#!/usr/bin/env python # coding: utf-8 # In[1]: get_ipython().run_cell_magic('bash', '', 'date\n') # In[2]: get_ipython().run_cell_magic('bash', '', 'system_profiler SPSoftwareDataType\n') # In[3]: get_ipython().run_cell_magic('bash', '', '#Uses grep to exclude lines that display serial number and hardware UUID\nsystem_profiler SPHardwareDataType | grep -v [SH][ea]\n') # #### Move to directory with GBS FASTQ files # In[20]: cd /Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks/ # #### List all FASTQ files for use in subsequent STACKS command # In[22]: get_ipython().run_cell_magic('bash', '', 'echo *_1.fq.gz\n') # In[23]: get_ipython().run_cell_magic('bash', '', 'echo *_2.fq.gz\n') # ### Run QC on files with `process_radtags` component # #### Cell below creates two lists (one list for each individual pair of FASTQs), loops through each as an array and assigns the corresponding FASTQ pairs to the variables "i" and "j". The values in "i" and "j" are used in the `process_radtags` command for matching the paired FASTQ files. # In[24]: get_ipython().run_cell_magic('bash', '', 'seq1=( 1HL_10A_1.fq.gz 1HL_11A_1.fq.gz 1HL_12A_1.fq.gz 1HL_13A_1.fq.gz 1HL_14A_1.fq.gz 1HL_15A_1.fq.gz 1HL_16A_1.fq.gz 1HL_17A_1.fq.gz 1HL_19A_1.fq.gz 1HL_1A_1.fq.gz 1HL_20A_1.fq.gz 1HL_21A_1.fq.gz 1HL_22A_1.fq.gz 1HL_23A_1.fq.gz 1HL_24A_1.fq.gz 1HL_25A_1.fq.gz 1HL_26A_1.fq.gz 1HL_27A_1.fq.gz 1HL_28A_1.fq.gz 1HL_29A_1.fq.gz 1HL_2A_1.fq.gz 1HL_31A_1.fq.gz 1HL_33A_1.fq.gz 1HL_34A_1.fq.gz 1HL_35A_1.fq.gz 1HL_3A_1.fq.gz 1HL_4A_1.fq.gz 1HL_5A_1.fq.gz 1HL_6A_1.fq.gz 1HL_7A_1.fq.gz 1HL_8A_1.fq.gz 1HL_9A_1.fq.gz 1NF_10A_1.fq.gz 1NF_11A_1.fq.gz 1NF_12A_1.fq.gz 1NF_13A_1.fq.gz 1NF_14A_1.fq.gz 1NF_15A_1.fq.gz 1NF_16A_1.fq.gz 1NF_17A_1.fq.gz 1NF_18A_1.fq.gz 1NF_19A_1.fq.gz 1NF_1A_1.fq.gz 1NF_20A_1.fq.gz 1NF_21A_1.fq.gz 1NF_22A_1.fq.gz 1NF_23A_1.fq.gz 1NF_24A_1.fq.gz 1NF_25A_1.fq.gz 1NF_26A_1.fq.gz 1NF_27A_1.fq.gz 