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-fastq_mergepairs A072-SU4-AGGTCTCC-Blomster-run20150513B_S72_L001_R1_001.fastq -fastqout mergedSU4.fq -relabel @ -log mergeSU4.log usearch -fastq_mergepairs A073-SU73-GGTGTCTT-Blomster-run20150513B_S73_L001_R1_001.fastq -fastqout mergedSU73.fq -relabel @ -log mergeSU73.log usearch -fastq_mergepairs A074-SU74-TGTACGAC-Blomster-run20150513B_S74_L001_R1_001.fastq -fastqout mergedSU74.fq -relabel @ -log mergeSU74.log usearch -fastq_mergepairs A075-SU81-CTGTAAGT-Blomster-run20150513B_S75_L001_R1_001.fastq -fastqout mergedSU81.fq -relabel @ -log mergeSU81.log usearch -fastq_mergepairs A076-SU9-TCAGGTAC-Blomster-run20150513B_S76_L001_R1_001.fastq -fastqout mergedSU9.fq -relabel @ -log mergeSU9.log usearch -fastq_mergepairs A077-SU28-ATCCGACG-Blomster-run20150513B_S77_L001_R1_001.fastq -fastqout mergedSU28.fq -relabel @ -log mergeSU28.log usearch -fastq_mergepairs A078-SU52-GCAAGAAG-Blomster-run20150513B_S78_L001_R1_001.fastq -fastqout mergedSU52.fq -relabel @ -log mergeSU52.log usearch -fastq_mergepairs A079-SU5-ACGTAGCC-Blomster-run20150513B_S79_L001_R1_001.fastq -fastqout mergedSU5.fq -relabel @ -log mergeSU5.log usearch -fastq_mergepairs A080-SU78-GGTCCATT-Blomster-run20150513B_S80_L001_R1_001.fastq -fastqout mergedSU78.fq -relabel @ -log mergeSU78.log usearch -fastq_mergepairs A081-SU18-CCAGTCAC-Blomster-run20150513B_S81_L001_R1_001.fastq -fastqout mergedSU18.fq -relabel @ -log mergeSU18.log usearch -fastq_mergepairs A082-SU7-GGCTTCAA-Blomster-run20150513B_S82_L001_R1_001.fastq -fastqout mergedSU7.fq -relabel @ -log mergeSU7.log usearch -fastq_mergepairs A083-SU62-AGACGAAC-Blomster-run20150513B_S83_L001_R1_001.fastq -fastqout mergedSU62.fq -relabel @ -log mergeSU62.log usearch -fastq_mergepairs A084-SU12-TCCGATGG-Blomster-run20150513B_S84_L001_R1_001.fastq -fastqout mergedSU12.fq -relabel @ -log mergeSU12.log usearch -fastq_mergepairs A085-SU17-GAATTCTC-Blomster-run20150513B_S85_L001_R1_001.fastq -fastqout mergedSU17.fq -relabel @ -log mergeSU17.log usearch -fastq_mergepairs A086-SU65-CTATCAAC-Blomster-run20150513B_S86_L001_R1_001.fastq -fastqout mergedSU65.fq -relabel @ -log mergeSU65.log usearch -fastq_mergepairs A087-SU34-TCCACACC-Blomster-run20150513B_S87_L001_R1_001.fastq -fastqout mergedSU34.fq -relabel @ -log mergeSU34.log usearch -fastq_mergepairs A088-SU46-GTTGCTCA-Blomster-run20150513B_S88_L001_R1_001.fastq -fastqout mergedSU46.fq -relabel @ -log mergeSU46.log usearch -fastq_mergepairs A089-SU79-CACGCACA-Blomster-run20150513B_S89_L001_R1_001.fastq -fastqout mergedSU79.fq -relabel @ -log mergeSU79.log usearch -fastq_mergepairs A090-SU80-CGCCACTT-Blomster-run20150513B_S90_L001_R1_001.fastq -fastqout mergedSU80.fq -relabel @ -log mergeSU80.log usearch -fastq_mergepairs A091-SU42-GAACACCG-Blomster-run20150513B_S91_L001_R1_001.fastq -fastqout mergedSU42.fq -relabel @ -log mergeSU42.log usearch -fastq_mergepairs A092-SU26-GTACATCC-Blomster-run20150513B_S92_L001_R1_001.fastq -fastqout mergedSU26.fq -relabel @ -log mergeSU26.log usearch -fastq_mergepairs A093-SU16-CTGGACAA-Blomster-run20150513B_S93_L001_R1_001.fastq -fastqout mergedSU16.fq -relabel @ -log mergeSU16.log usearch -fastq_mergepairs A094-SU75-GAATCAGC-Blomster-run20150513B_S94_L001_R1_001.fastq -fastqout mergedSU75.fq -relabel @ -log mergeSU75.log usearch -fastq_mergepairs A095-SU38-CCTTAGTC-Blomster-run20150513B_S95_L001_R1_001.fastq -fastqout mergedSU38.fq -relabel @ -log mergeSU38.log usearch -fastq_mergepairs A096-SU8-AGTTCCGC-Blomster-run20150513B_S96_L001_R1_001.fastq -fastqout mergedSU8.fq -relabel @ -log mergeSU8.log usearch -fastq_mergepairs A097-SU13-CTTGGTTG-Blomster-run20150513B_S97_L001_R1_001.fastq -fastqout mergedSU13.fq -relabel @ -log mergeSU13.log usearch -fastq_mergepairs A098-SU77-CCGCCTAA-Blomster-run20150513B_S98_L001_R1_001.fastq -fastqout mergedSU77.fq -relabel @ -log mergeSU77.log usearch -fastq_mergepairs A099-SU31-CTCACTTA-Blomster-run20150513B_S99_L001_R1_001.fastq -fastqout mergedSU31.fq -relabel @ -log mergeSU31.log usearch -fastq_mergepairs A100-SU39-TCGCCAGA-Blomster-run20150513B_S100_L001_R1_001.fastq -fastqout mergedSU39.fq -relabel @ -log mergeSU39.log usearch -fastq_mergepairs A101-SU55-ATGCCGCA-Blomster-run20150513B_S101_L001_R1_001.fastq -fastqout mergedSU55.fq -relabel @ -log mergeSU55.log usearch -fastq_mergepairs A102-SU25-GTAAGCCT-Blomster-run20150513B_S102_L001_R1_001.fastq -fastqout mergedSU25.fq -relabel @ -log mergeSU25.log usearch -fastq_mergepairs A103-SU11-CTGTTGGC-Blomster-run20150513B_S103_L001_R1_001.fastq -fastqout mergedSU11.fq -relabel @ -log mergeSU11.log usearch -fastq_mergepairs A104-SU49-GACTCGCA-Blomster-run20150513B_S104_L001_R1_001.fastq -fastqout mergedSU49.fq -relabel @ -log mergeSU49.log usearch -fastq_mergepairs A105-SU41-GCACTAGA-Blomster-run20150513B_S105_L001_R1_001.fastq -fastqout mergedSU41.fq -relabel @ -log mergeSU41.log usearch -fastq_mergepairs A106-SU15-TAACGGCT-Blomster-run20150513B_S106_L001_R1_001.fastq -fastqout mergedSU15.fq -relabel @ -log mergeSU15.log usearch -fastq_mergepairs A107-SU24-GTTAGGAA-Blomster-run20150513B_S107_L001_R1_001.fastq -fastqout mergedSU24.fq -relabel @ -log mergeSU24.log usearch -fastq_mergepairs A108-SU23-TCAACCGC-Blomster-run20150513B_S108_L001_R1_001.fastq -fastqout mergedSU23.fq -relabel @ -log mergeSU23.log usearch -fastq_mergepairs A109-SU10-ACCGAGTT-Blomster-run20150513B_S109_L001_R1_001.fastq -fastqout mergedSU10.fq -relabel @ -log mergeSU10.log usearch -fastq_mergepairs A110-SU14-CTACAAGA-Blomster-run20150513B_S110_L001_R1_001.fastq -fastqout mergedSU14.fq -relabel @ -log mergeSU14.log usearch -fastq_mergepairs A111-SU67-AGTCAGTT-Blomster-run20150513B_S111_L001_R1_001.fastq -fastqout mergedSU67.fq -relabel @ -log mergeSU67.log usearch -fastq_mergepairs A112-SU35-AGCCATGC-Blomster-run20150513B_S112_L001_R1_001.fastq -fastqout mergedSU35.fq -relabel @ -log mergeSU35.log usearch -fastq_mergepairs A113-SU66-TACATCTG-Blomster-run20150513B_S113_L001_R1_001.fastq -fastqout mergedSU66.fq -relabel @ -log mergeSU66.log usearch -fastq_mergepairs A114-SU47-GGTAGAAT-Blomster-run20150513B_S114_L001_R1_001.fastq -fastqout mergedSU47.fq -relabel @ -log mergeSU47.log usearch -fastq_mergepairs A115-SU50-CTTCGCTA-Blomster-run20150513B_S115_L001_R1_001.fastq -fastqout mergedSU50.fq -relabel @ -log mergeSU50.log usearch -fastq_mergepairs A116-SU63-TCCACCTT-Blomster-run20150513B_S116_L001_R1_001.fastq -fastqout mergedSU63.fq -relabel @ -log mergeSU63.log usearch -fastq_mergepairs A117-SU72-GAGGATAT-Blomster-run20150513B_S117_L001_R1_001.fastq -fastqout mergedSU72.fq -relabel @ -log mergeSU72.log usearch -fastq_mergepairs A118-SU33-GAGATTGT-Blomster-run20150513B_S118_L001_R1_001.fastq -fastqout mergedSU33.fq -relabel @ -log mergeSU33.log usearch -fastq_mergepairs A119-SU30-ACAGACAT-Blomster-run20150513B_S119_L001_R1_001.fastq -fastqout mergedSU30.fq -relabel @ -log mergeSU30.log usearch -fastq_mergepairs A120-SU48-TTCTCTCA-Blomster-run20150513B_S120_L001_R1_001.fastq -fastqout mergedSU48.fq -relabel @ -log mergeSU48.log usearch -fastq_mergepairs A121-SU76-TTGAGTCT-Blomster-run20150513B_S121_L001_R1_001.fastq -fastqout mergedSU76.fq -relabel @ -log mergeSU76.log usearch -fastq_mergepairs A122-SU64-TACGACCG-Blomster-run20150513B_S122_L001_R1_001.fastq -fastqout mergedSU64.fq -relabel @ -log mergeSU64.log usearch -fastq_mergepairs A123-SU21-TGCTCCGA-Blomster-run20150513B_S123_L001_R1_001.fastq -fastqout mergedSU21.fq -relabel @ -log mergeSU21.log usearch -fastq_mergepairs A124-SU60-CTTAGACA-Blomster-run20150513B_S124_L001_R1_001.fastq -fastqout mergedSU60.fq -relabel @ -log mergeSU60.log usearch -fastq_mergepairs