core_gene_alignment.aln missing

[nikolay12]

I just ran roary on a set of assemblies annotated by prokka. Got no error messages but the core_gene_alignment.aln was missing from the output.

Here is the output of roary -a:

$ roary -a
Please cite Roary if you use any of the results it produces:
Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
"Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693
doi: http://doi.org/10.1093/bioinformatics/btv421
Pubmed: 26198102
2016/10/13 12:45:43 Looking for 'Rscript' - found /usr/bin/Rscript
2016/10/13 12:45:43 Determined Rscript version is 3.2
2016/10/13 12:45:43 Looking for 'awk' - found /bin/awk
2016/10/13 12:45:43 Looking for 'bedtools' - found /app/Roary/build/bedtools2/bin/bedtools
2016/10/13 12:45:43 Determined bedtools version is 2.24
2016/10/13 12:45:43 Looking for 'blastp' - found /app/Roary/build/ncbi-blast-2.2.30+/bin/blastp
2016/10/13 12:45:43 Determined blastp version is 2.2.30
2016/10/13 12:45:43 Looking for 'grep' - found /bin/grep
2016/10/13 12:45:43 Optional tool 'kraken' not found in your $PATH
2016/10/13 12:45:43 Optional tool 'kraken-report' not found in your $PATH
2016/10/13 12:45:43 Looking for 'mafft' - found /app/Roary/build/mafft-7.271-without-extensions/build/bin/mafft
2016/10/13 12:45:43 Determined mafft version is 7.271
2016/10/13 12:45:43 Looking for 'makeblastdb' - found /app/Roary/build/ncbi-blast-2.2.30+/bin/makeblastdb
2016/10/13 12:45:43 Determined makeblastdb version is 2.2.30
2016/10/13 12:45:43 Looking for 'mcl' - found /app/Roary/build/mcl-14-137/src/shmcl/mcl
2016/10/13 12:45:43 Determined mcl version is 14-137
2016/10/13 12:45:43 Looking for 'parallel' - found /app/Roary/build/parallel-20150522/src/parallel
2016/10/13 12:45:44 Determined parallel version is 20150522
2016/10/13 12:45:44 Looking for 'prank' - found /app/Roary/build/prank-msa-master/src/prank
2016/10/13 12:45:44 Looking for 'sed' - found /bin/sed
2016/10/13 12:45:44 Looking for 'cd-hit' - found /projects/jpc/london/software/cd-hit/v4.6.5/cd-hit
2016/10/13 12:45:44 Determined cd-hit version is 4.6
2016/10/13 12:45:44 Looking for 'FastTree' - found /app/Roary/build/fasttree/FastTree
2016/10/13 12:45:44 Determined FastTree version is 2.1
2016/10/13 12:45:44 Roary version 1.006924
2016/10/13 12:45:44 Error: You need to provide at least 2 files to build a pan genome
Usage: roary [options] *.gff
Options: -p INT number of threads [1]
-o STR clusters output filename [clustered_proteins]
-f STR output directory [.]
-e create a multiFASTA alignment of core genes using PRANK
-n fast core gene alignment with MAFFT, use with -e
-i minimum percentage identity for blastp [95]
-cd FLOAT percentage of isolates a gene must be in to be core [99]
-qc generate QC report with Kraken
-k STR path to Kraken database for QC, use with -qc
-a check dependancies and print versions
-b STR blastp executable [blastp]
-c STR mcl executable [mcl]
-d STR mcxdeblast executable [mcxdeblast]
-g INT maximum number of clusters [50000]
-m STR makeblastdb executable [makeblastdb]
-r create R plots, requires R and ggplot2
-s dont split paralogs
-t INT translation table [11]
-z dont delete intermediate files
-v verbose output to STDOUT
-w print version and exit
-y add gene inference information to spreadsheet, doesnt work with -e
-h this help message
Example: Quickly generate a core gene alignment using 8 threads
roary -e --mafft -p 8 *.gff
For further info see: http://sanger-pathogens.github.io/Roary/