1NF_28A_1.fq.gz 1NF_29A_1.fq.gz 1NF_2A_1.fq.gz 1NF_30A_1.fq.gz 1NF_31A_1.fq.gz 1NF_32A_1.fq.gz 1NF_33A_1.fq.gz 1NF_4A_1.fq.gz 1NF_5A_1.fq.gz 1NF_6A_1.fq.gz 1NF_7A_1.fq.gz 1NF_8A_1.fq.gz 1NF_9A_1.fq.gz 1SN_10A_1.fq.gz 1SN_11A_1.fq.gz 1SN_12A_1.fq.gz 1SN_13A_1.fq.gz 1SN_14A_1.fq.gz 1SN_15A_1.fq.gz 1SN_16A_1.fq.gz 1SN_17A_1.fq.gz 1SN_18A_1.fq.gz 1SN_19A_1.fq.gz 1SN_1A_1.fq.gz 1SN_20A_1.fq.gz 1SN_21A_1.fq.gz 1SN_22A_1.fq.gz 1SN_23A_1.fq.gz 1SN_24A_1.fq.gz 1SN_25A_1.fq.gz 1SN_26A_1.fq.gz 1SN_27A_1.fq.gz 1SN_28A_1.fq.gz 1SN_29A_1.fq.gz 1SN_2A_1.fq.gz 1SN_30A_1.fq.gz 1SN_31A_1.fq.gz 1SN_32A_1.fq.gz 1SN_3A_1.fq.gz 1SN_4A_1.fq.gz 1SN_5A_1.fq.gz 1SN_6A_1.fq.gz 1SN_7A_1.fq.gz 1SN_8A_1.fq.gz 1SN_9A_1.fq.gz )\nseq2=( 1HL_10A_2.fq.gz 1HL_11A_2.fq.gz 1HL_12A_2.fq.gz 1HL_13A_2.fq.gz 1HL_14A_2.fq.gz 1HL_15A_2.fq.gz 1HL_16A_2.fq.gz 1HL_17A_2.fq.gz 1HL_19A_2.fq.gz 1HL_1A_2.fq.gz 1HL_20A_2.fq.gz 1HL_21A_2.fq.gz 1HL_22A_2.fq.gz 1HL_23A_2.fq.gz 1HL_24A_2.fq.gz 1HL_25A_2.fq.gz 1HL_26A_2.fq.gz 1HL_27A_2.fq.gz 1HL_28A_2.fq.gz 1HL_29A_2.fq.gz 1HL_2A_2.fq.gz 1HL_31A_2.fq.gz 1HL_33A_2.fq.gz 1HL_34A_2.fq.gz 1HL_35A_2.fq.gz 1HL_3A_2.fq.gz 1HL_4A_2.fq.gz 1HL_5A_2.fq.gz 1HL_6A_2.fq.gz 1HL_7A_2.fq.gz 1HL_8A_2.fq.gz 1HL_9A_2.fq.gz 1NF_10A_2.fq.gz 1NF_11A_2.fq.gz 1NF_12A_2.fq.gz 1NF_13A_2.fq.gz 1NF_14A_2.fq.gz 1NF_15A_2.fq.gz 1NF_16A_2.fq.gz 1NF_17A_2.fq.gz 1NF_18A_2.fq.gz 1NF_19A_2.fq.gz 1NF_1A_2.fq.gz 1NF_20A_2.fq.gz 1NF_21A_2.fq.gz 1NF_22A_2.fq.gz 1NF_23A_2.fq.gz 1NF_24A_2.fq.gz 1NF_25A_2.fq.gz 1NF_26A_2.fq.gz 1NF_27A_2.fq.gz 1NF_28A_2.fq.gz 1NF_29A_2.fq.gz 1NF_2A_2.fq.gz 1NF_30A_2.fq.gz 1NF_31A_2.fq.gz 1NF_32A_2.fq.gz 1NF_33A_2.fq.gz 1NF_4A_2.fq.gz 1NF_5A_2.fq.gz 1NF_6A_2.fq.gz 1NF_7A_2.fq.gz 1NF_8A_2.fq.gz 1NF_9A_2.fq.gz 1SN_10A_2.fq.gz 1SN_11A_2.fq.gz 1SN_12A_2.fq.gz 1SN_13A_2.fq.gz 1SN_14A_2.fq.gz 1SN_15A_2.fq.gz 1SN_16A_2.fq.gz 1SN_17A_2.fq.gz 1SN_18A_2.fq.gz 1SN_19A_2.fq.gz 1SN_1A_2.fq.gz 1SN_20A_2.fq.gz 