A125-SU70-GGTATATG-Blomster-run20150513B_S125_L001_R1_001.fastq -fastqout mergedSU70.fq -relabel @ -log mergeSU70.log usearch -fastq_mergepairs A126-SU40-TTCGTTGT-Blomster-run20150513B_S126_L001_R1_001.fastq -fastqout mergedSU40.fq -relabel @ -log mergeSU40.log usearch -fastq_mergepairs A127-SU32-TTACTGGC-Blomster-run20150513B_S127_L001_R1_001.fastq -fastqout mergedSU32.fq -relabel @ -log mergeSU32.log usearch -fastq_mergepairs A128-SU61-TTGGTCAC-Blomster-run20150513B_S128_L001_R1_001.fastq -fastqout mergedSU61.fq -relabel @ -log mergeSU61.log usearch -fastq_mergepairs A129-SU22-TGATTGCC-Blomster-run20150513B_S129_L001_R1_001.fastq -fastqout mergedSU22.fq -relabel @ -log mergeSU22.log usearch -fastq_mergepairs A130-SU51-CTTATGCT-Blomster-run20150513B_S130_L001_R1_001.fastq -fastqout mergedSU51.fq -relabel @ -log mergeSU51.log usearch -fastq_mergepairs A131-SU54-CAGAGTGC-Blomster-run20150513B_S131_L001_R1_001.fastq -fastqout mergedSU54.fq -relabel @ -log mergeSU54.log usearch -fastq_mergepairs A133-SU57-CCAGCAAA-Blomster-run20150513B_S132_L001_R1_001.fastq -fastqout mergedSU57.fq -relabel @ -log mergeSU57.log usearch -fastq_mergepairs A134-SU19-AACTGAGC-Blomster-run20150513B_S133_L001_R1_001.fastq -fastqout mergedSU19.fq -relabel @ -log mergeSU19.log usearch -fastq_mergepairs A136-SU58-GCAGTGTG-Blomster-run20150513B_S134_L001_R1_001.fastq -fastqout mergedSU58.fq -relabel @ -log mergeSU58.log usearch -fastq_mergepairs A137-SU37-GGATTTAC-Blomster-run20150513B_S135_L001_R1_001.fastq -fastqout mergedSU37.fq -relabel @ -log mergeSU37.log usearch -fastq_mergepairs A139-SU36-AGACTTAG-Blomster-run20150513B_S136_L001_R1_001.fastq -fastqout mergedSU36.fq -relabel @ -log mergeSU36.log usearch -fastq_mergepairs A142-SU27-TCTAGAAC-Blomster-run20150513B_S137_L001_R1_001.fastq -fastqout mergedSU27.fq -relabel @ -log mergeSU27.log usearch -fastq_mergepairs A143-SU69-TAACCAAG-Blomster-run20150513B_S138_L001_R1_001.fastq -fastqout mergedSU69.fq -relabel @ -log mergeSU69.log usearch -fastq_mergepairs A145-SU29-TCCATTCA-Blomster-run20150513B_S139_L001_R1_001.fastq -fastqout mergedSU29.fq -relabel @ -log mergeSU29.log usearch -fastq_mergepairs A146-SU20-ATACGGAT-Blomster-run20150513B_S140_L001_R1_001.fastq -fastqout mergedSU20.fq -relabel @ -log mergeSU20.log usearch -fastq_mergepairs A147-SU56-ATATGGGA-Blomster-run20150513B_S141_L001_R1_001.fastq -fastqout mergedSU56.fq -relabel @ -log mergeSU56.log usearch -fastq_mergepairs A151-SU43-CCGTGAGA-Blomster-run20150513B_S142_L001_R1_001.fastq -fastqout mergedSU43.fq -relabel @ -log mergeSU43.log usearch -fastq_mergepairs A158-SU71-GACACTAA-Blomster-run20150513B_S143_L001_R1_001.fastq -fastqout mergedSU71.fq -relabel @ -log mergeSU71.log usearch -fastq_mergepairs A162-SU45-GAAGCGAT-Blomster-run20150513B_S144_L001_R1_001.fastq -fastqout mergedSU45.fq -relabel @ -log mergeSU45.log usearch -fastq_mergepairs A164-SU44-ACAAACTG-Blomster-run20150513B_S145_L001_R1_001.fastq -fastqout mergedSU44.fq -relabel @ -log mergeSU44.log usearch -fastq_mergepairs A166-SU53-CCTATCAG-Blomster-run20150513B_S146_L001_R1_001.fastq -fastqout mergedSU53.fq -relabel @ -log mergeSU53.log usearch -fastq_filter mergedSU1.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU1.fa -log filterSU1.log usearch -fastq_filter mergedSU2.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU2.fa -log filterSU2.log usearch -fastq_filter mergedSU3.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU3.fa -log filterSU3.log usearch -fastq_filter mergedSU4.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU4.fa -log filterSU4.log usearch -fastq_filter mergedSU5.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU5.fa -log filterSU5.log usearch -fastq_filter mergedSU6.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU6.fa -log filterSU6.log usearch -fastq_filter mergedSU7.