Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cluster nodes: 4
Job counts:
	count	jobs
	1	all
	24	salmon_quant
	25

rule salmon_quant:
    input: reads/SAMEA103885262_1.fastq, reads/SAMEA103885262_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885262/quant.sf
    jobid: 1
    wildcards: sample=SAMEA103885262

Submitted job 1 with external jobid 'Submitted batch job 7366869'.

rule salmon_quant:
    input: reads/SAMEA103885392_1.fastq, reads/SAMEA103885392_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885392/quant.sf
    jobid: 24
    wildcards: sample=SAMEA103885392

Submitted job 24 with external jobid 'Submitted batch job 7366873'.

rule salmon_quant:
    input: reads/SAMEA103885043_1.fastq, reads/SAMEA103885043_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885043/quant.sf
    jobid: 21
    wildcards: sample=SAMEA103885043

Submitted job 21 with external jobid 'Submitted batch job 7366878'.

rule salmon_quant:
    input: reads/SAMEA103885347_1.fastq, reads/SAMEA103885347_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885347/quant.sf
    jobid: 22
    wildcards: sample=SAMEA103885347

Submitted job 22 with external jobid 'Submitted batch job 7366882'.
Finished job 24.
1 of 25 steps (4%) done

rule salmon_quant:
    input: reads/SAMEA103885368_1.fastq, reads/SAMEA103885368_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885368/quant.sf
    jobid: 12
    wildcards: sample=SAMEA103885368

Finished job 21.
2 of 25 steps (8%) done
Submitted job 12 with external jobid 'Submitted batch job 7374976'.

rule salmon_quant:
    input: reads/SAMEA103885102_1.fastq, reads/SAMEA103885102_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885102/quant.sf
    jobid: 20
    wildcards: sample=SAMEA103885102

Submitted job 20 with external jobid 'Submitted batch job 7374980'.
Finished job 22.
3 of 25 steps (12%) done

rule salmon_quant:
    input: reads/SAMEA103885182_1.fastq, reads/SAMEA103885182_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885182/quant.sf
    jobid: 7
    wildcards: sample=SAMEA103885182

Submitted job 7 with external jobid 'Submitted batch job 7375579'.
Finished job 1.
4 of 25 steps (16%) done

rule salmon_quant:
    input: reads/SAMEA103885228_1.fastq, reads/SAMEA103885228_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885228/quant.sf
    jobid: 13
    wildcards: sample=SAMEA103885228

Submitted job 13 with external jobid 'Submitted batch job 7375907'.
Finished job 13.
5 of 25 steps (20%) done

rule salmon_quant:
    input: reads/SAMEA103884949_1.fastq, reads/SAMEA103884949_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103884949/quant.sf
    jobid: 9
    wildcards: sample=SAMEA103884949

Submitted job 9 with external jobid 'Submitted batch job 7379265'.
Finished job 20.
6 of 25 steps (24%) done

rule salmon_quant:
    input: reads/SAMEA103885413_1.fastq, reads/SAMEA103885413_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885413/quant.sf
    jobid: 19
    wildcards: sample=SAMEA103885413

Submitted job 19 with external jobid 'Submitted batch job 7379271'.
Finished job 7.
7 of 25 steps (28%) done

rule salmon_quant:
    input: reads/SAMEA103885004_1.fastq, reads/SAMEA103885004_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885004/quant.sf
    jobid: 15
    wildcards: sample=SAMEA103885004

Submitted job 15 with external jobid 'Submitted batch job 7379277'.
Finished job 12.
8 of 25 steps (32%) done

rule salmon_quant:
    input: reads/SAMEA103885136_1.fastq, reads/SAMEA103885136_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885136/quant.sf
    jobid: 11
    wildcards: sample=SAMEA103885136

Submitted job 11 with external jobid 'Submitted batch job 7379283'.
Finished job 19.
9 of 25 steps (36%) done

rule salmon_quant:
    input: reads/SAMEA103884967_1.fastq, reads/SAMEA103884967_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103884967/quant.sf
    jobid: 16
    wildcards: sample=SAMEA103884967

Submitted job 16 with external jobid 'Submitted batch job 7382546'.
Finished job 9.
10 of 25 steps (40%) done

rule salmon_quant:
    input: reads/SAMEA103885218_1.fastq, reads/SAMEA103885218_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885218/quant.sf
    jobid: 3
    wildcards: sample=SAMEA103885218

Submitted job 3 with external jobid 'Submitted batch job 7383162'.
Finished job 15.
11 of 25 steps (44%) done

rule salmon_quant:
    input: reads/SAMEA103885308_1.fastq, reads/SAMEA103885308_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885308/quant.sf
    jobid: 10
    wildcards: sample=SAMEA103885308