1SN_21A_2.fq.gz 1SN_22A_2.fq.gz 1SN_23A_2.fq.gz 1SN_24A_2.fq.gz 1SN_25A_2.fq.gz 1SN_26A_2.fq.gz 1SN_27A_2.fq.gz 1SN_28A_2.fq.gz 1SN_29A_2.fq.gz 1SN_2A_2.fq.gz 1SN_30A_2.fq.gz 1SN_31A_2.fq.gz 1SN_32A_2.fq.gz 1SN_3A_2.fq.gz 1SN_4A_2.fq.gz 1SN_5A_2.fq.gz 1SN_6A_2.fq.gz 1SN_7A_2.fq.gz 1SN_8A_2.fq.gz 1SN_9A_2.fq.gz )\ntime for pair in "${!seq1[@]}"; do\n i=${seq1[$pair]}\n j=${seq2[$pair]}\n /usr/local/bioinformatics/stacks-1.37/process_radtags \\\n -1 $i \\\n -2 $j \\\n -o /Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks/ \\\n -e apeKI \\\n -c \\\n -q \\\n -i gzfastq \\\n >>radtags.stdout 2>>radtags.stderr\ndone\n') # ### Concatenate `process_radtags` output files into single FASTQ file # #### Create four lists - each of the four output files generated per individual for use in subsequent concatenation command. # In[ ]: # In[ ]: # In[ ]: # In[ ]: # In[25]: get_ipython().run_cell_magic('bash', '', 'list1=( 1HL_10A_1.1.fq.gz 1HL_11A_1.1.fq.gz 1HL_12A_1.1.fq.gz 1HL_13A_1.1.fq.gz 1HL_14A_1.1.fq.gz 1HL_15A_1.1.fq.gz 1HL_16A_1.1.fq.gz 1HL_17A_1.1.fq.gz 1HL_19A_1.1.fq.gz 1HL_1A_1.1.fq.gz 1HL_20A_1.1.fq.gz 1HL_21A_1.1.fq.gz 1HL_22A_1.1.fq.gz 1HL_23A_1.1.fq.gz 1HL_24A_1.1.fq.gz 1HL_25A_1.1.fq.gz 1HL_26A_1.1.fq.gz 1HL_27A_1.1.fq.gz 1HL_28A_1.1.fq.gz 1HL_29A_1.1.fq.gz 1HL_2A_1.1.fq.gz 1HL_31A_1.1.fq.gz 1HL_33A_1.1.fq.gz 1HL_34A_1.1.fq.gz 1HL_35A_1.1.fq.gz 1HL_3A_1.1.fq.gz 1HL_4A_1.1.fq.gz 1HL_5A_1.1.fq.gz 1HL_6A_1.1.fq.gz 1HL_7A_1.1.fq.gz 1HL_8A_1.1.fq.gz 1HL_9A_1.1.fq.gz 1NF_10A_1.1.fq.gz 1NF_11A_1.1.fq.gz 1NF_12A_1.1.fq.gz 1NF_13A_1.1.fq.gz 1NF_14A_1.1.fq.gz 1NF_15A_1.1.fq.gz 1NF_16A_1.1.fq.gz 1NF_17A_1.1.fq.gz 1NF_18A_1.1.fq.gz 1NF_19A_1.1.fq.gz 1NF_1A_1.1.fq.gz 1NF_20A_1.1.fq.gz 1NF_21A_1.1.fq.gz 1NF_22A_1.1.fq.gz 1NF_23A_1.1.fq.gz 1NF_24A_1.1.fq.gz 1NF_25A_1.1.fq.gz 1NF_26A_1.1.fq.gz 1NF_27A_1.1.fq.gz 1NF_28A_1.1.fq.gz 1NF_29A_1.1.fq.gz 1NF_2A_1.1.fq.gz 1NF_30A_1.1.fq.gz 1NF_31A_1.1.fq.gz 