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU7.fa -log filterSU7.log usearch -fastq_filter mergedSU8.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU8.fa -log filterSU8.log usearch -fastq_filter mergedSU9.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU9.fa -log filterSU9.log usearch -fastq_filter mergedSU10.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU10.fa -log filterSU10.log usearch -fastq_filter mergedSU11.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU11.fa -log filterSU11.log usearch -fastq_filter mergedSU12.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU12.fa -log filterSU12.log usearch -fastq_filter mergedSU13.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU13.fa -log filterSU13.log usearch -fastq_filter mergedSU14.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU14.fa -log filterSU14.log usearch -fastq_filter mergedSU15.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU15.fa -log filterSU15.log usearch -fastq_filter mergedSU16.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU16.fa -log filterSU16.log usearch -fastq_filter mergedSU17.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU17.fa -log filterSU17.log usearch -fastq_filter mergedSU18.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU18.fa -log filterSU18.log usearch -fastq_filter mergedSU19.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU19.fa -log filterSU19.log usearch -fastq_filter mergedSU20.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU20.fa -log filterSU20.log usearch -fastq_filter mergedSU21.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU21.fa -log filterSU21.log usearch -fastq_filter mergedSU22.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU22.fa -log filterSU22.log usearch -fastq_filter mergedSU23.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU23.fa -log filterSU23.log usearch -fastq_filter mergedSU24.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU24.fa -log filterSU24.log usearch -fastq_filter mergedSU25.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU25.fa -log filterSU25.log usearch -fastq_filter mergedSU26.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU26.fa -log filterSU26.log usearch -fastq_filter mergedSU27.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU27.fa -log filterSU27.log usearch -fastq_filter mergedSU28.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU28.fa -log filterSU28.log usearch -fastq_filter mergedSU29.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU29.fa -log filterSU29.log usearch -fastq_filter mergedSU30.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU30.fa -log filterSU30.log usearch -fastq_filter mergedSU31.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU31.fa -log filterSU31.log usearch -fastq_filter mergedSU32.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU32.fa -log filterSU32.log usearch -fastq_filter mergedSU33.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU33.fa -log filterSU33.log usearch -fastq_filter mergedSU34.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU34.fa -log filterSU34.log usearch -fastq_filter mergedSU35.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU35.fa -log filterSU35.log usearch -fastq_filter mergedSU36.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU36.fa -log filterSU36.log usearch -fastq_filter mergedSU37.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU37.fa -log filterSU37.log usearch -fastq_filter mergedSU38.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU38.fa -log filterSU38.log usearch -fastq_filter mergedSU39.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU39.fa -log filterSU39.log usearch -fastq_filter mergedSU40.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU40.fa -log filterSU40.log usearch -fastq_filter mergedSU41.