Submitted job 10 with external jobid 'Submitted batch job 7384000'.
Finished job 11.
12 of 25 steps (48%) done

rule salmon_quant:
    input: reads/SAMEA103885319_1.fastq, reads/SAMEA103885319_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885319/quant.sf
    jobid: 18
    wildcards: sample=SAMEA103885319

Submitted job 18 with external jobid 'Submitted batch job 7385744'.
Finished job 3.
13 of 25 steps (52%) done

rule salmon_quant:
    input: reads/SAMEA103885276_1.fastq, reads/SAMEA103885276_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885276/quant.sf
    jobid: 14
    wildcards: sample=SAMEA103885276

Submitted job 14 with external jobid 'Submitted batch job 7394007'.
Finished job 16.
14 of 25 steps (56%) done

rule salmon_quant:
    input: reads/SAMEA103885021_1.fastq, reads/SAMEA103885021_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885021/quant.sf
    jobid: 23
    wildcards: sample=SAMEA103885021

Finished job 10.
15 of 25 steps (60%) done
Submitted job 23 with external jobid 'Submitted batch job 7394303'.

rule salmon_quant:
    input: reads/SAMEA103885111_1.fastq, reads/SAMEA103885111_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885111/quant.sf
    jobid: 5
    wildcards: sample=SAMEA103885111

Submitted job 5 with external jobid 'Submitted batch job 7394307'.
Finished job 18.
16 of 25 steps (64%) done

rule salmon_quant:
    input: reads/SAMEA103885157_1.fastq, reads/SAMEA103885157_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885157/quant.sf
    jobid: 6
    wildcards: sample=SAMEA103885157

Submitted job 6 with external jobid 'Submitted batch job 7400770'.
Finished job 14.
17 of 25 steps (68%) done

rule salmon_quant:
    input: reads/SAMEA103884898_1.fastq, reads/SAMEA103884898_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103884898/quant.sf
    jobid: 8
    wildcards: sample=SAMEA103884898

Submitted job 8 with external jobid 'Submitted batch job 7404846'.
Finished job 23.
18 of 25 steps (72%) done

rule salmon_quant:
    input: reads/SAMEA103884919_1.fastq, reads/SAMEA103884919_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103884919/quant.sf
    jobid: 4
    wildcards: sample=SAMEA103884919

Finished job 5.
19 of 25 steps (76%) done
Submitted job 4 with external jobid 'Submitted batch job 7405321'.

rule salmon_quant:
    input: reads/SAMEA103885284_1.fastq, reads/SAMEA103885284_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885284/quant.sf
    jobid: 17
    wildcards: sample=SAMEA103885284

Submitted job 17 with external jobid 'Submitted batch job 7405325'.
Finished job 6.
20 of 25 steps (80%) done

rule salmon_quant:
    input: reads/SAMEA103885059_1.fastq, reads/SAMEA103885059_2.fastq, /proj/milovelab/anno/gencode.v29_salmon_0.12.0
    output: quants/SAMEA103885059/quant.sf
    jobid: 2
    wildcards: sample=SAMEA103885059

Submitted job 2 with external jobid 'Submitted batch job 7409464'.
Finished job 8.
21 of 25 steps (84%) done
Finished job 17.
22 of 25 steps (88%) done
Finished job 4.
23 of 25 steps (92%) done
Finished job 2.
24 of 25 steps (96%) done

localrule all:
    input: quants/SAMEA103884898/quant.sf, quants/SAMEA103884919/quant.sf, quants/SAMEA103884949/quant.sf, quants/SAMEA103884967/quant.sf, quants/SAMEA103885004/quant.sf, quants/SAMEA103885021/quant.sf, quants/SAMEA103885043/quant.sf, quants/SAMEA103885059/quant.sf, quants/SAMEA103885102/quant.sf, quants/SAMEA103885111/quant.sf, quants/SAMEA103885136/quant.sf, quants/SAMEA103885157/quant.sf, quants/SAMEA103885182/quant.sf, quants/SAMEA103885218/quant.sf, quants/SAMEA103885228/quant.sf, quants/SAMEA103885262/quant.sf, quants/SAMEA103885276/quant.sf, quants/SAMEA103885284/quant.sf, quants/SAMEA103885308/quant.sf, quants/SAMEA103885319/quant.sf, quants/SAMEA103885347/quant.sf, quants/SAMEA103885368/quant.sf, quants/SAMEA103885392/quant.sf, quants/SAMEA103885413/quant.sf
    jobid: 0

Finished job 0.
25 of 25 steps (100%) done
Complete log: .snakemake/log/2019-01-15T211329.585105.snakemake.log
