/data/results/tools/blast/ncbi-blast-2.2.25+/bin/makeblastdb -in RBCL_sequence.fasta -parse_seqids -dbtype nucl cat /mnt/max/b/genomics_facility/proton2/SPlab/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD1_300bpfrag1.IonXpress_049.fastq | awk -f ~/tools/formats/fastq2fasta.awk | /data/results/tools/blast/ncbi-blast-2.2.25+/bin/blastn -num_threads 17 -evalue 6 -max_target_seqs 1 -outfmt 0 -db /mnt/max/b/genomics_facility/proton2/SPlab/run431/blast/RBCL_sequence.fasta > SPD1.blast.txt ]0;/mnt/max/b/genomics_facility/proton2/SPlab/run431/diamondreczko@max:/mnt/max/b/genomics_facility/proton2/SPlab/run431/diamond$ ~/Elixir/metagenomics/diamond/diamond blastx -p 18 -c 2 -b5.0 --top 1 -d ~/Elixir/metagenomics/nr/nr -q R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD1_300bpfrag1.IonXpress_049.fastq -f 0 -o r431SPD1matches-top1.f0 Total time = 5233.4s Reported 10578526 pairwise alignments, 10626369 HSPs. 1431434 queries aligned. ~/Elixir/metagenomics/diamond/diamond blastx -p 18 -c 2 -b5.0 --top 1 -d ~/Elixir/metagenomics/nr/nr -q ../R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 0 -o r431SPD2matches-top1.f0 Total time = 40340.6s Reported 684986854 pairwise alignments, 685415644 HSPs. 1008656 queries aligned. (/ 40340 3600.0) 11.205555555555556 h 453119216 Sep 24 16:10 r431SPD1matches-top1-default.rma6 6890979334 Sep 18 20:50 r431SPD1matches-top1.f0 (/ 453119216 6890979334.0) 0.06575541647096746 (* 0.06575541647096746 475955635786) 31296661052.81253 (- 78661052 28661052) (/ 50000000 2) 25000000 (/ 31296661052.81253 25000000) (/ 1251.8664421125013 24) 52.16110175468756 days!! ~/Elixir/metagenomics/diamond/diamond blastx -k 1 -p 18 -c 2 -b5.0 --top 1 -d ~/Elixir/metagenomics/nr/nr -q ../R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD2_300bpfrag2.IonXpress_050.fastq -f 0 -o r431SPD2matches-k1.f0 SPD1: top5: Parsing file: /home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD1matches-top1.f0 Warning: Might not be a BLASTX file in TEXT format: /home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD1matches-top1.f0 Total reads: 1,953,579 Alignments: 2,829,012 Initializing binning... Using 'Naive LCA' algorithm for binning: Taxonomy Binning reads... Total reads: 1,953,579 With hits: 1,431,434 Alignments: 2,829,012 Assig. Taxonomy: 1,431,332 MinSupport set to: 976 Min-supp. changes: 2,008 Numb. Tax. classes: 406 Class. Taxonomy: 406 Info: Command completed (1466s): import blastFile='/home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD1matches-top1.f0' meganFile='/home/reczko/El... Induced tree has 554 of 2,127,533 nodes Induced tree has 554 of 2,127,533 nodes Executing: uncollapse nodes=subtree; Induced tree has 554 of 2,127,533 nodes top1 Warning: Might not be a BLASTX file in TEXT format: /home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD1matches-top1.f0 Total reads: 1,953,579 Alignments: 1,431,434 Initializing binning... Using 'Naive LCA' algorithm for binning: Taxonomy Binning reads... Total reads: 1,953,579 With hits: 1,431,434 Alignments: 1,431,434 Assig. Taxonomy: 1,431,223 MinSupport set to: 976 Min-supp. changes: 3,218 Numb. Tax. classes: 589 Class. Taxonomy: 589 Info: Command completed (858s): import blastFile='/home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD1matches-top1.f0' meganFile='/home/reczko/Eli... Induced tree has 789 of 2,127,533 nodes Induced tree has 789 of 2,127,533 nodes top1-95pctID Parsing file: /home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD1matches-top1.f0 Warning: Might not be a BLASTX file in TEXT format: /home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD1matches-top1.f0 Total reads: 1,953,579 Alignments: 1,431,434 Initializing binning... Using 'Naive LCA' algorithm for binning: Taxonomy Binning reads... Total reads: 1,953,579 With hits: 1,431,434 Alignments: 1,431,434 Assig. Taxonomy: 558,789 MinSupport set to: 976 Min-supp. changes: 1,624 Numb. Tax. classes: 291 Class. Taxonomy: 291 Info: Command completed (862s): import blastFile='/home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD1matches-top1.f0' meganFile='/home/reczko/Eli... Induced tree has 392 of 2,127,533 nodes Induced tree has 392 of 2,127,533 nodes # SPD2 Parsing file: /home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD2matches-top1.f0 Warning: Might not be a BLASTX file in TEXT format: /home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD2matches-top1.f0 Total reads: 1,172,322 Alignments: 1,008,656 Initializing binning... Using 'Naive LCA' algorithm for binning: Taxonomy Binning reads... Total reads: 1,172,322 With hits: 1,008,656 Alignments: 1,008,656 Assig. Taxonomy: 365,316 MinSupport set to: 586 Min-supp. changes: 1,667 Numb. Tax. classes: 281 Class. Taxonomy: 281 Info: Command completed (67036s): 'import''blastFile''=''/home/reczko/Elixir/metagenomics/SPlab/run431/diamond/r431SPD2matches-top1.f0''meganFile''=''/home/... Induced tree has 370 of 2,127,533 nodes Induced tree has 370 of 2,127,533 nodes Executing: uncollapse nodes=subtree; Induced tree has 370 of 2,127,533 nodes ~/Elixir/metagenomics/blat/blat ~/Elixir/metagenomics/SPlab/run431/blast/RBCL_sequence.fasta /mnt/max/b/genomics_facility/proton2/SPlab/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD1_300bpfrag1.IonXpress_049.fa -out=blast /mnt/max/b/genomics_facility/proton2/SPlab/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD1_300bpfrag1.IonXpress_049.blat #too sensitive ~/Elixir/metagenomics/blat/blat ~/Elixir/metagenomics/SPlab/run431/blast/RBCL_sequence.fasta /mnt/max/b/genomics_facility/proton2/SPlab/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD1_300bpfrag1.IonXpress_049.fa -minScore=100 -minIdentity=95 -out=blast9 /mnt/max/b/genomics_facility/proton2/SPlab/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD1_300bpfrag1.IonXpress_049.blat time /home/reczko/Elixir/metagenomics/mummer/mummer-4.0.0beta2/nucmer -t17 --save=rbcl-mummer --sam-short=spd1 ~/Elixir/metagenomics/SPlab/run431/blast/RBCL_sequence.fasta /mnt/max/b/genomics_facility/proton2/SPlab/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD1_300bpfrag1.IonXpress_049.fa #add header cd /home/reczko/Elixir/metagenomics/SPlab/run431/blast /data/results/tools/samtools/samtools-1.3/samtools faidx RBCL_sequence.fasta #cat spd1 | samtools view -bS -t ~/Elixir/metagenomics/SPlab/run431/blast/RBCL_sequence.fasta.fai - | samtools sort -o - - > spd1.bam cat spd1 | sort -k 1,1| samtools view -bS -t ~/Elixir/metagenomics/SPlab/run431/blast/RBCL_sequence.fasta.fai - > spd1.bam ~/Elixir/metagenomics/filterbam/filterBam --in spd1.bam --out spd1-flt.bam --minId 95 --uniq --uniqThresh 0.99 --verbose tail -n +3 spd1 | sort -k 1,1| samtools view -bS -t ~/Elixir/metagenomics/SPlab/run431/blast/RBCL_sequence.fasta.fai - > spd1.bam