(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	genome_prep
	1
(PYINSEQ INFO)
(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	demultiplex
	1
(PYINSEQ INFO)
534 reads demultiplexed
- E001_01 (GAAG): 252 reads
- E001_02 (CTTT): 274 reads
(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	bowtie_mapping
	1
(PYINSEQ INFO)
- Mapped reads from E001_02 to genome
BOWTIE OUTPUT:
# reads processed: 274
# reads with at least one reported alignment: 274
# reads that failed to align: 0
(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	bowtie_mapping
	1
(PYINSEQ INFO)
- Mapped reads from E001_01 to genome
BOWTIE OUTPUT:
# reads processed: 252
# reads with at least one reported alignment: 252
# reads that failed to align: 0
(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	map_sites
	1
(PYINSEQ INFO)
- E001_02: 274 aligned reads mapped to sites
(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	map_sites
	1
(PYINSEQ INFO)
- E001_01: 252 aligned reads mapped to sites
(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	map_genes
	1
(PYINSEQ INFO)
- E001_02: 204 of mapped reads fall in genes
(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	map_genes
	1
(PYINSEQ INFO)
- E001_01: 196 of mapped reads fall in genes
(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	build_gene_table
	1
(PYINSEQ INFO)
- Gene table contains 2 samples (columns) for 3987 genes (rows) 
(SNAKEMAKE INFO)
Job counts:
	count	jobs
	1	summarize
	1
(PYINSEQ INFO)
Print log path: results/example_pyinseq/log.txt
Print settings:
command: pyinseq
config_file: example_pyinseq-config.yaml
experiment: example_pyinseq
threads: 4
output_dir: results/example_pyinseq
path: results/example_pyinseq/
log: results/example_pyinseq/log.txt
summary_log: results/example_pyinseq/summary_log.txt
reads: ../data/input/example01.fastq
samples: ../data/input/example01.txt
samples_txt: results/example_pyinseq/samples.txt
samples_dict: {'E001_01': {'barcode': 'GAAG'}, 'E001_02': {'barcode': 'CTTT'}}
samples_info_yml: results/example_pyinseq/samples_info.yml
raw_path: results/example_pyinseq/raw_data/
reference_genome: ../data/input/ES114v2.gb
genome_path: results/example_pyinseq/genome_lookup/
map_to_genome: True
gff: False
summary_table: results/example_pyinseq/summary_gene_table.txt
disruption: 0.9
barcode_length: 4
transposon_seq: ACAGGTTG
min_counts: 3
max_ratio: 10
settings_pickle: results/example_pyinseq/settings.pickle
organism: genome
snakefile: /Users/emanuelburgos/Dropbox/Mandel_Lab/Projects/Project_Pyinseq/pyinseq/pyinseq/workflows/PyinseqWorkflow/Snakefile
snakemake_cmd: snakemake --config experiment=example_pyinseq -s /Users/emanuelburgos/Dropbox/Mandel_Lab/Projects/Project_Pyinseq/pyinseq/pyinseq/workflows/PyinseqWorkflow/Snakefile --cores 3
process_reads: False
process_sample_list: False
parse_genebank: False
generate_bowtie_index: False
write_trimmed_reads: True
Print samples detail
E001_01:
  barcode: GAAG
  demultiplexed_reads: 252
  gene hits: 182
  site hits: 252
E001_02:
  barcode: CTTT
  demultiplexed_reads: 274
  gene hits: 204
  site hits: 274