1NF_32A_1.1.fq.gz 1NF_33A_1.1.fq.gz 1NF_4A_1.1.fq.gz 1NF_5A_1.1.fq.gz 1NF_6A_1.1.fq.gz 1NF_7A_1.1.fq.gz 1NF_8A_1.1.fq.gz 1NF_9A_1.1.fq.gz 1SN_10A_1.1.fq.gz 1SN_11A_1.1.fq.gz 1SN_12A_1.1.fq.gz 1SN_13A_1.1.fq.gz 1SN_14A_1.1.fq.gz 1SN_15A_1.1.fq.gz 1SN_16A_1.1.fq.gz 1SN_17A_1.1.fq.gz 1SN_18A_1.1.fq.gz 1SN_19A_1.1.fq.gz 1SN_1A_1.1.fq.gz 1SN_20A_1.1.fq.gz 1SN_21A_1.1.fq.gz 1SN_22A_1.1.fq.gz 1SN_23A_1.1.fq.gz 1SN_24A_1.1.fq.gz 1SN_25A_1.1.fq.gz 1SN_26A_1.1.fq.gz 1SN_27A_1.1.fq.gz 1SN_28A_1.1.fq.gz 1SN_29A_1.1.fq.gz 1SN_2A_1.1.fq.gz 1SN_30A_1.1.fq.gz 1SN_31A_1.1.fq.gz 1SN_32A_1.1.fq.gz 1SN_3A_1.1.fq.gz 1SN_4A_1.1.fq.gz 1SN_5A_1.1.fq.gz 1SN_6A_1.1.fq.gz 1SN_7A_1.1.fq.gz 1SN_8A_1.1.fq.gz 1SN_9A_1.1.fq.gz )\nlist2=( 1HL_10A_1.rem.1.fq.gz 1HL_11A_1.rem.1.fq.gz 1HL_12A_1.rem.1.fq.gz 1HL_13A_1.rem.1.fq.gz 1HL_14A_1.rem.1.fq.gz 1HL_15A_1.rem.1.fq.gz 1HL_16A_1.rem.1.fq.gz 1HL_17A_1.rem.1.fq.gz 1HL_19A_1.rem.1.fq.gz 1HL_1A_1.rem.1.fq.gz 1HL_20A_1.rem.1.fq.gz 1HL_21A_1.rem.1.fq.gz 1HL_22A_1.rem.1.fq.gz 1HL_23A_1.rem.1.fq.gz 1HL_24A_1.rem.1.fq.gz 1HL_25A_1.rem.1.fq.gz 1HL_26A_1.rem.1.fq.gz 1HL_27A_1.rem.1.fq.gz 1HL_28A_1.rem.1.fq.gz 1HL_29A_1.rem.1.fq.gz 1HL_2A_1.rem.1.fq.gz 1HL_31A_1.rem.1.fq.gz 1HL_33A_1.rem.1.fq.gz 1HL_34A_1.rem.1.fq.gz 1HL_35A_1.rem.1.fq.gz 1HL_3A_1.rem.1.fq.gz 1HL_4A_1.rem.1.fq.gz 1HL_5A_1.rem.1.fq.gz 1HL_6A_1.rem.1.fq.gz 1HL_7A_1.rem.1.fq.gz 1HL_8A_1.rem.1.fq.gz 1HL_9A_1.rem.1.fq.gz 1NF_10A_1.rem.1.fq.gz 1NF_11A_1.rem.1.fq.gz 1NF_12A_1.rem.1.fq.gz 1NF_13A_1.rem.1.fq.gz 1NF_14A_1.rem.1.fq.gz 1NF_15A_1.rem.1.fq.gz 1NF_16A_1.rem.1.fq.gz 1NF_17A_1.rem.1.fq.gz 1NF_18A_1.rem.1.fq.gz 1NF_19A_1.rem.1.fq.gz 1NF_1A_1.rem.1.fq.gz 1NF_20A_1.rem.1.fq.gz 1NF_21A_1.rem.1.fq.gz 1NF_22A_1.rem.1.fq.gz 1NF_23A_1.rem.1.fq.gz 1NF_24A_1.rem.1.fq.gz 1NF_25A_1.rem.1.fq.gz 1NF_26A_1.rem.1.fq.gz 1NF_27A_1.rem.1.fq.gz 1NF_28A_1.rem.1.fq.gz 1NF_29A_1.rem.1.fq.gz 1NF_2A_1.rem.1.fq.gz 