Here is the output of the actual roary run:

drwxr-xr-x 4 nnikolo1 zusers 4096 Oct 13 10:42 ..
-rw-rw-r-- 1 nnikolo1 zusers 53093 Oct 13 11:13 accessory_binary_genes.fa
-rw-rw-r-- 1 nnikolo1 zusers 453 Oct 13 11:13 accessory_binary_genes.fa.newick
-rw-rw-r-- 1 nnikolo1 zusers 545768 Oct 13 11:14 accessory_graph.dot
-rw-rw-r-- 1 nnikolo1 zusers 1181741 Oct 13 11:14 accessory.header.embl
-rw-rw-r-- 1 nnikolo1 zusers 1381819 Oct 13 11:14 accessory.tab
-rw-rw-r-- 1 nnikolo1 zusers 48 Oct 13 11:13 blast_identity_frequency.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 409236 Oct 13 11:13 clustered_proteins
-rw-rw-r-- 1 nnikolo1 zusers 664203 Oct 13 11:14 core_accessory_graph.dot
-rw-rw-r-- 1 nnikolo1 zusers 1253693 Oct 13 11:14 core_accessory.header.embl
-rw-rw-r-- 1 nnikolo1 zusers 1554420 Oct 13 11:14 core_accessory.tab
-rw-rw-r-- 1 nnikolo1 zusers 1537923 Oct 13 11:14 gene_presence_absence.csv
-rw-rw-r-- 1 nnikolo1 zusers 331951 Oct 13 11:14 gene_presence_absence.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 534 Oct 13 11:14 number_of_conserved_genes.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 650 Oct 13 11:14 number_of_genes_in_pan_genome.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 522 Oct 13 11:14 number_of_new_genes.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 650 Oct 13 11:14 number_of_unique_genes.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 201 Oct 13 11:14 summary_statistics.txt

Here is the log:

2016/10/13 11:13:55 Creating accessory binary gene presence and absence tree
2016/10/13 11:13:55 Running command: /app/Roary/build/fasttree/FastTree -fastest -nt accessory_binary_genes.fa > accessory_binary_genes.fa.newick
FastTree Version 2.1.8 SSE3
Alignment: accessory_binary_genes.fa
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Fastest+2nd +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.50
ML Model: Jukes-Cantor, CAT approximation with 20 rate categories
Initial topology in 0.03 seconds
Refining topology: 15 rounds ME-NNIs, 2 rounds ME-SPRs, 7 rounds ML-NNIs
0.26 seconds: ME NNI round 6 of 15, 1 of 11 splits ^M 0.47 seconds: ME NNI round 11 of 15, 1 of 11 splits ^MTotal branch-length 1.997 after 0.50 sec
0.60 seconds: ML NNI round 1 of 7, 1 of 11 splits ^MML-NNI round 1: LogLk = -29742.679 NNIs 2 max delta 38.57 Time 0.89
0.89 seconds: Site likelihoods with rate category 1 of 20 ^MSwitched to using 20 rate categories (CAT approximation)
Rate categories were divided by 0.751 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
0.99 seconds: ML NNI round 2 of 7, 1 of 11 splits ^MML-NNI round 2: LogLk = -29155.713 NNIs 0 max delta 0.00 Time 1.10
Turning off heuristics for final round of ML NNIs (converged)
1.10 seconds: ML NNI round 3 of 7, 1 of 11 splits ^MML-NNI round 3: LogLk = -29151.158 NNIs 0 max delta 0.00 Time 1.39 (final)
1.38 seconds: ML Lengths 1 of 11 splits ^MOptimize all lengths: LogLk = -29151.146 Time 1.48
Total time: 2.32 seconds Unique: 13/13 Bad splits: 0/10

What to do now? I would like to produce an output that I can use with raxml.

[andrewjpage]

Hi,
Everything looks fine. Could you try rerunning it with -e -n as parameters,
that should produce the core alignment

On 13 Oct 2016 17:56, "nikolay12" notifications@github.com wrote:

I just ran roary on a set of assemblies annotated by prokka. Got no error
messages but the core_gene_alignment.aln was missing from the output.

