
2021-05-17 CRAC_Pipeline_SE
20:21:48 - CRAC_Pipeline_SE -   INFO - analysing the following files:
/home/parallels/Documents/CRAC_Pipelines/test_data/test_1.fastq

20:21:49 - CRAC_Pipeline_SE -   INFO - No demultiplexing requested. Trimming reads
20:21:49 - CRAC_Pipeline_SE -   INFO - Collapsing reads
20:21:49 - CRAC_Pipeline_SE -   INFO - Aligning reads
20:21:49 - CRAC_Pipeline_SE -   INFO - Mapping reads to genomic features
20:21:49 - CRAC_Pipeline_SE -   INFO - Making bedgraph files
20:21:49 - CRAC_Pipeline_SE -   INFO - flexbar -r '/home/parallels/Documents/CRAC_Pipelines/test_data/test_1.fastq' -qf i1.8 -n 10 -ao 7 --output-reads '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/flexbar_trimmed/test_1_trimmed.fastq' --adapters '../adapter_sequences/three_prime_adapters.fasta' -qt 30
20:21:50 - CRAC_Pipeline_SE -   INFO - pyFastqDuplicateRemover.py -f '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/flexbar_trimmed/test_1_trimmed.fastq' -o '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/collapsed/test_1_trimmed.fasta'
20:21:51 - CRAC_Pipeline_SE -   INFO - novoalign -d '../genome_files/Staphylococcus_aureus_usa300_FPR3757_corrected.novoindex' -f '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/collapsed/test_1_trimmed.fasta' -r Random > '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/novo_files/test_1_trimmed.novo'
20:21:56 - CRAC_Pipeline_SE -   INFO - pyReadCounters.py -f '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/novo_files/test_1_trimmed.novo' --gtf '../genome_files/Staphylococcus_aureus_usa300_FPR3757_1.3_with_intergenic.gtf' -v --rpkm -o '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/pyReadCounters_analyses/test_1_trimmed' ''
20:21:56 - CRAC_Pipeline_SE -   INFO - pyReadCounters.py -f '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/novo_files/test_1_trimmed.novo' --gtf '../genome_files/Staphylococcus_aureus_usa300_FPR3757_1.3_with_intergenic.gtf' -v --rpkm -o '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/pyReadCounters_blocks_nomuts_analyses/test_1_trimmed_blocks_nomuts' --mutations  nomuts --blocks
20:21:58 - CRAC_Pipeline_SE -   INFO - pyGTF2bedGraph.py --gtf '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/pyReadCounters_blocks_nomuts_analyses/test_1_trimmed_blocks_nomuts_count_output_cDNAs.gtf' --count -v --permillion -o '/home/parallels/Documents/CRAC_Pipelines/test_code/test_single_end_run/bedgraph_files/test_1_trimmed_blocks_nomuts' -c '../genome_files/Staphylococcus_aureus_usa300_FPR3757_corrected.length'