1NF_30A_1.rem.1.fq.gz 1NF_31A_1.rem.1.fq.gz 1NF_32A_1.rem.1.fq.gz 1NF_33A_1.rem.1.fq.gz 1NF_4A_1.rem.1.fq.gz 1NF_5A_1.rem.1.fq.gz 1NF_6A_1.rem.1.fq.gz 1NF_7A_1.rem.1.fq.gz 1NF_8A_1.rem.1.fq.gz 1NF_9A_1.rem.1.fq.gz 1SN_10A_1.rem.1.fq.gz 1SN_11A_1.rem.1.fq.gz 1SN_12A_1.rem.1.fq.gz 1SN_13A_1.rem.1.fq.gz 1SN_14A_1.rem.1.fq.gz 1SN_15A_1.rem.1.fq.gz 1SN_16A_1.rem.1.fq.gz 1SN_17A_1.rem.1.fq.gz 1SN_18A_1.rem.1.fq.gz 1SN_19A_1.rem.1.fq.gz 1SN_1A_1.rem.1.fq.gz 1SN_20A_1.rem.1.fq.gz 1SN_21A_1.rem.1.fq.gz 1SN_22A_1.rem.1.fq.gz 1SN_23A_1.rem.1.fq.gz 1SN_24A_1.rem.1.fq.gz 1SN_25A_1.rem.1.fq.gz 1SN_26A_1.rem.1.fq.gz 1SN_27A_1.rem.1.fq.gz 1SN_28A_1.rem.1.fq.gz 1SN_29A_1.rem.1.fq.gz 1SN_2A_1.rem.1.fq.gz 1SN_30A_1.rem.1.fq.gz 1SN_31A_1.rem.1.fq.gz 1SN_32A_1.rem.1.fq.gz 1SN_3A_1.rem.1.fq.gz 1SN_4A_1.rem.1.fq.gz 1SN_5A_1.rem.1.fq.gz 1SN_6A_1.rem.1.fq.gz 1SN_7A_1.rem.1.fq.gz 1SN_8A_1.rem.1.fq.gz 1SN_9A_1.rem.1.fq.gz )\nlist3=( 1HL_10A_2.2.fq.gz 1HL_11A_2.2.fq.gz 1HL_12A_2.2.fq.gz 1HL_13A_2.2.fq.gz 1HL_14A_2.2.fq.gz 1HL_15A_2.2.fq.gz 1HL_16A_2.2.fq.gz 1HL_17A_2.2.fq.gz 1HL_19A_2.2.fq.gz 1HL_1A_2.2.fq.gz 1HL_20A_2.2.fq.gz 1HL_21A_2.2.fq.gz 1HL_22A_2.2.fq.gz 1HL_23A_2.2.fq.gz 1HL_24A_2.2.fq.gz 1HL_25A_2.2.fq.gz 1HL_26A_2.2.fq.gz 1HL_27A_2.2.fq.gz 1HL_28A_2.2.fq.gz 1HL_29A_2.2.fq.gz 1HL_2A_2.2.fq.gz 1HL_31A_2.2.fq.gz 1HL_33A_2.2.fq.gz 1HL_34A_2.2.fq.gz 1HL_35A_2.2.fq.gz 1HL_3A_2.2.fq.gz 1HL_4A_2.2.fq.gz 1HL_5A_2.2.fq.gz 1HL_6A_2.2.fq.gz 1HL_7A_2.2.fq.gz 1HL_8A_2.2.fq.gz 1HL_9A_2.2.fq.gz 1NF_10A_2.2.fq.gz 1NF_11A_2.2.fq.gz 1NF_12A_2.2.fq.gz 1NF_13A_2.2.fq.gz 1NF_14A_2.2.fq.gz 1NF_15A_2.2.fq.gz 1NF_16A_2.2.fq.gz 1NF_17A_2.2.fq.gz 1NF_18A_2.2.fq.gz 1NF_19A_2.2.fq.gz 1NF_1A_2.2.fq.gz 1NF_20A_2.2.fq.gz 1NF_21A_2.2.fq.gz 1NF_22A_2.2.fq.gz 1NF_23A_2.2.fq.gz 1NF_24A_2.2.fq.gz 1NF_25A_2.2.fq.gz 1NF_26A_2.2.fq.gz 1NF_27A_2.2.fq.gz 1NF_28A_2.2.fq.gz 1NF_29A_2.2.fq.gz 1NF_2A_2.2.fq.gz 1NF_30A_2.2.fq.gz 1NF_31A_2.2.fq.gz 