Here is the output of roary -a:

$ roary -a
Please cite Roary if you use any of the results it produces:
Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra
Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A.
Keane, Julian Parkhill,
"Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics,
2015 Nov 15;31(22):3691-3693
doi: http://doi.org/10.1093/bioinformatics/btv421
Pubmed: 26198102
2016/10/13 12:45:43 Looking for 'Rscript' - found /usr/bin/Rscript
2016/10/13 12:45:43 Determined Rscript version is 3.2
2016/10/13 12:45:43 Looking for 'awk' - found /bin/awk
2016/10/13 12:45:43 Looking for 'bedtools' - found
/app/Roary/build/bedtools2/bin/bedtools
2016/10/13 12:45:43 Determined bedtools version is 2.24
2016/10/13 12:45:43 Looking for 'blastp' - found
/app/Roary/build/ncbi-blast-2.2.30+/bin/blastp
2016/10/13 12:45:43 Determined blastp version is 2.2.30
2016/10/13 12:45:43 Looking for 'grep' - found /bin/grep
2016/10/13 12:45:43 Optional tool 'kraken' not found in your $PATH
2016/10/13 12:45:43 Optional tool 'kraken-report' not found in your $PATH
2016/10/13 12:45:43 Looking for 'mafft' - found
/app/Roary/build/mafft-7.271-without-extensions/build/bin/mafft
2016/10/13 12:45:43 Determined mafft version is 7.271
2016/10/13 12:45:43 Looking for 'makeblastdb' - found
/app/Roary/build/ncbi-blast-2.2.30+/bin/makeblastdb
2016/10/13 12:45:43 Determined makeblastdb version is 2.2.30
2016/10/13 12:45:43 Looking for 'mcl' - found /app/Roary/build/mcl-14-137/
src/shmcl/mcl
2016/10/13 12:45:43 Determined mcl version is 14-137
2016/10/13 12:45:43 Looking for 'parallel' - found
/app/Roary/build/parallel-20150522/src/parallel
2016/10/13 12:45:44 Determined parallel version is 20150522
2016/10/13 12:45:44 Looking for 'prank' - found /app/Roary/build/prank-msa-
master/src/prank
2016/10/13 12:45:44 Looking for 'sed' - found /bin/sed
2016/10/13 12:45:44 Looking for 'cd-hit' - found
/projects/jpc/london/software/cd-hit/v4.6.5/cd-hit
2016/10/13 12:45:44 Determined cd-hit version is 4.6
2016/10/13 12:45:44 Looking for 'FastTree' - found
/app/Roary/build/fasttree/FastTree
2016/10/13 12:45:44 Determined FastTree version is 2.1
2016/10/13 12:45:44 Roary version 1.006924
2016/10/13 12:45:44 Error: You need to provide at least 2 files to build a
pan genome
Usage: roary [options] *.gff
Options: -p INT number of threads [1]
-o STR clusters output filename [clustered_proteins]
-f STR output directory [.]
-e create a multiFASTA alignment of core genes using PRANK
-n fast core gene alignment with MAFFT, use with -e
-i minimum percentage identity for blastp [95]
-cd FLOAT percentage of isolates a gene must be in to be core [99]
-qc generate QC report with Kraken
-k STR path to Kraken database for QC, use with -qc
-a check dependancies and print versions
-b STR blastp executable [blastp]
-c STR mcl executable [mcl]
-d STR mcxdeblast executable [mcxdeblast]
-g INT maximum number of clusters [50000]
-m STR makeblastdb executable [makeblastdb]
-r create R plots, requires R and ggplot2
-s dont split paralogs
-t INT translation table [11]
-z dont delete intermediate files
-v verbose output to STDOUT
-w print version and exit
-y add gene inference information to spreadsheet, doesnt work with -e
-h this help message
Example: Quickly generate a core gene alignment using 8 threads
roary -e --mafft -p 8 *.gff
For further info see: http://sanger-pathogens.github.io/Roary/

Here is the output of the actual roary run:

drwxr-xr-x 4 nnikolo1 zusers 4096 Oct 13 10:42 ..
-rw-rw-r-- 1 nnikolo1 zusers 53093 Oct 13 11:13 accessory_binary_genes.fa
-rw-rw-r-- 1 nnikolo1 zusers 453 Oct 13 11:13 accessory_binary_genes.fa.
newick
-rw-rw-r-- 1 nnikolo1 zusers 545768 Oct 13 11:14 accessory_graph.dot
-rw-rw-r-- 1 nnikolo1 zusers 1181741 Oct 13 11:14 accessory.header.embl
-rw-rw-r-- 1 nnikolo1 zusers 1381819 Oct 13 11:14 accessory.tab
-rw-rw-r-- 1 nnikolo1 zusers 48 Oct 13 11:13 blast_identity_frequency.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 409236 Oct 13 11:13 clustered_proteins
-rw-rw-r-- 1 nnikolo1 zusers 664203 Oct 13 11:14 core_accessory_graph.dot
-rw-rw-r-- 1 nnikolo1 zusers 1253693 Oct 13 11:14 core_accessory.header.embl
-rw-rw-r-- 1 nnikolo1 zusers 1554420 Oct 13 11:14 core_accessory.tab
-rw-rw-r-- 1 nnikolo1 zusers 1537923 Oct 13 11:14 gene_presence_absence.csv
-rw-rw-r-- 1 nnikolo1 zusers 331951 Oct 13 11:14 gene_presence_absence.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 534 Oct 13 11:14 number_of_conserved_genes.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 650 Oct 13 11:14 number_of_genes_in_pan_genome.
Rtab
-rw-rw-r-- 1 nnikolo1 zusers 522 Oct 13 11:14 number_of_new_genes.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 650 Oct 13 11:14 number_of_unique_genes.Rtab
-rw-rw-r-- 1 nnikolo1 zusers 201 Oct 13 11:14 summary_statistics.txt

Here is the log:

2016/10/13 11:13:55 Creating accessory binary gene presence and absence tree
2016/10/13 11:13:55 Running command: /app/Roary/build/fasttree/FastTree
-fastest -nt accessory_binary_genes.fa > accessory_binary_genes.fa.newick
FastTree Version 2.1.8 SSE3
Alignment: accessory_binary_genes.fa
Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000
Search: Fastest+2nd +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.50
ML Model: Jukes-Cantor, CAT approximation with 20 rate categories
Initial topology in 0.03 seconds
Refining topology: 15 rounds ME-NNIs, 2 rounds ME-SPRs, 7 rounds ML-NNIs
0.26 seconds: ME NNI round 6 of 15, 1 of 11 splits ^M 0.47 seconds: ME NNI
round 11 of 15, 1 of 11 splits ^MTotal branch-length 1.997 after 0.50 sec
0.60 seconds: ML NNI round 1 of 7, 1 of 11 splits ^MML-NNI round 1: LogLk =
-29742.679 NNIs 2 max delta 38.57 Time 0.89
0.89 seconds: Site likelihoods with rate category 1 of 20 ^MSwitched to
using 20 rate categories (CAT approximation)
Rate categories were divided by 0.751 so that average rate = 1.0
CAT-based log-likelihoods may not be comparable across runs
Use -gamma for approximate but comparable Gamma(20) log-likelihoods
0.99 seconds: ML NNI round 2 of 7, 1 of 11 splits ^MML-NNI round 2: LogLk =
-29155.713 NNIs 0 max delta 0.00 Time 1.10
Turning off heuristics for final round of ML NNIs (converged)
1.10 seconds: ML NNI round 3 of 7, 1 of 11 splits ^MML-NNI round 3: LogLk =
-29151.158 NNIs 0 max delta 0.00 Time 1.39 (final)
1.38 seconds: ML Lengths 1 of 11 splits ^MOptimize all lengths: LogLk =
-29151.146 Time 1.48
Total time: 2.32 seconds Unique: 13/13 Bad splits: 0/10

What to do now? I would like to produce an output that I can use with raxml.

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[nikolay12]

Thanks. That was it - I ran roary without the "-e" and "-n" flags. When I re-ran it with these flags the aln file was generated.

[yihandqx]

Hi, Everything looks fine. Could you try rerunning it with -e -n as parameters, that should produce the core alignment

On 13 Oct 2016 17:56, "nikolay12" notifications@github.com wrote:

I just ran roary on a set of assemblies annotated by prokka. Got no error messages but the core_gene_alignment.aln was missing from the output.

Here is the output of roary -a:

$ roary -a Please cite Roary if you use any of the results it produces: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693 doi: http://doi.org/10.1093/bioinformatics/btv421 Pubmed: 26198102 2016/10/13 12:45:43 Looking for 'Rscript' - found /usr/bin/Rscript 2016/10/13 12:45:43 Determined Rscript version is 3.2 2016/10/13 12:45:43 Looking for 'awk' - found /bin/awk 2016/10/13 12:45:43 Looking for 'bedtools' - found /app/Roary/build/bedtools2/bin/bedtools 2016/10/13 12:45:43 Determined bedtools version is 2.24 2016/10/13 12:45:43 Looking for 'blastp' - found /app/Roary/build/ncbi-blast-2.2.30+/bin/blastp 2016/10/13 12:45:43 Determined blastp version is 2.2.30 2016/10/13 12:45:43 Looking for 'grep' - found /bin/grep 2016/10/13 12:45:43 Optional tool 'kraken' not found in your $PATH 2016/10/13 12:45:43 Optional tool 'kraken-report' not found in your $PATH 2016/10/13 12:45:43 Looking for 'mafft' - found /app/Roary/build/mafft-7.271-without-extensions/build/bin/mafft 2016/10/13 12:45:43 Determined mafft version is 7.271 2016/10/13 12:45:43 Looking for 'makeblastdb' - found /app/Roary/build/ncbi-blast-2.2.30+/bin/makeblastdb 2016/10/13 12:45:43 Determined makeblastdb version is 2.2.30 2016/10/13 12:45:43 Looking for 'mcl' - found /app/Roary/build/mcl-14-137/ src/shmcl/mcl 2016/10/13 12:45:43 Determined mcl version is 14-137 2016/10/13 12:45:43 Looking for 'parallel' - found /app/Roary/build/parallel-20150522/src/parallel 2016/10/13 12:45:44 Determined parallel version is 20150522 2016/10/13 12:45:44 Looking for 'prank' - found /app/Roary/build/prank-msa- master/src/prank 2016/10/13 12:45:44 Looking for 'sed' - found /bin/sed 2016/10/13 12:45:44 Looking for 'cd-hit' - found /projects/jpc/london/software/cd-hit/v4.6.5/cd-hit 2016/10/13 12:45:44 Determined cd-hit version is 4.6 2016/10/13 12:45:44 Looking for 'FastTree' - found /app/Roary/build/fasttree/FastTree 2016/10/13 12:45:44 Determined FastTree version is 2.1 2016/10/13 12:45:44 Roary version 1.006924 2016/10/13 12:45:44 Error: You need to provide at least 2 files to build a pan genome Usage: roary [options] *.gff Options: -p INT number of threads [1] -o STR clusters output filename [clustered_proteins] -f STR output directory [.] -e create a multiFASTA alignment of core genes using PRANK -n fast core gene alignment with MAFFT, use with -e -i minimum percentage identity for blastp [95] -cd FLOAT percentage of isolates a gene must be in to be core [99] -qc generate QC report with Kraken -k STR path to Kraken database for QC, use with -qc -a check dependancies and print versions -b STR blastp executable [blastp] -c STR mcl executable [mcl] -d STR mcxdeblast executable [mcxdeblast] -g INT maximum number of clusters [50000] -m STR makeblastdb executable [makeblastdb] -r create R plots, requires R and ggplot2 -s dont split paralogs -t INT translation table [11] -z dont delete intermediate files -v verbose output to STDOUT -w print version and exit -y add gene inference information to spreadsheet, doesnt work with -e -h this help message Example: Quickly generate a core gene alignment using 8 threads roary -e --mafft -p 8 *.gff For further info see: http://sanger-pathogens.github.io/Roary/

Here is the output of the actual roary run:

drwxr-xr-x 4 nnikolo1 zusers 4096 Oct 13 10:42 .. -rw-rw-r-- 1 nnikolo1 zusers 53093 Oct 13 11:13 accessory_binary_genes.fa -rw-rw-r-- 1 nnikolo1 zusers 453 Oct 13 11:13 accessory_binary_genes.fa. newick -rw-rw-r-- 1 nnikolo1 zusers 545768 Oct 13 11:14 accessory_graph.dot -rw-rw-r-- 1 nnikolo1 zusers 1181741 Oct 13 11:14 accessory.header.embl -rw-rw-r-- 1 nnikolo1 zusers 1381819 Oct 13 11:14 accessory.tab -rw-rw-r-- 1 nnikolo1 zusers 48 Oct 13 11:13 blast_identity_frequency.Rtab -rw-rw-r-- 1 nnikolo1 zusers 409236 Oct 13 11:13 clustered_proteins -rw-rw-r-- 1 nnikolo1 zusers 664203 Oct 13 11:14 core_accessory_graph.dot -rw-rw-r-- 1 nnikolo1 zusers 1253693 Oct 13 11:14 core_accessory.header.embl -rw-rw-r-- 1 nnikolo1 zusers 1554420 Oct 13 11:14 core_accessory.tab -rw-rw-r-- 1 nnikolo1 zusers 1537923 Oct 13 11:14 gene_presence_absence.csv -rw-rw-r-- 1 nnikolo1 zusers 331951 Oct 13 11:14 gene_presence_absence.Rtab -rw-rw-r-- 1 nnikolo1 zusers 534 Oct 13 11:14 number_of_conserved_genes.Rtab -rw-rw-r-- 1 nnikolo1 zusers 650 Oct 13 11:14 number_of_genes_in_pan_genome. Rtab -rw-rw-r-- 1 nnikolo1 zusers 522 Oct 13 11:14 number_of_new_genes.Rtab -rw-rw-r-- 1 nnikolo1 zusers 650 Oct 13 11:14 number_of_unique_genes.Rtab -rw-rw-r-- 1 nnikolo1 zusers 201 Oct 13 11:14 summary_statistics.txt