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU41.fa -log filterSU41.log usearch -fastq_filter mergedSU42.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU42.fa -log filterSU42.log usearch -fastq_filter mergedSU43.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU43.fa -log filterSU43.log usearch -fastq_filter mergedSU44.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU44.fa -log filterSU44.log usearch -fastq_filter mergedSU45.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU45.fa -log filterSU45.log usearch -fastq_filter mergedSU46.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU46.fa -log filterSU46.log usearch -fastq_filter mergedSU47.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU47.fa -log filterSU47.log usearch -fastq_filter mergedSU48.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU48.fa -log filterSU48.log usearch -fastq_filter mergedSU49.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU49.fa -log filterSU49.log usearch -fastq_filter mergedSU50.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU50.fa -log filterSU50.log usearch -fastq_filter mergedSU51.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU51.fa -log filterSU51.log usearch -fastq_filter mergedSU52.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU52.fa -log filterSU52.log usearch -fastq_filter mergedSU53.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU53.fa -log filterSU53.log usearch -fastq_filter mergedSU54.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU54.fa -log filterSU54.log usearch -fastq_filter mergedSU55.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU55.fa -log filterSU55.log usearch -fastq_filter mergedSU56.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU56.fa -log filterSU56.log usearch -fastq_filter mergedSU57.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU57.fa -log filterSU57.log usearch -fastq_filter mergedSU58.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU58.fa -log filterSU58.log usearch -fastq_filter mergedSU59.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU59.fa -log filterSU59.log usearch -fastq_filter mergedSU60.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU60.fa -log filterSU60.log usearch -fastq_filter mergedSU61.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU61.fa -log filterSU61.log usearch -fastq_filter mergedSU62.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU62.fa -log filterSU62.log usearch -fastq_filter mergedSU63.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU63.fa -log filterSU63.log usearch -fastq_filter mergedSU64.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU64.fa -log filterSU64.log usearch -fastq_filter mergedSU65.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU65.fa -log filterSU65.log usearch -fastq_filter mergedSU66.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU66.fa -log filterSU66.log usearch -fastq_filter mergedSU67.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU67.fa -log filterSU67.log usearch -fastq_filter mergedSU68.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU68.fa -log filterSU68.log usearch -fastq_filter mergedSU69.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU69.fa -log filterSU69.log usearch -fastq_filter mergedSU70.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU70.fa -log filterSU70.log usearch -fastq_filter mergedSU71.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU71.fa -log filterSU71.log usearch -fastq_filter mergedSU72.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU72.fa -log filterSU72.log usearch -fastq_filter mergedSU73.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU73.fa -log filterSU73.log usearch -fastq_filter mergedSU74.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU74.fa -log filterSU74.log usearch -fastq_filter mergedSU75.