
2021-05-17 CRAC_pipeline_PE
20:20:58 - CRAC_pipeline_PE -   INFO - pyFastqJoiner.py -f '/home/parallels/Documents/CRAC_Pipelines/test_data/test_1.fastq' '/home/parallels/Documents/CRAC_Pipelines/test_data/test_2.fastq' -c '|' | pyFastqDuplicateRemover.py | pyFastqSplitter.py -c '|' --file_type fasta -o '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/collapsed/test_1.fasta' '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/collapsed/test_2.fasta'
20:20:58 - CRAC_pipeline_PE -   INFO - flexbar -r '/home/parallels/Documents/CRAC_Pipelines/test_data/test_1.fastq' -p '/home/parallels/Documents/CRAC_Pipelines/test_data/test_2.fastq' -qf i1.8 -n 10 -ao 7 --adapters '../adapter_sequences/three_prime_adapters.fasta' --adapters2 '../adapter_sequences/five_prime_adapters_reverse_complemented.fasta' --output-reads '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/flexbar_trimmed/test_trimmed_1.fastq' --output-reads2 '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/flexbar_trimmed/test_trimmed_2.fastq' -qt 30 -ap ON
20:21:03 - CRAC_pipeline_PE -   INFO - novoalign -d '../genome_files/Staphylococcus_aureus_usa300_FPR3757_corrected.novoindex' -f '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/collapsed/test_1.fasta' '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/collapsed/test_2.fasta' -r Random > '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/novo_files/test_1.novo'
20:21:42 - CRAC_pipeline_PE -   INFO - pyReadCounters.py -f '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/novo_files/test_1.novo' --gtf '../genome_files/Staphylococcus_aureus_usa300_FPR3757_1.3_with_intergenic.gtf' -v -o '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/pyReadCounters_blocks_nomuts_analyses/test_1_blocks_nomuts' --mutations	nomuts --blocks
20:21:42 - CRAC_pipeline_PE -   INFO - pyReadCounters.py -f '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/novo_files/test_1.novo' --gtf '../genome_files/Staphylococcus_aureus_usa300_FPR3757_1.3_with_intergenic.gtf' -v -o '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/pyReadCounters_analyses/test_1' ''
20:21:47 - CRAC_pipeline_PE -   INFO - pyGTF2bedGraph.py --gtf '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/pyReadCounters_blocks_nomuts_analyses/test_1_blocks_nomuts_count_output_cDNAs.gtf' --count -v --permillion -o '/home/parallels/Documents/CRAC_Pipelines/test_code/test_run/bedgraph_files/test_1_blocks_nomuts' -c '../genome_files/Staphylococcus_aureus_usa300_FPR3757_corrected.length'
