/data/images/proton2/run425/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq reczko@fix:~/Elixir/metagenomics/nr$ time ../diamond/diamond blastx -d nr -q /data/images/proton2/run425/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq -o matches.m8 Processing query chunk 0, reference chunk 39, shape 0, index chunk 0. Total time = 375.439s Reported 15211 pairwise alignments, 17694 HSPs. 614 queries aligned. real 6m15.478s user 68m43.028s sys 2m33.976s Processing query chunk 0, reference chunk 3, shape 0, index chunk 0. Total time = 380.785s Reported 15210 pairwise alignments, 17707 HSPs. 614 queries aligned. real 6m20.853s user 63m53.160s sys 2m36.140s time ../diamond/diamond blastx -c 1 -b25.0 -d nr -q /data/images/proton2/run425/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq -f 0 -o matches.m8 Reported 15210 pairwise alignments, 17707 HSPs. 614 queries aligned. real 6m8.566s user 63m58.812s sys 2m30.492s time ../diamond/diamond blastx -c 1 -b50.0 -d nr -q /data/images/proton2/run425/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq -f 100 -o matches.daa Total time = 368.349s Reported 15205 pairwise alignments, 17719 HSPs. 614 queries aligned. real 6m8.503s user 59m38.824s sys 2m33.572s cp matches.daa ../SPlab/blast/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq.m8-b25.0-c1-f0.daa time ../diamond/diamond blastx -c 1 -b50.0 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches.daa Failed to allocate sufficient memory. Please refer to the manual for instructions on memory usage. real 4m9.844s time ../diamond/diamond blastx -c 1 -b25.0 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches.daa Failed to allocate sufficient memory. Please refer to the manual for instructions on memory usage. time ../diamond/diamond blastx -c 2 -b25.0 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches.daa time ../diamond/diamond blastx -c 2 -b5.0 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches.daa -p 30 time ../diamond/diamond blastx -c 2 -b5.0 --frameshift 15 --range-culling --top 10 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches-longreads.daa /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD1_300bpfrag1.IonXpress_049.fastq R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD3_fragDNA1.IonXpress_031.fastq R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq # get nr wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz #make index reczko@fix:~/Elixir/metagenomics/nr$ fg ../diamond/diamond makedb --in nr.gz -d nr --taxonmap prot.accession2taxid.gz --taxonnodes taxdmp.zip # align diamond blastx -d nr -q reads.fna -o matches.m8 --sensitive This mode is a lot more sensitive that the default and generally recommended for aligning longer sequences. The default mode is mainly designed for short read alignment, i.e. finding significant matches of >50 bits on 30-40aa fragments. --more-sensitive This mode provides some additional sensitivity compared to the sensitive mode. Input options --db/-d Path to the DIAMOND database file. --query/-q Path to the query input file in FASTA or FASTQ format (may be gzip compressed). If this parameter is omitted, the input will be read from stdin. # long reads setting for diamond -F 15 —range-culling —top 10 /data/images/proton2/run425/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq reczko@fix:~/Elixir/metagenomics/nr$ time ../diamond/diamond blastx -d nr -q /data/images/proton2/run425/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq -o matches.m8 Processing query chunk 0, reference chunk 39, shape 0, index chunk 0. Total time = 375.439s Reported 15211 pairwise alignments, 17694 HSPs. 614 queries aligned. real 6m15.478s user 68m43.028s sys 2m33.976s reczko@platia:~/Elixir/metagenomics/nr$ time ../diamond/diamond blastx -d nr -q /mnt/max/b/genomics_facility/proton2/run425/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq -f 102 -o matches.f102 -t temp2 Total time = 2027.61s Reported 31526285 pairwise alignments, 33991037 HSPs. 614 queries aligned. real 33m47.674s user 80m31.128s sys 3m17.952s Processing query chunk 0, reference chunk 3, shape 0, index chunk 0. Total time = 380.785s Reported 15210 pairwise alignments, 17707 HSPs. 614 queries aligned. real 6m20.853s user 63m53.160s sys 2m36.140s time ../diamond/diamond blastx -c 1 -b25.0 -d nr -q /data/images/proton2/run425/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq -f 0 -o matches.m8 Reported 15210 pairwise alignments, 17707 HSPs. 614 queries aligned. real 6m8.566s user 63m58.812s sys 2m30.492s time ../diamond/diamond blastx -c 1 -b50.0 -d nr -q /data/images/proton2/run425/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq -f 100 -o matches.daa Total time = 368.349s Reported 15205 pairwise alignments, 17719 HSPs. 614 queries aligned. real 6m8.503s user 59m38.824s sys 2m33.572s cp matches.daa ../SPlab/blast/R_2019_07_23_14_35_17_user_IONAS-425-GKlab_SPlab_190722_GK3R249-264_SPD1-2.SPD2_300bpfrag.IonXpress_050.fastq.m8-b25.0-c1-f0.daa time ../diamond/diamond blastx -c 1 -b50.0 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches.daa Failed to allocate sufficient memory. Please refer to the manual for instructions on memory usage. real 4m9.844s time ../diamond/diamond blastx -c 1 -b25.0 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches.daa Failed to allocate sufficient memory. Please refer to the manual for instructions on memory usage. time ../diamond/diamond blastx -c 2 -b25.0 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches.daa time ../diamond/diamond blastx -c 2 -b5.0 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches.daa -p 30 time ../diamond/diamond blastx -c 2 -b5.0 --frameshift 15 --range-culling --top 10 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches-longreads.daa /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD1_300bpfrag1.IonXpress_049.fastq R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD3_fragDNA1.IonXpress_031.fastq R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq time ../diamond/diamond blastx -c 2 -b5.0 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches.daa -p 30 Total time = 36278.4s Reported 22769234 pairwise alignments, 22889963 HSPs. 1008779 queries aligned. real 604m38.594s user 8438m20.504s sys 36m47.700s time ../diamond/diamond blastx -c 2 -b5.0 --frameshift 15 --range-culling --top 10 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 100 -o matches-longreads.daa -t temp1 Total time = 37275.8s Reported 13327383448 pairwise alignments, 13327383448 HSPs. 1028494 queries aligned. real 621m15.949s user 9692m16.420s sys 112m17.360s #@ Quality-trimmed cd ~/Elixir/metagenomics/nr time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 1 -d nr -q /data/images/proton2/run431/wwwSPlab/QC/trim/SPD4.s10q20l20.fastq.gz -f 100 -o /data/images/proton2/run431/wwwSPlab/QC/trim/SPD4.s10q20l20.fastq.matches-longreads.daa Total time = 2071.31s Reported 2564274 pairwise alignments, 2564274 HSPs. 225810 queries aligned. real 34m31.619s time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 1 -d nr -q /data/images/proton2/run431/wwwSPlab/QC/trim/SPD3.s10q20l20.fastq.gz -f 100 -o /data/images/proton2/run431/wwwSPlab/QC/trim/SPD3.s10q20l20.fastq.matches-longreads.daa Total time = 3015.34s Reported 8893470 pairwise alignments, 8893475 HSPs. 835765 queries aligned. real 50m16.076s time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 1 -d nr -q /data/images/proton2/run431/wwwSPlab/QC/trim/SPD4.s10q20l20.fastq.gz -f 100 -o /data/images/proton2/run431/wwwSPlab/QC/trim/SPD4.s10q20l20.fastq.matches-longreads.daa Total time = 2071.31s Reported 2564274 pairwise alignments, 2564274 HSPs. 225810 queries aligned. real 34m31.619s time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 1 -d nr -q /data/images/proton2/run431/wwwSPlab/QC/trim/SPD3.s10q20l20.fastq.gz -f 100 -o /data/images/proton2/run431/wwwSPlab/QC/trim/SPD3.s10q20l20.fastq.matches-longreads.daa Total time = 3015.34s Reported 8893470 pairwise alignments, 8893475 HSPs. 835765 queries aligned. real 50m16.076s time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 1 -d nr -q /data/images/proton2/run431/wwwSPlab/QC/trim/SPD2.s10q20l20.fastq.gz -f 100 -o /data/images/proton2/run431/wwwSPlab/QC/trim/SPD2.s10q20l20.fastq.matches-longreads.daa Total time = 12061.7s Reported 527710728 pairwise alignments, 527710728 HSPs. 425644 queries aligned. real 201m1.755s time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 1 -d nr -q /data/images/proton2/run431/wwwSPlab/QC/trim/SPD1.s10q20l20.fastq.gz -f 100 -o /data/images/proton2/run431/wwwSPlab/QC/trim/SPD1.s10q20l20.fastq.matches-longreads.daa #@ asm time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 1 -d nr -q /data/images/proton2/run431/wwwSPlab/spd3/asm/SPD3.k51.ForMGRAST.fasta.gz -f 100 -o /data/images/proton2/run431/wwwSPlab/spd3/asm/SPD3.k51.ForMGRAST.fasta.matches-longreads.daa Total time = 1626.6s Reported 192905 pairwise alignments, 192921 HSPs. 23906 queries aligned. real 27m6.713s time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 1 -d nr -q /data/images/proton2/run431/wwwSPlab/spd4/asm/SPD4.k17.ForMGRAST.fasta.gz -f 100 -o /data/images/proton2/run431/wwwSPlab/spd4/asm/SPD4.k17.ForMGRAST.fasta.matches-longreads.daa Total time = 1655.73s Reported 524827 pairwise alignments, 524828 HSPs. 32382 queries aligned. real 27m35.875s @ --top 10 time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 10 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD4_fragDNA2.IonXpress_032.fastq -f 100 -o /data/images/proton2/run431/wwwSPlab/spd4/SPD4.top10.matches-longreads.daa Total time = 2589.67s Reported 35529993 pairwise alignments, 35529996 HSPs. 406839 queries aligned. real 43m11.652s time ../diamond/diamond blastx -c 2 -b5.0 -p 20 --frameshift 15 --range-culling --top 10 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD3_fragDNA1.IonXpress_031.fastq -f 100 -o /data/images/proton2/run431/wwwSPlab/spd3/SPD3.top10.matches-longreads.daa