Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cluster nodes: 4
Job counts:
	count	jobs
	1	all
	12	salmon_quant
	13

rule salmon_quant:
    input: reads/SRX2236952_1.fastq, reads/SRX2236952_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236952/quant.sf
    jobid: 5
    wildcards: sample=SRX2236952

Submitted job 5 with external jobid 'Submitted batch job 7148798'.

rule salmon_quant:
    input: reads/SRX2236955_1.fastq, reads/SRX2236955_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236955/quant.sf
    jobid: 4
    wildcards: sample=SRX2236955

Submitted job 4 with external jobid 'Submitted batch job 7148799'.

rule salmon_quant:
    input: reads/SRX2236946_1.fastq, reads/SRX2236946_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236946/quant.sf
    jobid: 7
    wildcards: sample=SRX2236946

Submitted job 7 with external jobid 'Submitted batch job 7148800'.

rule salmon_quant:
    input: reads/SRX2236945_1.fastq, reads/SRX2236945_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236945/quant.sf
    jobid: 2
    wildcards: sample=SRX2236945

Submitted job 2 with external jobid 'Submitted batch job 7148801'.
Finished job 5.
1 of 13 steps (8%) done

rule salmon_quant:
    input: reads/SRX2236951_1.fastq, reads/SRX2236951_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236951/quant.sf
    jobid: 10
    wildcards: sample=SRX2236951

Finished job 7.
2 of 13 steps (15%) done
Submitted job 10 with external jobid 'Submitted batch job 7149281'.

rule salmon_quant:
    input: reads/SRX2236950_1.fastq, reads/SRX2236950_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236950/quant.sf
    jobid: 1
    wildcards: sample=SRX2236950

Submitted job 1 with external jobid 'Submitted batch job 7149282'.
Finished job 4.
3 of 13 steps (23%) done

rule salmon_quant:
    input: reads/SRX2236953_1.fastq, reads/SRX2236953_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236953/quant.sf
    jobid: 12
    wildcards: sample=SRX2236953

Submitted job 12 with external jobid 'Submitted batch job 7149288'.
Finished job 2.
4 of 13 steps (31%) done

rule salmon_quant:
    input: reads/SRX2236947_1.fastq, reads/SRX2236947_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236947/quant.sf
    jobid: 6
    wildcards: sample=SRX2236947

Submitted job 6 with external jobid 'Submitted batch job 7149292'.
Finished job 12.
5 of 13 steps (38%) done

rule salmon_quant:
    input: reads/SRX2236956_1.fastq, reads/SRX2236956_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236956/quant.sf
    jobid: 9
    wildcards: sample=SRX2236956

Submitted job 9 with external jobid 'Submitted batch job 7149565'.
Finished job 1.
6 of 13 steps (46%) done

rule salmon_quant:
    input: reads/SRX2236948_1.fastq, reads/SRX2236948_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236948/quant.sf
    jobid: 11
    wildcards: sample=SRX2236948

Submitted job 11 with external jobid 'Submitted batch job 7149577'.
Finished job 6.
7 of 13 steps (54%) done

rule salmon_quant:
    input: reads/SRX2236949_1.fastq, reads/SRX2236949_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236949/quant.sf
    jobid: 8
    wildcards: sample=SRX2236949

Submitted job 8 with external jobid 'Submitted batch job 7149582'.
Finished job 10.
8 of 13 steps (62%) done

rule salmon_quant:
    input: reads/SRX2236954_1.fastq, reads/SRX2236954_2.fastq, /proj/milovelab/anno/gencode.vM20_salmon_0.12.0
    output: quants/SRX2236954/quant.sf
    jobid: 3
    wildcards: sample=SRX2236954

Submitted job 3 with external jobid 'Submitted batch job 7149629'.
Finished job 11.
9 of 13 steps (69%) done
Finished job 9.
10 of 13 steps (77%) done
Finished job 8.
11 of 13 steps (85%) done
Finished job 3.
12 of 13 steps (92%) done

localrule all:
    input: quants/SRX2236945/quant.sf, quants/SRX2236946/quant.sf, quants/SRX2236947/quant.sf, quants/SRX2236948/quant.sf, quants/SRX2236949/quant.sf, quants/SRX2236950/quant.sf, quants/SRX2236951/quant.sf, quants/SRX2236952/quant.sf, quants/SRX2236953/quant.sf, quants/SRX2236954/quant.sf, quants/SRX2236955/quant.sf, quants/SRX2236956/quant.sf
    jobid: 0

Finished job 0.
13 of 13 steps (100%) done
Complete log: .snakemake/log/2019-01-15T110901.756642.snakemake.log