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU75.fa -log filterSU75.log usearch -fastq_filter mergedSU76.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU76.fa -log filterSU76.log usearch -fastq_filter mergedSU77.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU77.fa -log filterSU77.log usearch -fastq_filter mergedSU78.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU78.fa -log filterSU78.log usearch -fastq_filter mergedSU79.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU79.fa -log filterSU79.log usearch -fastq_filter mergedSU80.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU80.fa -log filterSU80.log usearch -fastq_filter mergedSU81.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU81.fa -log filterSU81.log usearch -fastq_filter mergedSU82.fq -fastq_maxee 1.0 -fastq_minlen 200 -fastaout filteredSU82.fa -log filterSU82.log There were barcode sequences before primer sequences, so to get rid of them, opened in Aliview, removed 25 first bases to remove forward primer sequences, made reverse complement saved as filteredA061_2.fa, removed 20 bases to remove reverse primer sequences made reverse complement and saved as filteredA061_4.fa, etc. usearch -derep_fulllength filteredSU1_4.fa -sizeout -fastaout uniquesSU1.fa -log derepSU1.log usearch -derep_fulllength filteredSU2_4.fa -sizeout -fastaout uniquesSU2.fa -log derepSU2.log usearch -derep_fulllength filteredSU3_4.fa -sizeout -fastaout uniquesSU3.fa -log derepSU3.log usearch -derep_fulllength filteredSU4_4.fa -sizeout -fastaout uniquesSU4.fa -log derepSU4.log usearch -derep_fulllength filteredSU5_4.fa -sizeout -fastaout uniquesSU5.fa -log derepSU5.log usearch -derep_fulllength filteredSU6_4.fa -sizeout -fastaout uniquesSU6.fa -log derepSU6.log usearch -derep_fulllength filteredSU7_4.fa -sizeout -fastaout uniquesSU7.fa -log derepSU7.log usearch -derep_fulllength filteredSU8_4.fa -sizeout -fastaout uniquesSU8.fa -log derepSU8.log usearch -derep_fulllength filteredSU9_4.fa -sizeout -fastaout uniquesSU9.fa -log derepSU9.log usearch -derep_fulllength filteredSU10_4.fa -sizeout -fastaout uniquesSU10.fa -log derepSU10.log usearch -derep_fulllength filteredSU11_4.fa -sizeout -fastaout uniquesSU11.fa -log derepSU11.log usearch -derep_fulllength filteredSU12_4.fa -sizeout -fastaout uniquesSU12.fa -log derepSU12.log usearch -derep_fulllength filteredSU13_4.fa -sizeout -fastaout uniquesSU13.fa -log derepSU13.log usearch -derep_fulllength filteredSU14_4.fa 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filteredSU55_4.fa -sizeout -fastaout uniquesSU55.fa -log derepSU55.log usearch -derep_fulllength filteredSU56_4.fa -sizeout -fastaout uniquesSU56.fa -log derepSU56.log usearch -derep_fulllength filteredSU57_4.fa -sizeout -fastaout uniquesSU57.fa -log derepSU57.log usearch -derep_fulllength filteredSU58_4.fa -sizeout -fastaout uniquesSU58.fa -log derepSU58.log usearch -derep_fulllength filteredSU59_4.fa -sizeout -fastaout uniquesSU59.fa -log derepSU59.log usearch -derep_fulllength filteredSU60_4.fa -sizeout -fastaout uniquesSU60.fa -log derepSU60.log usearch -derep_fulllength filteredSU61_4.fa -sizeout -fastaout uniquesSU61.fa -log derepSU61.log usearch -derep_fulllength filteredSU62_4.fa -sizeout -fastaout uniquesSU62.fa -log derepSU62.log usearch -derep_fulllength filteredSU63_4.fa -sizeout -fastaout uniquesSU63.fa -log derepSU63.log usearch -derep_fulllength filteredSU64_4.fa -sizeout -fastaout uniquesSU64.fa -log derepSU64.log usearch -derep_fulllength filteredSU65_4.fa -sizeout -fastaout uniquesSU65.fa -log derepSU65.log usearch -derep_fulllength filteredSU66_4.fa -sizeout -fastaout uniquesSU66.fa -log derepSU66.log usearch -derep_fulllength filteredSU67_4.fa -sizeout -fastaout uniquesSU67.fa -log derepSU67.log usearch -derep_fulllength filteredSU68_4.fa -sizeout -fastaout uniquesSU68.fa -log derepSU68.log usearch -derep_fulllength filteredSU69_4.fa -sizeout -fastaout uniquesSU69.fa -log derepSU69.log usearch -derep_fulllength filteredSU70_4.fa -sizeout -fastaout uniquesSU70.fa -log derepSU70.log usearch -derep_fulllength filteredSU71_4.fa -sizeout -fastaout uniquesSU71.fa -log derepSU71.log usearch -derep_fulllength filteredSU72_4.fa -sizeout -fastaout uniquesSU72.fa -log derepSU72.log usearch -derep_fulllength filteredSU73_4.fa -sizeout -fastaout uniquesSU73.fa -log derepSU73.log usearch -derep_fulllength filteredSU74_4.fa -sizeout -fastaout uniquesSU74.fa -log derepSU74.log usearch -derep_fulllength filteredSU75_4.fa -sizeout -fastaout uniquesSU75.fa -log 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-cluster_otus uniquesSU4.fa -minsize 2 -sizeout -otus otusSU4.fa -log cluster_otusSU4.log usearch -cluster_otus uniquesSU5.fa -minsize 2 -sizeout -otus otusSU5.fa -log cluster_otusSU5.log usearch -cluster_otus uniquesSU6.fa -minsize 2 -sizeout -otus otusSU6.fa -log cluster_otusSU6.log usearch -cluster_otus uniquesSU7.fa -minsize 2 -sizeout -otus otusSU7.fa -log cluster_otusSU7.log usearch -cluster_otus uniquesSU8.fa -minsize 2 -sizeout -otus otusSU8.fa -log cluster_otusSU8.log usearch -cluster_otus uniquesSU9.fa -minsize 2 -sizeout -otus otusSU9.fa -log cluster_otusSU9.log usearch -cluster_otus uniquesSU10.fa -minsize 2 -sizeout -otus otusSU10.fa -log cluster_otusSU10.log usearch -cluster_otus uniquesSU11.fa -minsize 2 -sizeout -otus otusSU11.fa -log cluster_otusSU11.log usearch -cluster_otus uniquesSU12.fa -minsize 2 -sizeout -otus otusSU12.fa -log cluster_otusSU12.log usearch -cluster_otus uniquesSU13.fa -minsize 2 -sizeout -otus otusSU13.fa -log cluster_otusSU13.log usearch -cluster_otus uniquesSU14.fa -minsize 2 -sizeout -otus otusSU14.fa -log cluster_otusSU14.log usearch -cluster_otus uniquesSU15.fa -minsize 2 -sizeout -otus otusSU15.fa -log cluster_otusSU15.log usearch -cluster_otus uniquesSU16.fa -minsize 2 -sizeout -otus otusSU16.fa -log cluster_otusSU16.log usearch -cluster_otus uniquesSU17.fa -minsize 2 -sizeout -otus otusSU17.fa -log cluster_otusSU17.log usearch -cluster_otus uniquesSU18.fa -minsize 2 -sizeout -otus otusSU18.fa -log cluster_otusSU18.log usearch -cluster_otus uniquesSU19.fa -minsize 2 -sizeout -otus otusSU19.fa -log cluster_otusSU19.log usearch -cluster_otus uniquesSU20.fa -minsize 2 -sizeout -otus otusSU20.fa -log cluster_otusSU20.log usearch -cluster_otus uniquesSU21.fa -minsize 2 -sizeout -otus otusSU21.fa -log cluster_otusSU21.log usearch -cluster_otus uniquesSU22.fa -minsize 2 -sizeout -otus otusSU22.fa -log cluster_otusSU22.log usearch -cluster_otus uniquesSU23.fa -minsize 2 -sizeout -otus otusSU23.fa -log 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-sizeout -otus otusSU43.fa -log cluster_otusSU43.log usearch -cluster_otus uniquesSU44.fa -minsize 2 -sizeout -otus otusSU44.fa -log cluster_otusSU44.log usearch -cluster_otus uniquesSU45.fa -minsize 2 -sizeout -otus otusSU45.fa -log cluster_otusSU45.log usearch -cluster_otus uniquesSU46.fa -minsize 2 -sizeout -otus otusSU46.fa -log cluster_otusSU46.log usearch -cluster_otus uniquesSU47.fa -minsize 2 -sizeout -otus otusSU47.fa -log cluster_otusSU47.log usearch -cluster_otus uniquesSU48.fa -minsize 2 -sizeout -otus otusSU48.fa -log cluster_otusSU48.log usearch -cluster_otus uniquesSU49.fa -minsize 2 -sizeout -otus otusSU49.fa -log cluster_otusSU49.log usearch -cluster_otus uniquesSU50.fa -minsize 2 -sizeout -otus otusSU50.fa -log cluster_otusSU50.log usearch -cluster_otus uniquesSU51.fa -minsize 2 -sizeout -otus otusSU51.fa -log cluster_otusSU51.log usearch -cluster_otus uniquesSU52.fa -minsize 2 -sizeout -otus otusSU52.fa -log cluster_otusSU52.log usearch -cluster_otus uniquesSU53.fa 