Version   MEGAN Community Edition (version 6.18.0, built 28 Oct 2019)
Copyright (C) 2019 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
This is free software, licensed under the terms of the GNU General Public License, Version 3.
Sources available at: https://github.com/danielhuson/megan-ce
Java version: 11.0.7

Opening startup files
Loading ncbi.map: 2,175,506
Loading ncbi.tre: 2,175,510
Induced tree has 2,175,510 of 2,175,510 nodes
Executing: add file='/home/samb/data/metagenomics/Library_Geoduck_MG_1_S3_L002_R1.rma6';add file='/home/samb/data/metagenomics/Library_Geoduck_MG_2_S4_L002_R1.rma6';add file='/home/samb/data/metagenomics/Library_Geoduck_MG_3_S1_L002_R1.rma6';add file='/home/samb/data/metagenomics/Library_Geoduck_MG_5_S6_L002_R1.rma6';add file='/home/samb/data/metagenomics/Library_Geoduck_MG_6_S5_L002_R1.rma6';add file='/home/samb/data/metagenomics/Library_Geoduck_MG_7_S2_L002_R1.rma6';
Loading MEGAN File: Library_Geoduck_MG_1_S3_L002_R1.rma6
Loading MEGAN File: Library_Geoduck_MG_2_S4_L002_R1.rma6
Loading MEGAN File: Library_Geoduck_MG_3_S1_L002_R1.rma6
Loading MEGAN File: Library_Geoduck_MG_5_S6_L002_R1.rma6
Loading MEGAN File: Library_Geoduck_MG_6_S5_L002_R1.rma6
Loading MEGAN File: Library_Geoduck_MG_7_S2_L002_R1.rma6
Induced tree has 2,175,510 of 2,175,510 nodes
Executing: set mode=ABSOLUTE;
Executing: apply;
Selected: 6
Executing: compare mode=ABSOLUTE readAssignmentMode=readCount keep1=false ignoreUnassigned=false meganFile='/home/samb/data/metagenomics/Library_Geoduck_MG_1_S3_L002_R1.rma6', '/home/samb/data/metagenomics/Library_Geoduck_MG_2_S4_L002_R1.rma6', '/home/samb/data/metagenomics/Library_Geoduck_MG_3_S1_L002_R1.rma6', '/home/samb/data/metagenomics/Library_Geoduck_MG_5_S6_L002_R1.rma6', '/home/samb/data/metagenomics/Library_Geoduck_MG_6_S5_L002_R1.rma6', '/home/samb/data/metagenomics/Library_Geoduck_MG_7_S2_L002_R1.rma6';
Executing: open file='/home/samb/data/metagenomics/Library_Geoduck_MG_1_S3_L002_R1.rma6' readOnly=true;update;
Loading MEGAN File: Library_Geoduck_MG_1_S3_L002_R1.rma6
Info: Opened file 'Library_Geoduck_MG_1_S3_L002_R1.rma6' with 78,338,406 reads
updating viewer
Induced tree has 371 of 2,175,510 nodes
Induced tree has 371 of 2,175,510 nodes
Executing: open file='/home/samb/data/metagenomics/Library_Geoduck_MG_2_S4_L002_R1.rma6' readOnly=true;update;
Loading MEGAN File: Library_Geoduck_MG_2_S4_L002_R1.rma6
Opened file '/home/samb/data/metagenomics/Library_Geoduck_MG_2_S4_L002_R1.rma6' with 80,708,846 reads
updating viewer
Induced tree has 319 of 2,175,510 nodes
Induced tree has 319 of 2,175,510 nodes
Executing: open file='/home/samb/data/metagenomics/Library_Geoduck_MG_3_S1_L002_R1.rma6' readOnly=true;update;
Loading MEGAN File: Library_Geoduck_MG_3_S1_L002_R1.rma6
Opened file '/home/samb/data/metagenomics/Library_Geoduck_MG_3_S1_L002_R1.rma6' with 41,066,115 reads
updating viewer
Induced tree has 398 of 2,175,510 nodes
Induced tree has 398 of 2,175,510 nodes
Executing: open file='/home/samb/data/metagenomics/Library_Geoduck_MG_5_S6_L002_R1.rma6' readOnly=true;update;
Loading MEGAN File: Library_Geoduck_MG_5_S6_L002_R1.rma6
Opened file '/home/samb/data/metagenomics/Library_Geoduck_MG_5_S6_L002_R1.rma6' with 80,636,117 reads
updating viewer
Induced tree has 253 of 2,175,510 nodes
Induced tree has 253 of 2,175,510 nodes
Executing: open file='/home/samb/data/metagenomics/Library_Geoduck_MG_6_S5_L002_R1.rma6' readOnly=true;update;
Loading MEGAN File: Library_Geoduck_MG_6_S5_L002_R1.rma6
Opened file '/home/samb/data/metagenomics/Library_Geoduck_MG_6_S5_L002_R1.rma6' with 83,337,226 reads
updating viewer
Induced tree has 284 of 2,175,510 nodes
Induced tree has 284 of 2,175,510 nodes
Executing: open file='/home/samb/data/metagenomics/Library_Geoduck_MG_7_S2_L002_R1.rma6' readOnly=true;update;
Loading MEGAN File: Library_Geoduck_MG_7_S2_L002_R1.rma6
Opened file '/home/samb/data/metagenomics/Library_Geoduck_MG_7_S2_L002_R1.rma6' with 101,937,343 reads
updating viewer
Induced tree has 281 of 2,175,510 nodes
Induced tree has 281 of 2,175,510 nodes
Computing comparison: 
Total assigned:  466,024,048
Induced tree has 585 of 2,175,510 nodes
Induced tree has 585 of 2,175,510 nodes
Executing: show window=samplesViewer;
Executing: new attribute='pH' position=6;
Executing: new attribute='Day' position=6;
Executing: show window=samplesViewer;
Executing: move sample= 'Library_Geoduck_MG_3_S1_L002_R1' direction=down;
Executing: update reinduce=true;select samples name='Library_Geoduck_MG_3_S1_L002_R1';
Selected 1 rows
Executing: colorBy attribute='pH';
Induced tree has 585 of 2,175,510 nodes
Induced tree has 585 of 2,175,510 nodes
Executing: shapeBy attribute='Day';
