localrules directive specifies rules that are not present in the Snakefile:
	filterResults
	mergeTblm
	makeFastaFromTab
	mergeRef
	mergeCollapsed

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Unlimited resources: mfree, IO
Job counts:
	count	jobs
	1	map_mm
	1

[Wed May  5 09:40:25 2021]
rule map_mm:
    input: Iso_data/SBY20366_t0_input_r1.flnc.fa, /net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/iso-seq/YeastCen/genomes/sacCer3/sacCer3.fa
    output: alignments/sacCer3_mm.SBY20366_t0_input_r1.flnc.fa.bam
    jobid: 0
    wildcards: target=sacCer3, ID=SBY20366_t0_input_r1.flnc.fa
    resources: mfree=4, IO=300


		IN=$PWD/Iso_data/SBY20366_t0_input_r1.flnc.fa
		OUT=$PWD/alignments/sacCer3_mm.SBY20366_t0_input_r1.flnc.fa.bam

		source ~/modules.sh
		minimap2 			-ax splice 			-t 4 			-G2k -uf -C5 			/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/iso-seq/YeastCen/genomes/sacCer3/sacCer3.fa $IN | 			samtools view -bS -F 2308 - | 			samtools sort -m 4G -o $OUT
		
/net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/iso-seq/YeastCen/210504_Round4/data/mapping/env_python3.cfg: line 10: activate: No such file or directory
[M::mm_idx_gen::1.056*0.53] collected minimizers
[M::mm_idx_gen::1.192*0.88] sorted minimizers
[M::main::1.192*0.88] loaded/built the index for 17 target sequence(s)
[M::mm_mapopt_update::1.259*0.89] mid_occ = 33
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 17
[M::mm_idx_stat::1.309*0.89] distinct minimizers: 3788481 (95.52% are singletons); average occurrences: 1.095; average spacing: 2.930
[M::worker_pipeline::20.748*2.67] mapped 96509 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -ax splice -t 4 -G2k -uf -C5 /net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/iso-seq/YeastCen/genomes/sacCer3/sacCer3.fa /net/eichler/vol27/projects/AlphaSatelliteMapping/nobackups/FindingAlphaSat/iso-seq/YeastCen/210504_Round4/data/mapping/Iso_data/SBY20366_t0_input_r1.flnc.fa
[M::main] Real time: 20.779 sec; CPU: 55.393 sec; Peak RSS: 0.410 GB
[Wed May  5 09:40:49 2021]
Finished job 0.
1 of 1 steps (100%) done