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-cluster_otus uniquesSU73.fa -minsize 2 -sizeout -otus otusSU73.fa -log cluster_otusSU73.log usearch -cluster_otus uniquesSU74.fa -minsize 2 -sizeout -otus otusSU74.fa -log cluster_otusSU74.log usearch -cluster_otus uniquesSU75.fa -minsize 2 -sizeout -otus otusSU75.fa -log cluster_otusSU75.log usearch -cluster_otus uniquesSU76.fa -minsize 2 -sizeout -otus otusSU76.fa -log cluster_otusSU76.log usearch -cluster_otus uniquesSU77.fa -minsize 2 -sizeout -otus otusSU77.fa -log cluster_otusSU77.log usearch -cluster_otus uniquesSU78.fa -minsize 2 -sizeout -otus otusSU78.fa -log cluster_otusSU78.log usearch -cluster_otus uniquesSU79.fa -minsize 2 -sizeout -otus otusSU79.fa -log cluster_otusSU79.log usearch -cluster_otus uniquesSU80.fa -minsize 2 -sizeout -otus otusSU80.fa -log cluster_otusSU80.log usearch -cluster_otus uniquesSU81.fa -minsize 2 -sizeout -otus otusSU81.fa -log cluster_otusSU81.log usearch -cluster_otus uniquesSU82.fa -minsize 2 -sizeout -otus otusSU82.fa -log cluster_otusSU82.log mothur> merge.files(input=otusSU1.fa-otusSU2.fa-otusSU3.fa-otusSU4.fa-otusSU5.fa-otusSU6.fa-otusSU7.fa-otusSU8.fa-otusSU9.fa-otusSU10.fa-otusSU11.fa-otusSU12.fa-otusSU13.fa-otusSU14.fa-otusSU15.fa-otusSU16.fa-otusSU17.fa-otusSU18.fa-otusSU19.fa-otusSU20.fa-otusSU21.fa-otusSU22.fa-otusSU23.fa-otusSU24.fa-otusSU25.fa-otusSU26.fa-otusSU27.fa-otusSU28.fa-otusSU29.fa-otusSU30.fa-otusSU31.fa-otusSU32.fa-otusSU33.fa-otusSU34.fa-otusSU35.fa-otusSU36.fa-otusSU37.fa-otusSU38.fa-otusSU39.fa-otusSU40.fa-otusSU41.fa-otusSU42.fa-otusSU43.fa-otusSU44.fa-otusSU45.fa-otusSU46.fa-otusSU47.fa-otusSU48.fa-otusSU49.fa-otusSU50.fa-otusSU51.fa-otusSU52.fa-otusSU53.fa-otusSU54.fa-otusSU55.fa-otusSU56.fa-otusSU57.fa-otusSU58.fa-otusSU59.fa-otusSU60.fa-otusSU61.fa-otusSU62.fa-otusSU63.fa-otusSU64.fa-otusSU65.fa-otusSU66.fa-otusSU67.fa-otusSU68.fa-otusSU69.fa-otusSU70.fa-otusSU71.fa-otusSU72.fa-otusSU73.fa-otusSU74.fa-otusSU75.fa-otusSU76.fa-otusSU77.fa-otusSU78.fa-otusSU79.fa-otusSU80.fa-otusSU81.fa-otusSU82.fa, output=otusALL.fa) usearch -sortbysize otusALL.fa -fastaout otusALL_sorted.fa usearch -cluster_otus otusALL_sorted.fa -minsize 2 -sizein -otus otusALL_sorted_clustered.fa -sizeout -log cluster_otusALLclustered.log usearch -usearch_global otusALL.fa -db otusALL_sorted_clustered.fa -strand plus -id 0.97 -mothur_shared_out otutab.shared blastn -db nt -query D:\Miseq\Successionpaper\otusALL_sorted_clustered.fa -evalue 1e-20 -num_descriptions 100 -num_alignments 100 -out D:\Miseq\Successionpaper\otusALL_sorted_clustered.taxonomy.txt -remote MEGAN6: import otusALL_sorted_clustered.taxonomy.txt minimum bit score 400.0 top percentage 3.0 Minimum support percentage 0.0001 minimum support 1 Total: 1760 Not assigned: 583 (33.1%) No hits 59 (3.4%) Results put together with OTU-table, manually. mothur> classify.seqs(fasta=otusALL_sorted_clustered.fa, template=gb203_pr2_all_10_28_99p.fasta, taxonomy=gb203_pr2_all_10_28_99p.tax) Not assigned OTUs removed (372). Sequence names and taxonomy put together to name the OTUs. A new shared file: otutab.referenced.shared.txt. Lowest amount of sequences/sample was 27591. Thus, the number of reads per sample will be normalized to that number. mothur > sub.sample(shared=otutab.referenced.shared.txt, size=27591) otutab.referenced.shared.usearch.subsample.txt will be used for multivariate analyses (in excel removed singletons and otus in less than two samples and saved as otutab.multivariate). mothur> collect.single(shared=otutab.referenced.usearch.subsample.shared, freq=1) This just to check whether the curves get horizontal, if do, we can take summary.single command with subsampling. mothur > summary.single(shared=otutab.referenced.shared.txt, calc=nseqs-coverage-sobs-ace-shannon-invsimpson, subsample=27573) calculate diversity metrics for phases.