Executing: set nodeShape=Oval sample= 'Library_Geoduck_MG_2_S4_L002_R1' 'Library_Geoduck_MG_7_S2_L002_R1';set nodeShape=Diamond sample= 'Library_Geoduck_MG_3_S1_L002_R1';set nodeShape=Triangle sample= 'Library_Geoduck_MG_5_S6_L002_R1';set nodeShape=Rectangle sample= 'Library_Geoduck_MG_1_S3_L002_R1' 'Library_Geoduck_MG_6_S5_L002_R1';
Executing: open viewer=INTERPRO2GO;
Loading interpro2go.map:    13,501
Loading interpro2go.tre:    29,204
Induced tree has 25,735 of 29,204 nodes
Induced tree has 25,735 of 29,204 nodes
Executing: uncollapse nodes=selected;
Induced tree has 25,735 of 29,204 nodes
Induced tree has 25,735 of 29,204 nodes
Executing: uncollapse nodes=selected;
Induced tree has 25,735 of 29,204 nodes
Induced tree has 25,735 of 29,204 nodes
Executing: uncollapse nodes=selected;
Induced tree has 25,735 of 29,204 nodes
Induced tree has 25,735 of 29,204 nodes
Executing: export what=CSV format=interpro2goName_to_count separator=tab counts=assigned file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_NameToCount.txt';
Info: Wrote 62 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_NameToCount.txt
Executing: export what=CSV format=interpro2goPath_to_count separator=tab counts=assigned file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_interpro2goPathToCount.txt';
Info: Wrote 62 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_interpro2goPathToCount.txt
Executing: export what=CSV format=interpro2goName_to_percent separator=tab counts=assigned file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_interpro2goNameToPercent.txt';
Info: Wrote 62 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_interpro2goNameToPercent.txt
Executing: export what=CSV format=interpro2goPath_to_percent separator=tab counts=assigned file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_interpro2goPathToPercent.txt';
Info: Wrote 62 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_interpro2goPathToPercent.txt
Executing: save file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH.megan' summary=true;
done
Executing: compareBy attribute='Day' mode=absolute samples='Library_Geoduck_MG_1_S3_L002_R1' 'Library_Geoduck_MG_2_S4_L002_R1' 'Library_Geoduck_MG_5_S6_L002_R1' 'Library_Geoduck_MG_3_S1_L002_R1' 'Library_Geoduck_MG_6_S5_L002_R1' 'Library_Geoduck_MG_7_S2_L002_R1';
Loading seed.map:    13,662
Loading seed.tre:    21,085
Loading eggnog.map:    30,875
Loading eggnog.tre:    30,986
Info: Wrote 463,244,224 reads to file '/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH-Day.megan'
Executing: update reprocess=true reinduce=true;
Induced tree has 584 of 2,175,510 nodes
Induced tree has 584 of 2,175,510 nodes
Executing: open viewer=INTERPRO2GO;
Induced tree has 25,734 of 29,204 nodes
Induced tree has 25,734 of 29,204 nodes
Executing: uncollapse nodes=selected;
Induced tree has 25,734 of 29,204 nodes
Induced tree has 25,734 of 29,204 nodes
Executing: uncollapse nodes=selected;
Induced tree has 25,734 of 29,204 nodes
Induced tree has 25,734 of 29,204 nodes
Executing: uncollapse nodes=selected;
Induced tree has 25,734 of 29,204 nodes
Induced tree has 25,734 of 29,204 nodes
Executing: export what=CSV format=interpro2goName_to_count separator=tab counts=assigned file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_interpro2goNameToCount.txt';
Info: Wrote 62 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_interpro2goNameToCount.txt
Executing: export what=CSV format=interpro2goPath_to_count separator=tab counts=assigned file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_interpro2goPathToCount.txt';
Info: Wrote 62 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_interpro2goPathToCount.txt
Executing: export what=CSV format=interpro2goName_to_percent separator=tab counts=assigned file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_interpro2goNameToPercent.txt';
Info: Wrote 62 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_interpro2goNameToPercent.txt
Executing: export what=CSV format=interpro2goPath_to_percent separator=tab counts=assigned file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_interpro2goPathToPercent.txt';
Info: Wrote 62 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_interpro2goPathToPercent.txt
Executing: show window=mainViewer;
Executing: collapse rank='Class';select rank='Class';
Induced tree has 584 of 2,175,510 nodes
Induced tree has 584 of 2,175,510 nodes
Executing: collapse nodes=selected;
Induced tree has 584 of 2,175,510 nodes
Induced tree has 584 of 2,175,510 nodes
Executing: collapse nodes=top;
Induced tree has 584 of 2,175,510 nodes
Induced tree has 584 of 2,175,510 nodes
Executing: uncollapse nodes=selected;
