Re-splitting libraries for Illumina GOM data

Trying to see if I can get better outputs for the _2 PE read files. Libraries were originally split using QIIME 1.4 on my iMac, but now I am re-processing them on a HiMem Cloud instance (QIIME 1.5, 68 GB memory, oh yeah). Now using minimum PHRED scores of 20 (-q 20) and specifically specifying max 1.5 errors in the barcode sequence. Commands run are as follows:

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-1_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-1_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_1_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-1_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-1_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_1_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-2_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-2_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_2_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-2_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-2_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_2_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-3_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-3_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_3_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-3_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-3_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_3_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-4_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-4_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_4_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-4_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-4_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_4_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-5_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-5_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_5_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-5_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-5_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_5_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-6_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-6_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_6_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-6_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-6_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_6_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-7_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-7_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_7_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-7_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-7_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_7_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-8_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-8_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_8_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-8_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-8_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_8_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-9_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-9_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_9_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-9_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-9_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_9_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-10_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-10_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_10_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-10_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-10_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_10_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-11_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-11_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_11_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-11_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-11_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_11_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-12_1_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-12_1_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_12_1/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

split_libraries_fastq.py -i /home/ubuntu/fastx_trimmed_files/1926-KO-12_2_trimmed.txt -b /home/ubuntu/fastx_trimmed_files/1926-KO-12_2_barcode.txt -o /home/ubuntu/GOM_demultiplexed/KO_12_2/ -m /home/ubuntu/QIIME_mapping_files/1926_KO_1.txt –barcode_type=5 –max_barcode_errors=1.5 -q 20

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