indexing is not occurring in tutorial
splaisan opened this issue · comments
Stephane Plaisance commented
I deleted the two results folders and re-ran the full script but the bam's do not get indexed
What I am missing?
Thanks
rule bwa_map:
input:
"data/genome.fa",
"data/samples/{sample}.fastq"
output:
"mapped_reads/{sample}.bam"
shell:
"bwa mem {input} | samtools view -Sb - > {output}"
rule samtools_sort:
input:
"mapped_reads/{sample}.bam"
output:
"sorted_reads/{sample}.bam"
shell:
"samtools sort -T sorted_reads/{wildcards.sample} "
"-O bam {input} > {output}"
rule samtools_index:
input:
"sorted_reads/{sample}.bam"
output:
"sorted_reads/{sample}.bam.bai"
shell:
"samtools index {input}"
> snakemake sorted_reads/{A,B}.bam
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
2 samtools_sort
2
[Mon Oct 22 11:40:17 2018]
rule samtools_sort:
input: mapped_reads/B.bam
output: sorted_reads/B.bam
jobid: 0
wildcards: sample=B
[Mon Oct 22 11:40:17 2018]
Finished job 0.
1 of 2 steps (50%) done
[Mon Oct 22 11:40:17 2018]
rule samtools_sort:
input: mapped_reads/A.bam
output: sorted_reads/A.bam
jobid: 1
wildcards: sample=A
[Mon Oct 22 11:40:17 2018]
Finished job 1.
2 of 2 steps (100%) done
Complete log: /data/NC_projects/snakemake-tutorial/.snakemake/log/2018-10-22T114017.262317.snakemake.log
# is leading to
> ls -lah sorted_reads/
total 4.4M
drwxr-xr-x 2 u0002316 domain users 4.0K Oct 22 11:30 .
drwxr-xr-x 6 u0002316 domain users 4.0K Oct 22 11:39 ..
-rw-r--r-- 1 u0002316 domain users 2.2M Oct 22 11:30 A.bam
-rw-r--r-- 1 u0002316 domain users 2.2M Oct 22 11:30 B.bam
Johannes Köster commented
Duplicate of #10.