1NF_32A_2.2.fq.gz 1NF_33A_2.2.fq.gz 1NF_4A_2.2.fq.gz 1NF_5A_2.2.fq.gz 1NF_6A_2.2.fq.gz 1NF_7A_2.2.fq.gz 1NF_8A_2.2.fq.gz 1NF_9A_2.2.fq.gz 1SN_10A_2.2.fq.gz 1SN_11A_2.2.fq.gz 1SN_12A_2.2.fq.gz 1SN_13A_2.2.fq.gz 1SN_14A_2.2.fq.gz 1SN_15A_2.2.fq.gz 1SN_16A_2.2.fq.gz 1SN_17A_2.2.fq.gz 1SN_18A_2.2.fq.gz 1SN_19A_2.2.fq.gz 1SN_1A_2.2.fq.gz 1SN_20A_2.2.fq.gz 1SN_21A_2.2.fq.gz 1SN_22A_2.2.fq.gz 1SN_23A_2.2.fq.gz 1SN_24A_2.2.fq.gz 1SN_25A_2.2.fq.gz 1SN_26A_2.2.fq.gz 1SN_27A_2.2.fq.gz 1SN_28A_2.2.fq.gz 1SN_29A_2.2.fq.gz 1SN_2A_2.2.fq.gz 1SN_30A_2.2.fq.gz 1SN_31A_2.2.fq.gz 1SN_32A_2.2.fq.gz 1SN_3A_2.2.fq.gz 1SN_4A_2.2.fq.gz 1SN_5A_2.2.fq.gz 1SN_6A_2.2.fq.gz 1SN_7A_2.2.fq.gz 1SN_8A_2.2.fq.gz 1SN_9A_2.2.fq.gz )\nlist4=( 1HL_10A_2.rem.2.fq.gz 1HL_11A_2.rem.2.fq.gz 1HL_12A_2.rem.2.fq.gz 1HL_13A_2.rem.2.fq.gz 1HL_14A_2.rem.2.fq.gz 1HL_15A_2.rem.2.fq.gz 1HL_16A_2.rem.2.fq.gz 1HL_17A_2.rem.2.fq.gz 1HL_19A_2.rem.2.fq.gz 1HL_1A_2.rem.2.fq.gz 1HL_20A_2.rem.2.fq.gz 1HL_21A_2.rem.2.fq.gz 1HL_22A_2.rem.2.fq.gz 1HL_23A_2.rem.2.fq.gz 1HL_24A_2.rem.2.fq.gz 1HL_25A_2.rem.2.fq.gz 1HL_26A_2.rem.2.fq.gz 1HL_27A_2.rem.2.fq.gz 1HL_28A_2.rem.2.fq.gz 1HL_29A_2.rem.2.fq.gz 1HL_2A_2.rem.2.fq.gz 1HL_31A_2.rem.2.fq.gz 1HL_33A_2.rem.2.fq.gz 1HL_34A_2.rem.2.fq.gz 1HL_35A_2.rem.2.fq.gz 1HL_3A_2.rem.2.fq.gz 1HL_4A_2.rem.2.fq.gz 1HL_5A_2.rem.2.fq.gz 1HL_6A_2.rem.2.fq.gz 1HL_7A_2.rem.2.fq.gz 1HL_8A_2.rem.2.fq.gz 1HL_9A_2.rem.2.fq.gz 1NF_10A_2.rem.2.fq.gz 1NF_11A_2.rem.2.fq.gz 1NF_12A_2.rem.2.fq.gz 1NF_13A_2.rem.2.fq.gz 1NF_14A_2.rem.2.fq.gz 1NF_15A_2.rem.2.fq.gz 1NF_16A_2.rem.2.fq.gz 1NF_17A_2.rem.2.fq.gz 1NF_18A_2.rem.2.fq.gz 1NF_19A_2.rem.2.fq.gz 1NF_1A_2.rem.2.fq.gz 1NF_20A_2.rem.2.fq.gz 1NF_21A_2.rem.2.fq.gz 1NF_22A_2.rem.2.fq.gz 1NF_23A_2.rem.2.fq.gz 1NF_24A_2.rem.2.fq.gz 1NF_25A_2.rem.2.fq.gz 1NF_26A_2.rem.2.fq.gz 1NF_27A_2.rem.2.fq.gz 1NF_28A_2.rem.2.fq.gz 1NF_29A_2.rem.2.fq.gz 1NF_2A_2.rem.2.fq.gz 1NF_30A_2.rem.2.fq.gz 