(base) veeral@wangikarlab:/media/wangikarlab/Veeral/Seq_data$ snakemake -s /home/veeral/lathe/Snakefile --configfile config_1.txt -n                                                                             {'V1': ['/media/wangikarlab/Veeral/Seq_data/illuminaclean/V1_clean1.fastq', '/media/wangikarlab/Veeral/Seq_data/illuminaclean/V1_clean2.fastq']}
Building DAG of jobs...
Job counts:
        count   jobs
        3       align_bam
        1       all
        1       assemble_final
        2       assemble_flye
        3       bam_idx
        1       circularize_final
        1       extract_bigtigs
        5       faidx
        1       final
        1       merge
        3       misassemblies_correct
        3       misassemblies_detect
        1       nanoplot
        1       pilon_aggregate_vcf
        1       pilon_consensus
        1       pilon_ranges
        1       polish_final
        30

[Wed May  5 11:51:51 2021]
rule assemble_flye:
    input: /media/wangikarlab/Veeral/Seq_data/nanoporeclean/v1q7.fastq
    output: V1/1.assemble/assemble_2m/assembly.fasta
    jobid: 11
    wildcards: sample=V1, genome_size=2m
    resources: mem=100, time=100


[Wed May  5 11:51:51 2021]
rule nanoplot:
    input: /media/wangikarlab/Veeral/Seq_data/nanoporeclean/v1q7.fastq
    output: V1/0.basecall/nanoplots/Weighted_LogTransformed_HistogramReadlength.png
    jobid: 29
    wildcards: sample=V1
    resources: time=4


[Wed May  5 11:51:51 2021]
rule assemble_flye:
    input: /media/wangikarlab/Veeral/Seq_data/nanoporeclean/v1q7.fastq
    output: V1/1.assemble/assemble_4m/assembly.fasta
    jobid: 17
    wildcards: sample=V1, genome_size=4m
    resources: mem=100, time=100


[Wed May  5 11:51:51 2021]
localrule faidx:
    input: V1/1.assemble/assemble_2m/assembly.fasta
    output: V1/1.assemble/assemble_2m/assembly.fasta.fai
    jobid: 12
    wildcards: something=V1/1.assemble/assemble_2m/assembly, asta=asta


[Wed May  5 11:51:51 2021]
localrule faidx:
    input: V1/1.assemble/assemble_4m/assembly.fasta
    output: V1/1.assemble/assemble_4m/assembly.fasta.fai
    jobid: 18
    wildcards: something=V1/1.assemble/assemble_4m/assembly, asta=asta


[Wed May  5 11:51:51 2021]
rule align_bam:
    input: V1/1.assemble/assemble_2m/assembly.fasta, /media/wangikarlab/Veeral/Seq_data/nanoporeclean/v1q7.fastq
    output: V1/1.assemble/assemble_2m/assembly.fasta.bam
    jobid: 13
    wildcards: ref=V1/1.assemble/assemble_2m/assembly, asta=asta
    resources: time=6, mem=16


[Wed May  5 11:51:51 2021]
rule align_bam:
    input: V1/1.assemble/assemble_4m/assembly.fasta, /media/wangikarlab/Veeral/Seq_data/nanoporeclean/v1q7.fastq
    output: V1/1.assemble/assemble_4m/assembly.fasta.bam
    jobid: 19
    wildcards: ref=V1/1.assemble/assemble_4m/assembly, asta=asta
    resources: time=6, mem=16


[Wed May  5 11:51:51 2021]
rule bam_idx:
    input: V1/1.assemble/assemble_2m/assembly.fasta.bam
    output: V1/1.assemble/assemble_2m/assembly.fasta.bam.bai
    jobid: 14
    wildcards: some=V1/1.assemble/assemble_2m/assembly.fasta


[Wed May  5 11:51:51 2021]
rule bam_idx:
    input: V1/1.assemble/assemble_4m/assembly.fasta.bam
    output: V1/1.assemble/assemble_4m/assembly.fasta.bam.bai
    jobid: 20
    wildcards: some=V1/1.assemble/assemble_4m/assembly.fasta


