SRR31291448.ke.tsv
  52636 SRR31291448.se.tsv
 161919 total
==> SRR31291448.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

==> SRR31291448.se.tsv <==
ENSMUSG00000102693	0
ENSMUSG00000064842	0
ENSMUSG00000051951	465
ENSMUSG00000102851	0
ENSMUSG00000103377	30
ENSMUSG00000104017	17
ENSMUSG00000103025	8
ENSMUSG00000089699	0
ENSMUSG00000103201	0
ENSMUSG00000103147	1
SRR31291448 completed mapping pipeline successfully