1NF_31A_2.rem.2.fq.gz 1NF_32A_2.rem.2.fq.gz 1NF_33A_2.rem.2.fq.gz 1NF_4A_2.rem.2.fq.gz 1NF_5A_2.rem.2.fq.gz 1NF_6A_2.rem.2.fq.gz 1NF_7A_2.rem.2.fq.gz 1NF_8A_2.rem.2.fq.gz 1NF_9A_2.rem.2.fq.gz 1SN_10A_2.rem.2.fq.gz 1SN_11A_2.rem.2.fq.gz 1SN_12A_2.rem.2.fq.gz 1SN_13A_2.rem.2.fq.gz 1SN_14A_2.rem.2.fq.gz 1SN_15A_2.rem.2.fq.gz 1SN_16A_2.rem.2.fq.gz 1SN_17A_2.rem.2.fq.gz 1SN_18A_2.rem.2.fq.gz 1SN_19A_2.rem.2.fq.gz 1SN_1A_2.rem.2.fq.gz 1SN_20A_2.rem.2.fq.gz 1SN_21A_2.rem.2.fq.gz 1SN_22A_2.rem.2.fq.gz 1SN_23A_2.rem.2.fq.gz 1SN_24A_2.rem.2.fq.gz 1SN_25A_2.rem.2.fq.gz 1SN_26A_2.rem.2.fq.gz 1SN_27A_2.rem.2.fq.gz 1SN_28A_2.rem.2.fq.gz 1SN_29A_2.rem.2.fq.gz 1SN_2A_2.rem.2.fq.gz 1SN_30A_2.rem.2.fq.gz 1SN_31A_2.rem.2.fq.gz 1SN_32A_2.rem.2.fq.gz 1SN_3A_2.rem.2.fq.gz 1SN_4A_2.rem.2.fq.gz 1SN_5A_2.rem.2.fq.gz 1SN_6A_2.rem.2.fq.gz 1SN_7A_2.rem.2.fq.gz 1SN_8A_2.rem.2.fq.gz 1SN_9A_2.rem.2.fq.gz )\n\ntime for index in "${!list1[@]}"; do\n i=${list1[$index]}\n j=${list2[$index]}\n k=${list3[$index]}\n l=${list4[$index]}\n cat $i $j $k $l > ${i/_1.1/}\n \ndone\n') # In[26]: get_ipython().run_cell_magic('bash', '', 'echo *A.fq.gz\n') # In[ ]: get_ipython().run_cell_magic('bash', '', '#Runs ustacks and appends sql ID to each file for downstream analysis.\nsql_id=0\ntime for i in *A.fq.gz; do\n ((sql_id++))\n /usr/local/bioinformatics/stacks-1.37/ustacks \\\n -t gzfastq \\\n -f $i \\\n -o /Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks/stacks/ \\\n -i $sql_id \\\n -d \\\n -r \\\n -p 16\ndone\n') # #### The command above continually failed with a segmentation fault 11 error. Additionally, the external HDD this operation was reading/writing to became unresponsive on 5/4/2016. Will proceed with whatever data has been completed for this analysis. # ### List file names and format for subsequent use in cstacks command # In[1]: cd /Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks/stacks/ # In[2]: get_ipython().run_cell_magic('bash', '', '#Uses printf statement to print just the first part of each filename, without the extension, and ads a "-s" and a " \\"\n#to each line for use in the subsequent cstacks command.