2021-05-21 11:13 - INFO - gbk_convert - Converting genebank ../data/input/ES114v2.gb to fasta nucleotide (.fna) and feature table (.ftt).
2021-05-21 11:18 - INFO - gbk_convert - Converting genebank ../data/input/ES114v2.gb to fasta nucleotide (.fna) and feature table (.ftt).
2021-05-21 11:18 - INFO - gbk_convert - Nucleotides stored in results/example_pyinseq_unique_transposon_barcode/genome_lookup/genome.fna
2021-05-21 11:18 - INFO - gbk_convert - Features table stored in results/example_pyinseq_unique_transposon_barcode/genome_lookup/genome.ftt
2021-05-21 11:18 - INFO - demultiplex - Preparing to demultiplex reads
2021-05-21 11:18 - INFO - demultiplex - Total reads demultiplexed: 534
2021-05-21 11:18 - INFO - map_reads - Mapping reads in results/example_pyinseq_unique_transposon_barcode/E001_02_trimmed.fastq to genome using bowtie
2021-05-21 11:18 - INFO - map_reads - Bowtie results for E001_02:
# reads processed: 274
# reads with at least one reported alignment: 274 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 274 alignments

2021-05-21 11:18 - INFO - map_reads - Mapping reads in results/example_pyinseq_unique_transposon_barcode/E001_01_trimmed.fastq to genome using bowtie
2021-05-21 11:18 - INFO - map_reads - Bowtie results for E001_01:
# reads processed: 252
# reads with at least one reported alignment: 252 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 252 alignments

2021-05-21 11:18 - INFO - process_mapping - Sample E001_02: summarize the site data from the bowtie results into sites file.
2021-05-21 11:18 - INFO - process_mapping - Sample E001_01: summarize the site data from the bowtie results into sites file.
2021-05-21 11:18 - INFO - process_mapping - Sample E001_02: map site data to genes
2021-05-21 11:18 - INFO - process_mapping - Sample E001_01: map site data to genes
2021-05-21 11:18 - INFO - process_mapping - Aggregate gene mapping from all samples into the summary_data_table
2021-05-21 11:19 - INFO - pipeline - Print log path: results/example_pyinseq_unique_transposon_barcode/log.txt
2021-05-21 11:19 - INFO - pipeline - Print settings:
command: pyinseq
config_file: example_pyinseq_unique_transposon_barcode-config.yaml
experiment: example_pyinseq_unique_transposon_barcode
threads: 4
output_dir: results/example_pyinseq_unique_transposon_barcode
path: results/example_pyinseq_unique_transposon_barcode/
log: results/example_pyinseq_unique_transposon_barcode/log.txt
summary_log: results/example_pyinseq_unique_transposon_barcode/summary_log.txt
reads: ../data/input/example03.fastq
samples: ../data/input/example03.txt
samples_txt: results/example_pyinseq_unique_transposon_barcode/samples.txt
samples_dict: {'E001_01': {'barcode': 'CTAGAGAAG'}, 'E001_02': {'barcode': 'AAGTCCTTT'}}
samples_info_yml: results/example_pyinseq_unique_transposon_barcode/samples_info.yml
raw_path: results/example_pyinseq_unique_transposon_barcode/raw_data/
reference_genome: ../data/input/ES114v2.gb
genome_path: results/example_pyinseq_unique_transposon_barcode/genome_lookup/
map_to_genome: True
gff: False
summary_table: results/example_pyinseq_unique_transposon_barcode/summary_gene_table.txt
disruption: 0.9
barcode_length: 9
transposon_seq: TCGCACGG
min_counts: 3
max_ratio: 10
settings_pickle: results/example_pyinseq_unique_transposon_barcode/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_unique_transposon_barcode -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

2021-05-21 11:19 - INFO - pipeline - Print samples detail
E001_01:
  barcode: CTAGAGAAG
  demultiplexed_reads: 252
  gene hits: 182
  site hits: 252
E001_02:
  barcode: AAGTCCTTT
  demultiplexed_reads: 274
  gene hits: 204
  site hits: 274


