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Copy path2. Unzipping bz2 to fastq
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2. Unzipping bz2 to fastq
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#!/bin/bash
#SBATCH --job-name=bunzip
#SBATCH --partition=highmem_p
#SBATCH --ntasks=1
#SBATCH --mem=200gb
#SBATCH --time=20:00:00
#SBATCH --output=bunzip.%j.out
#SBATCH --error=bunzip.%j.err
cd $SLURM_SUBMIT_DIR
ml bzip2/1.0.6-GCCcore-6.4.0
#bunzip2 -d IXBR_RNAseq_3_Control_1_24hr_TACCGAGG_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXBR_RNAseq_3_Control_1_24hr_TACCGAGG_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXBS_RNAseq_4_Control_1_48hr_CGTTAGAA_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXBS_RNAseq_4_Control_1_48hr_CGTTAGAA_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXBT_RNAseq_6_Control_1_96hr_AGCCTCAT_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXBT_RNAseq_6_Control_1_96hr_AGCCTCAT_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXBU_RNAseq_10_Control_2_24hr_GATTCTGC_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXBU_RNAseq_10_Control_2_24hr_GATTCTGC_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXBW_RNAseq_11_Control_2_48hr_TCGTAGTG_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXBW_RNAseq_11_Control_2_48hr_TCGTAGTG_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXBX_RNAseq_13_Control_2_96hr_CTACGACA_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXBX_RNAseq_13_Control_2_96hr_CTACGACA_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXBY_RNAseq_17_Control_3_24hr_TAAGTGGT_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXBY_RNAseq_17_Control_3_24hr_TAAGTGGT_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXBZ_RNAseq_18_Control_3_48hr_CGGACAAC_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXBZ_RNAseq_18_Control_3_48hr_CGGACAAC_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCA_RNAseq_20_Control_3_96hr_ATATGGAT_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCA_RNAseq_20_Control_3_96hr_ATATGGAT_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCB_RNAseq_24_Pa-OK-11_1_24hr_GCGCAAGC_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCB_RNAseq_24_Pa-OK-11_1_24hr_GCGCAAGC_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCC_RNAseq_25_Pa-OK-11_1_48hr_AAGATACT_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCC_RNAseq_25_Pa-OK-11_1_48hr_AAGATACT_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCD_RNAseq_27_Pa-OK-11_1_96hr_GGAGCGTC_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCD_RNAseq_27_Pa-OK-11_1_96hr_GGAGCGTC_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXCE_RNAseq_31_Pa-OK-11_2_24hr_ATGGCATG_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXCE_RNAseq_31_Pa-OK-11_2_24hr_ATGGCATG_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXCF_RNAseq_32_Pa-OK-11_2_48hr_GCAATGCA_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXCF_RNAseq_32_Pa-OK-11_2_48hr_GCAATGCA_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCG_RNAseq_34_Pa-OK-11_2_96hr_GTTCCAAT_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCG_RNAseq_34_Pa-OK-11_2_96hr_GTTCCAAT_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCH_RNAseq_38_Pa-OK-11_3_24hr_ACCTTGGC_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCH_RNAseq_38_Pa-OK-11_3_24hr_ACCTTGGC_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXCI_RNAseq_39_Pa-OK-11_3_48hr_ATATCTCG_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXCI_RNAseq_39_Pa-OK-11_3_48hr_ATATCTCG_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCJ_RNAseq_41_Pa-OK-11_3_96hr_GCGCTCTA_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCJ_RNAseq_41_Pa-OK-11_3_96hr_GCGCTCTA_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXCK_RNAseq_45_De-Tif-11_1_24hr_AACAGGTT_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXCK_RNAseq_45_De-Tif-11_1_24hr_AACAGGTT_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXCL_RNAseq_46_De-Tif-11_1_48hr_GGTGAACC_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXCL_RNAseq_46_De-Tif-11_1_48hr_GGTGAACC_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCM_RNAseq_48_De-Tif-11_1_96hr_CAACAATG_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCM_RNAseq_48_De-Tif-11_1_96hr_CAACAATG_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCN_RNAseq_52_De-Tif-11_2_24hr_TGGTGGCA_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCN_RNAseq_52_De-Tif-11_2_24hr_TGGTGGCA_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXCP_RNAseq_53_De-Tif-11_2_48hr_AGGCAGAG_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXCP_RNAseq_53_De-Tif-11_2_48hr_AGGCAGAG_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXCQ_RNAseq_55_De-Tif-11_2_96hr_GAATGAGA_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXCQ_RNAseq_55_De-Tif-11_2_96hr_GAATGAGA_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCR_RNAseq_59_De-Tif-11_3_24hr_TGCGGCGT_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCR_RNAseq_59_De-Tif-11_3_24hr_TGCGGCGT_Carya_illinoinensis_I972_L2_R2.fastq.bz2
#bunzip2 -d IXCS_RNAseq_60_De-Tif-11_3_48hr_CATAATAC_Carya_illinoinensis_I972_L2_R1.fastq.bz2
#bunzip2 -d IXCS_RNAseq_60_De-Tif-11_3_48hr_CATAATAC_Carya_illinoinensis_I972_L2_R2.fastq.bz2
bunzip2 -d IXCT_RNAseq_62_De-Tif-11_3_96hr_GATCTATC_Carya_illinoinensis_I972_L2_R1.fastq.bz2
bunzip2 -d IXCT_RNAseq_62_De-Tif-11_3_96hr_GATCTATC_Carya_illinoinensis_I972_L2_R2.fastq.bz2