\nfor fname in *; do printf " %s\\n" "-s ${fname%%.*} \\\\" >> tmp.txt; done\ncat tmp.txt | uniq\nrm tmp.txt\n') # In[3]: get_ipython().run_cell_magic('bash', '', '#cstacks command.\ntime /usr/local/bioinformatics/stacks-1.37/cstacks -b 1 -o . \\\n-p 16 \\\n -s 1HL_10A \\\n -s 1HL_11A \\\n -s 1HL_12A \\\n -s 1HL_13A \\\n -s 1HL_14A \\\n -s 1HL_15A \\\n -s 1HL_16A \\\n -s 1HL_17A \\\n -s 1HL_19A \\\n -s 1HL_1A \\\n -s 1HL_20A \\\n -s 1HL_21A \\\n -s 1HL_22A \\\n -s 1HL_23A \\\n -s 1HL_24A \\\n -s 1HL_25A \\\n -s 1HL_26A \\\n -s 1HL_27A \\\n -s 1HL_28A \\\n -s 1HL_29A \\\n -s 1HL_2A \\\n -s 1HL_31A \\\n -s 1HL_33A \\\n -s 1HL_34A \\\n -s 1HL_35A \\\n -s 1HL_3A \\\n -s 1HL_4A \\\n -s 1HL_5A \\\n -s 1HL_6A \\\n -s 1HL_7A \\\n -s 1HL_8A \\\n -s 1HL_9A \\\n -s 1NF_10A \\\n -s 1NF_11A \\\n -s 1NF_12A \\\n -s 1NF_13A \\\n -s 1NF_14A \\\n -s 1NF_15A \\\n -s 1NF_16A \\\n -s 1NF_17A \\\n -s 1NF_18A \\\n -s 1NF_19A \\\n -s 1NF_1A \\\n -s 1NF_20A \\\n -s 1NF_21A \\\n -s 1NF_22A \\\n -s 1NF_23A \\\n -s 1NF_24A \\\n -s 1NF_25A \\\n -s 1NF_26A \\\n -s 1NF_27A \\\n -s 1NF_28A \\\n -s 1NF_29A \\\n -s 1NF_2A \\\n -s 1NF_30A \\\n -s 1NF_31A \\\n -s 1NF_32A \\\n -s 1NF_33A \\\n -s 1NF_4A \\\n -s 1NF_5A \\\n -s 1NF_6A \\\n -s 1NF_7A \\\n -s 1NF_8A \\\n -s 1NF_9A \\\n -s 1SN_10A \\\n -s 1SN_11A \\\n -s 1SN_12A \\\n -s 1SN_13A \\\n -s 1SN_14A \\\n -s 1SN_15A \\\n -s 1SN_16A \\\n -s 1SN_17A \\\n -s 1SN_18A \\\n -s 1SN_19A \\\n -s 1SN_1A \\\n -s 1SN_20A \\\n -s 1SN_21A \\\n -s 1SN_22A \\\n -s 1SN_23A \\\n -s 1SN_24A \\\n -s 1SN_25A \\\n -s 1SN_26A \\\n -s 1SN_27A \\\n -s 1SN_28A \\\n -s 1SN_29A \\\n -s 1SN_2A \\\n -s 1SN_30A \\\n -s 1SN_31A \\\n -s 1SN_32A \\\n -s 1SN_3A\n') # In[ ]: