(base) Jeremies-MacBook-Pro:rawReads jeremieauger$ cat Mock10-Mix1-reads.fastq | grep "@" | cut -f1 | sort | uniq @HA-119-25 amplicon=367..831 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus plantarum." @R0011-1 amplicon=335..799 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus rhamnosus." @R0026-31 amplicon=352..816 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Enterococcaceae; G_Enterococcus; S_Enterococcus faecium." @R0070-58 amplicon=328..777 position=1..450 description="K_Bacteria; P_Actinobacteria; C_Actinobacteria; O_Bifidobacteriales; F_Bifidobacteriaceae; G_Bifidobacterium; S_Bifidobacterium breve." @R0071-41 amplicon=333..779 position=1..447 description="K_Bacteria; P_Actinobacteria; C_Actinobacteria; O_Bifidobacteriales; F_Bifidobacteriaceae; G_Bifidobacterium; S_Bifidobacterium bifidum." @R0083-1 amplicon=340..804 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Streptococcaceae; G_Streptococcus; S_Streptococcus thermophilus." @R0175-3 amplicon=327..771 position=1..445 description="K_Bacteria; P_Actinobacteria; C_Actinobacteria; O_Bifidobacteriales; F_Bifidobacteriaceae; G_Bifidobacterium; S_Bifidobacterium longum subsp. longum" @R0179-27 amplicon=349..814 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Bacillales; F_Bacillaceae; G_Bacillus; S_Bacillus subtilis." @R0215-1 amplicon=368..832 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus casei." @R1001-10 amplicon=368..832 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Pediococcus; S_Pediococcus acidilactici." # From grinder's fastq (base) Jeremies-MacBook-Pro:rawReads jeremieauger$ cat Mock10-Mix1-reads.fastq | grep "@" | cut -f1 | sort | uniq K_Bacteria; P_Actinobacteria; C_Actinobacteria; O_Bifidobacteriales; F_Bifidobacteriaceae; G_Bifidobacterium; S_Bifidobacterium bifidum." K_Bacteria; P_Actinobacteria; C_Actinobacteria; O_Bifidobacteriales; F_Bifidobacteriaceae; G_Bifidobacterium; S_Bifidobacterium breve." K_Bacteria; P_Actinobacteria; C_Actinobacteria; O_Bifidobacteriales; F_Bifidobacteriaceae; G_Bifidobacterium; S_Bifidobacterium longum subsp. longum" K_Bacteria; P_Firmicutes; C_Bacilli; O_Bacillales; F_Bacillaceae; G_Bacillus; S_Bacillus subtilis." K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Enterococcaceae; G_Enterococcus; S_Enterococcus faecium." K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus casei." K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus plantarum." K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus rhamnosus." K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Pediococcus; S_Pediococcus acidilactici." K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Streptococcaceae; G_Streptococcus; S_Streptococcus thermophilus." # From the tax-plot.qzv index Mock10-Mix1 Mock10-Mix2 Mock10-Mix3 Mock10-Mix4 k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__breve 49875 24376 92900 51726 k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus;s__ 49922 24682 92443 25983 k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;__ 50088 49451 61498 129948 k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;__ 49924 74413 30810 25652 k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__zeae 59630 88078 36561 77514 k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus;s__acidilactici 49830 74423 92618 129470 k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__ 50135 24884 31111 2649 # Even confirming the counts -- in the fastq (base) Jeremies-MacBook-Pro:rawReads jeremieauger$ cat Mock10-Mix1-reads.fastq | grep "@" | cut -f1 | sort | uniq -c 50005 K_Bacteria; P_Actinobacteria; C_Actinobacteria; O_Bifidobacteriales; F_Bifidobacteriaceae; G_Bifidobacterium; S_Bifidobacterium bifidum." @R0071-41 49875 K_Bacteria; P_Actinobacteria; C_Actinobacteria; O_Bifidobacteriales; F_Bifidobacteriaceae; G_Bifidobacterium; S_Bifidobacterium breve." @R0070-58 49435 K_Bacteria; P_Actinobacteria; C_Actinobacteria; O_Bifidobacteriales; F_Bifidobacteriaceae; G_Bifidobacterium; S_Bifidobacterium longum subsp. longum" @R0175-3 49922 K_Bacteria; P_Firmicutes; C_Bacilli; O_Bacillales; F_Bacillaceae; G_Bacillus; S_Bacillus subtilis." @R0179-27 50088 K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Enterococcaceae; G_Enterococcus; S_Enterococcus faecium." @R0026-31 50311 K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus casei." @R0215-1 49924 K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus plantarum." @HA-119-25 50475 K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus rhamnosus." @R0011-1 49830 K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Pediococcus; S_Pediococcus acidilactici." @R1001-10 50135 K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Streptococcaceae; G_Streptococcus; S_Streptococcus thermophilus." @R0083-1 # Had already lost 2 at the Rep-seq (table from Deblur) -- total 8 ASVs 5e3543852dd1a53f27cfc8970ee88588 450 CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGAGGGATGGAGGCCTTCGGGTTGTAAACCTCTTTTGTTAGGGAGCAAGGCACTTTGTGTTGAGTGTACCTTTCGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTC 7ebe1f70f865404ddbb73e67b089eb10 450 CCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGCAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAGCTCTGTTGTTAAAGAAGAACGTGGGTGAGAGTAACTGTTCACCCAGTGACGGTATTTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTCTTTTAAGTCTAATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTA 081d5114bfb4d638e542507d092de667 450 CCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATT 08fb8c11b48072aea183f944ffa76caf 450 CCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAACTCTGTTGTTAGAGAAGAACAAGGATGAGAGTAACTGTTCATCCCTTGACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTA 5c0840c0a2b80126d9df751d5c682b90 450 CCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGGGGGCAACCCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTAAGTCAAGAACGGGTGTGAGAGTGGAAAGTTCACACTGTGACGGTAGCTTACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTGATAAGTCTGAAGTTAAAGGCTGTGGCTCAACCATAGTTCGCTTTGGAAACTGTCAAACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGGATTA 5b6c26aa614309ab7481a418b3300a7a 450 CCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAACTCTGTTGTTAAAGAAGAACATATCTGAGAGTAACTGTTCAGGTATTGACGGTATTTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGTATGGGTAGCAAACAGGATTA b6c042f25d0246963390d96d12b4a7f5 450 CCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGCAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGCTTTCGGGTCGTAAAACTCTGTTGTTGGAGAAGAATGGTCGGCAGAGTAACTGTTGTCGGCGTGACGGTATCCAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCTCGGCTTAACCGAGGAAGCGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTA c388d8a25b87f59558bf9ff408a1de3e 450 CCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGCAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGCTTTCGGGTCGTAAAACTCTGTTGTTGGAGAAGAATGGTCGGCAGAGTAACTGTTGTCGGCGTGACGGTATCCAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCTCGGCTTAACCGAGGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTA # Sample of my generated Fastq -[augerjer@beluga2 dada-qiime]$ zcat /home/augerjer/scratch/mock10/rawReads/Mock10-Mix2-reads.fastq.gz | head @1 reference=HA-119-25 amplicon=367..831 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus plantarum." CCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAACTCTGTTGTTAAAGAAGAACATATCTGAGAGTAACTGTTCAGGTATTGACGGTATTTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGTATGGGTAGCAAACAGGATTAGATACCCTGG + ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? @2 reference=R0215-1 amplicon=368..832 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus casei." CCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGCAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGCTTTCGGGTCGTAAAACTCTGTTGTTGGAGAAGAATGGTCGGCAGAGTAACTGTTGTCGGCGTGACGGTATCCAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCTCGGCTTAACCGAGGAAGCGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGGATTAGATACCCTGG + ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? @3 reference=HA-119-25 amplicon=367..831 position=1..460 description="K_Bacteria; P_Firmicutes; C_Bacilli; O_Lactobacillales; F_Lactobacillaceae; G_Lactobacillus; S_Lactobacillus plantarum." CCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGACGAAAGTCTGATGGAGCAACGCCGCGTGAGTGAAGAAGGGTTTCGGCTCGTAAAACTCTGTTGTTAAAGAAGAACATATCTGAGAGTAACTGTTCAGGTATTGACGGTATTTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCTTCGGCTCAACCGAAGAAGTGCATCGGAAACTGGGAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGTATGGGTAGCAAACAGGATTAGATACCCTGG