Induced tree has 584 of 2,175,510 nodes
Induced tree has 584 of 2,175,510 nodes
Executing: collapse rank='Class';select rank='Class';
Induced tree has 584 of 2,175,510 nodes
Induced tree has 584 of 2,175,510 nodes
Executing: export what=CSV format=taxonName_to_count separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_readsNameToCount.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_readsNameToCount.txt
Executing: export what=CSV format=taxonRank_to_count separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_readsTaxonRankToCount.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_readsTaxonRankToCount.txt
Executing: export what=CSV format=taxonPath_to_count separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_readsTaxonPathToCount.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_readsTaxonPathToCount.txt
Executing: export what=CSV format=taxonPath_to_percent separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_readsTaxonPathToPercent.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_day_readsTaxonPathToPercent.txt
Executing: close what=current;
Executing: save file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_Day.megan' summary=true;
done
Executing: show window=mainViewer;
Executing: uncollapse nodes=selected;
Induced tree has 585 of 2,175,510 nodes
Induced tree has 585 of 2,175,510 nodes
Executing: collapse rank='Class';select rank='Class';
Induced tree has 585 of 2,175,510 nodes
Induced tree has 585 of 2,175,510 nodes
Executing: show window=mainViewer;
Executing: close what=current;
Executing: collapse rank='Class';select rank='Class';
Induced tree has 585 of 2,175,510 nodes
Induced tree has 585 of 2,175,510 nodes
Using experimental comparison data access
Executing: export what=CSV format=taxonName_to_count separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsNameToCount.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsNameToCount.txt
Executing: export what=CSV format=taxonRank_to_count separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToCount.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToCount.txt
Executing: export what=CSV format=taxonPath_to_count separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToCount.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToCount.txt
Executing: export what=CSV format=taxonRank_to_count separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonRankToCount.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonRankToCount.txt
Executing: export what=CSV format=taxonPath_to_count separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToCount.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToCount.txt
Executing: export what=CSV format=taxonPath_to_percent separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToPercent.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToPercent.txt
Executing: close what=current;
Executing: quit;
Executing: save file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH.megan' summary=true;
done
Induced tree has 2,175,510 of 2,175,510 nodes
Executing: open file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH.megan';
Loading MEGAN File: abs-reads_abs-comparison_pH.megan
Info: Opened file 'abs-reads_abs-comparison_pH.megan' with 466,024,064 reads
Induced tree has 585 of 2,175,510 nodes
Induced tree has 585 of 2,175,510 nodes
Executing: show window=samplesViewer;
Executing: compareBy attribute='pH' mode=absolute samples='Library_Geoduck_MG_1_S3_L002_R1' 'Library_Geoduck_MG_2_S4_L002_R1' 'Library_Geoduck_MG_5_S6_L002_R1' 'Library_Geoduck_MG_3_S1_L002_R1' 'Library_Geoduck_MG_6_S5_L002_R1' 'Library_Geoduck_MG_7_S2_L002_R1';
Info: Wrote 463,244,160 reads to file '/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH-pH.megan'
Executing: update reprocess=true reinduce=true;
Induced tree has 584 of 2,175,510 nodes
Induced tree has 584 of 2,175,510 nodes
Executing: uncollapse nodes=selected;
Induced tree has 584 of 2,175,510 nodes
Induced tree has 584 of 2,175,510 nodes
Executing: collapse rank='Class';select rank='Class';
Induced tree has 584 of 2,175,510 nodes
Induced tree has 584 of 2,175,510 nodes
Save canceled
Executing: export what=CSV format=taxonPath_to_count separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToCount.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToCount.txt
Executing: export what=CSV format=taxonPath_to_percent separator=tab counts=summarized file='/home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToPercent.txt';
Info: Wrote 26 line(s) to file: /home/samb/analyses/20200618_metagenomics_megan_tables/abs-reads_abs-comparison_pH_readsTaxonPathToPercent.txt
Executing: close what=current;