Here is the log:

2016/10/13 11:13:55 Creating accessory binary gene presence and absence tree 2016/10/13 11:13:55 Running command: /app/Roary/build/fasttree/FastTree -fastest -nt accessory_binary_genes.fa > accessory_binary_genes.fa.newick FastTree Version 2.1.8 SSE3 Alignment: accessory_binary_genes.fa Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000 Search: Fastest+2nd +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 TopHits: 1.00*sqrtN close=default refresh=0.50 ML Model: Jukes-Cantor, CAT approximation with 20 rate categories Initial topology in 0.03 seconds Refining topology: 15 rounds ME-NNIs, 2 rounds ME-SPRs, 7 rounds ML-NNIs 0.26 seconds: ME NNI round 6 of 15, 1 of 11 splits ^M 0.47 seconds: ME NNI round 11 of 15, 1 of 11 splits ^MTotal branch-length 1.997 after 0.50 sec 0.60 seconds: ML NNI round 1 of 7, 1 of 11 splits ^MML-NNI round 1: LogLk = -29742.679 NNIs 2 max delta 38.57 Time 0.89 0.89 seconds: Site likelihoods with rate category 1 of 20 ^MSwitched to using 20 rate categories (CAT approximation) Rate categories were divided by 0.751 so that average rate = 1.0 CAT-based log-likelihoods may not be comparable across runs Use -gamma for approximate but comparable Gamma(20) log-likelihoods 0.99 seconds: ML NNI round 2 of 7, 1 of 11 splits ^MML-NNI round 2: LogLk = -29155.713 NNIs 0 max delta 0.00 Time 1.10 Turning off heuristics for final round of ML NNIs (converged) 1.10 seconds: ML NNI round 3 of 7, 1 of 11 splits ^MML-NNI round 3: LogLk = -29151.158 NNIs 0 max delta 0.00 Time 1.39 (final) 1.38 seconds: ML Lengths 1 of 11 splits ^MOptimize all lengths: LogLk = -29151.146 Time 1.48 Total time: 2.32 seconds Unique: 13/13 Bad splits: 0/10

What to do now? I would like to produce an output that I can use with raxml.

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Hi, I have run roary with -e -n flags but still didn't get the core_gene_alignment.aln file. The number of my input genomes is about 3,500, is that probably the reason why the file was missing? The files in the output dir as follows:
accessory_binary_genes.fa
accessory_binary_genes.fa.newick
_accessory_clusters
_accessory_clusters.clstr
accessory_graph.dot
accessory.header.embl
accessory.tab
Ah_2bXxwwK
b33Q5wBpOQ
bBsogkRUyU
bDWuGOIHN0
blast_identity_frequency.Rtab
_blast_results
_clustered
_clustered.clstr
clustered_proteins
_combined_files
_combined_files.groups
core_accessory_graph.dot
core_accessory.header.embl
core_accessory.tab
gene_presence_absence.csv
gene_presence_absence.Rtab
_inflated_mcl_groups
_inflated_unsplit_mcl_groups
JidzILfCGx
_labeled_mcl_groups
number_of_conserved_genes.Rtab
number_of_genes_in_pan_genome.Rtab
number_of_new_genes.Rtab
number_of_unique_genes.Rtab
pan_genome_reference.fa
pan_genome_sequences
QtL893WRo2
sP7T9F1EOg
summary_statistics.txt
_uninflated_mcl_groups