[Wed May  5 11:51:51 2021]
rule misassemblies_detect:
    input: V1/1.assemble/assemble_2m/assembly.fasta, V1/1.assemble/assemble_2m/assembly.fasta.fai, V1/1.assemble/assemble_2m/assembly.fasta.bam, V1/1.assemble/assemble_2m/assembly.fasta.bam.bai
    output: V1/1.assemble/assemble_2m/assembly.fasta.misassemblies.tsv
    jobid: 10
    wildcards: sample=V1/1.assemble/assemble_2m, sequence=assembly, sta=sta
    resources: mem=24, time=24


[Wed May  5 11:51:51 2021]
rule misassemblies_detect:
    input: V1/1.assemble/assemble_4m/assembly.fasta, V1/1.assemble/assemble_4m/assembly.fasta.fai, V1/1.assemble/assemble_4m/assembly.fasta.bam, V1/1.assemble/assemble_4m/assembly.fasta.bam.bai
    output: V1/1.assemble/assemble_4m/assembly.fasta.misassemblies.tsv
    jobid: 16
    wildcards: sample=V1/1.assemble/assemble_4m, sequence=assembly, sta=sta
    resources: mem=24, time=24


[Wed May  5 11:51:51 2021]
rule misassemblies_correct:
    input: V1/1.assemble/assemble_4m/assembly.fasta.misassemblies.tsv, V1/1.assemble/assemble_4m/assembly.fasta.fai, V1/1.assemble/assemble_4m/assembly.fasta
    output: V1/1.assemble/assemble_4m/assembly.corrected.fasta
    jobid: 15
    wildcards: sample=V1/1.assemble/assemble_4m, sequence=assembly, sta=sta


[Wed May  5 11:51:51 2021]
rule misassemblies_correct:
    input: V1/1.assemble/assemble_2m/assembly.fasta.misassemblies.tsv, V1/1.assemble/assemble_2m/assembly.fasta.fai, V1/1.assemble/assemble_2m/assembly.fasta
    output: V1/1.assemble/assemble_2m/assembly.corrected.fasta
    jobid: 9
    wildcards: sample=V1/1.assemble/assemble_2m, sequence=assembly, sta=sta


[Wed May  5 11:51:51 2021]
rule merge:
    input: V1/1.assemble/assemble_2m/assembly.corrected.fasta, V1/1.assemble/assemble_4m/assembly.corrected.fasta
    output: V1/1.assemble/V1_merged.fasta
    jobid: 8
    wildcards: sample=V1
    resources: time=6, mem=24


[Wed May  5 11:51:51 2021]
localrule assemble_final:
    input: V1/1.assemble/V1_merged.fasta
    output: V1/1.assemble/V1_raw_assembly.fa
    jobid: 7
    wildcards: sample=V1


[Wed May  5 11:51:51 2021]
localrule faidx:
    input: V1/1.assemble/V1_raw_assembly.fa
    output: V1/1.assemble/V1_raw_assembly.fa.fai
    jobid: 23
    wildcards: something=V1/1.assemble/V1_raw_assembly, asta=a


[Wed May  5 11:51:51 2021]
localcheckpoint pilon_ranges:
    input: V1/1.assemble/V1_raw_assembly.fa, V1/1.assemble/V1_raw_assembly.fa.fai
    output: V1/2.polish/pilon/ranges
    jobid: 22
    wildcards: sample=V1
Downstream jobs will be updated after completion.


[Wed May  5 11:51:51 2021]
localrule pilon_aggregate_vcf:
    input: <TBD>
    output: V1/2.polish/pilon/corrections.vcf.gz
    jobid: 21
    wildcards: sample=V1
    resources: time=4, mem=8


[Wed May  5 11:51:51 2021]
rule pilon_consensus:
    input: V1/1.assemble/V1_raw_assembly.fa, V1/2.polish/pilon/corrections.vcf.gz
    output: V1/2.polish/pilon/V1_pilon.fa
    jobid: 6
    wildcards: sample=V1


[Wed May  5 11:51:51 2021]
localrule polish_final:
    input: V1/2.polish/pilon/V1_pilon.fa
    output: V1/2.polish/V1_polished.fasta
    jobid: 5
    wildcards: sample=V1


[Wed May  5 11:51:51 2021]
localrule faidx:
    input: V1/2.polish/V1_polished.fasta
    output: V1/2.polish/V1_polished.fasta.fai
    jobid: 24
    wildcards: something=V1/2.polish/V1_polished, asta=asta


[Wed May  5 11:51:51 2021]
localcheckpoint extract_bigtigs:
    input: V1/2.polish/V1_polished.fasta, V1/2.polish/V1_polished.fasta.fai
    output: V1/3.circularization/1.candidate_genomes
    jobid: 25
    wildcards: sample=V1
Downstream jobs will be updated after completion.


[Wed May  5 11:51:51 2021]
localrule circularize_final:
    input: V1/2.polish/V1_polished.fasta, V1/2.polish/V1_polished.fasta.fai, <TBD>, <TBD>
    output: V1/3.circularization/4.V1_circularized.fasta
    jobid: 4
    wildcards: sample=V1


[Wed May  5 11:51:51 2021]
localrule faidx:
    input: V1/3.circularization/4.V1_circularized.fasta
    output: V1/3.circularization/4.V1_circularized.fasta.fai
    jobid: 26
    wildcards: something=V1/3.circularization/4.V1_circularized, asta=asta


[Wed May  5 11:51:51 2021]
rule align_bam:
    input: V1/3.circularization/4.V1_circularized.fasta, /media/wangikarlab/Veeral/Seq_data/nanoporeclean/v1q7.fastq
    output: V1/3.circularization/4.V1_circularized.fasta.bam
    jobid: 27
    wildcards: ref=V1/3.circularization/4.V1_circularized, asta=asta
    resources: time=6, mem=16


[Wed May  5 11:51:51 2021]
rule bam_idx:
    input: V1/3.circularization/4.V1_circularized.fasta.bam
    output: V1/3.circularization/4.V1_circularized.fasta.bam.bai
    jobid: 28
    wildcards: some=V1/3.circularization/4.V1_circularized.fasta


[Wed May  5 11:51:51 2021]
rule misassemblies_detect:
    input: V1/3.circularization/4.V1_circularized.fasta, V1/3.circularization/4.V1_circularized.fasta.fai, V1/3.circularization/4.V1_circularized.fasta.bam, V1/3.circularization/4.V1_circularized.fasta.bam.bai
    output: V1/3.circularization/4.V1_circularized.fasta.misassemblies.tsv
    jobid: 3
    wildcards: sample=V1/3.circularization, sequence=4.V1_circularized, sta=sta
    resources: mem=24, time=24


[Wed May  5 11:51:51 2021]
rule misassemblies_correct:
    input: V1/3.circularization/4.V1_circularized.fasta.misassemblies.tsv, V1/3.circularization/4.V1_circularized.fasta.fai, V1/3.circularization/4.V1_circularized.fasta
    output: V1/3.circularization/4.V1_circularized.corrected.fasta
    jobid: 2
    wildcards: sample=V1/3.circularization, sequence=4.V1_circularized, sta=sta


[Wed May  5 11:51:51 2021]
rule final:
    input: V1/3.circularization/4.V1_circularized.corrected.fasta
    output: V1/5.final/V1_final.fa
    jobid: 1
    wildcards: sample=V1


[Wed May  5 11:51:51 2021]
localrule all:
    input: V1/5.final/V1_final.fa, V1/0.basecall/nanoplots/Weighted_LogTransformed_HistogramReadlength.png
    jobid: 0

Job counts:
        count   jobs
        3       align_bam
        1       all
        1       assemble_final
        2       assemble_flye
        3       bam_idx
        1       circularize_final
        1       extract_bigtigs
        5       faidx
        1       final
        1       merge
        3       misassemblies_correct
        3       misassemblies_detect
        1       nanoplot
        1       pilon_aggregate_vcf
        1       pilon_consensus
        1       pilon_ranges
        1       polish_final
        30
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.