Datamonkey Adaptive Evolution Server

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3232115.new-silverback

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Standard Error Message

[2K
Working on site pattern 1/61 in partition 1[2K
Working on site pattern 2/61 in partition 1[2K
Working on site pattern 3/61 in partition 1[2K
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Working on site pattern 59/61 in partition 1[2K
Working on site pattern 60/61 in partition 1[2K
Working on site pattern 61/61 in partition 1[2K
                                            [2K
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


HYPHYMPI terminated.
Error:
HyPhy killed by signal 15


[n6:72321] 31 more processes have sent help message help-mpi-api.txt / mpi-abort
[n6:72321] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[warn] Epoll MOD(1) on fd 24 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 24 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 25 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 25 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 28 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 28 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 30 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 30 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 40 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 40 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 32 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 32 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 36 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 36 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 48 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 48 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 46 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 46 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 38 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 38 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 44 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 44 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 42 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 42 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 52 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 52 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 56 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 56 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 50 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 50 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 58 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 58 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 54 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 54 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 26 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 26 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 60 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 60 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 76 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 76 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 72 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 72 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 68 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 68 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 70 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 70 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 78 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 78 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 62 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 62 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 66 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 66 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 74 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 74 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 64 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 64 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 82 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 82 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 80 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 80 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor
[warn] Epoll MOD(1) on fd 84 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 84 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor

Analysis Description -------------------- MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and uses a likelihood ratio test to determine if β+ > α at a site. The estimates aggregate information over a proportion of branches at a site, so the signal is derived from episodic diversification, which is a combination of strength of selection [effect size] and the proportion of the tree affected. A subset of branches can be selected for testing as well, in which case an additional (nuisance) parameter will be inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported for recombination - aware analysis. Version 3.0 adds a different format for ancestral state reconstruction, branch-site posterior storage, and site-level heterogeneity testing. Version 4 adds support for multiple hits and more than 2 rate classes on omega, as well as site-level imputation option - __Requirements__: in-frame codon alignment and a phylogenetic tree - __Citation__: Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764. - __Written by__: Sergei L. Kosakovsky Pond, Steven Weaver - __Contact Information__: spond@temple.edu - __Analysis Version__: 4.0 >code => Universal >Loaded a multiple sequence alignment with **29** sequences, **510** codons, and **6** partitions from `/home/datamonkey/datamonkey-js-server/production/app/meme/output/65956336ba6f2072cc42574f` >branches => All >Select the p-value threshold to use when testing for selection (permissible range = [0,1], default value = 0.1): >pvalue => 0.1 >[Advanced setting, will result in MUCH SLOWER run time] Perform parametric bootstrap resampling to derive site-level null LRT distributions up to this many replicates per site. Recommended use for small to medium (<30 sequences) datasets (permissible range = [0,1000], default value = 50, integer): >resample => 0 The number omega rate classes to include in the model [2 is the strongly recommended default] (permissible range = [2,4], default value = 2, integer): >rates => 2 >multiple-hits => None >impute-states => No >precision => standard ### Branches to include in the MEME analysis Selected 55 branches to include in the MEME analysis: `MK448824_1_CDS_0063_ENDOLYSIN, MK448712_1_CDS_0028_ENDOLYSIN, NODE19, DQ386162_1_CDS_0019_ENDOLYSIN, NODE18, MT430910_1_CDS_0024_ENDOLYSIN, NODE17, KR153145_1_CDS_0019_ENDOLYSIN, NODE16, MH892358_1_CDS_0022_ENDOLYSIN, NODE15, MH937482_1_CDS_0021_ENDOLYSIN, NODE14, NC_070693_1_CDS_0022_ENDOLYSIN, NODE13, NC_070664_1_CDS_0022_ENDOLYSIN, NODE12, NC_071075_1_CDS_0024_ENDOLYSIN, NODE11, MK448933_1_CDS_0072_ENDOLYSIN, NODE10, MK448837_1_CDS_0053_ENDOLYSIN, JX409894_1_CDS_0017_ENDOLYSIN, JX409895_1_CDS_0041_ENDOLYSIN, NODE33, NODE31, NODE9, MH853355_1_CDS_0038_ENDOLYSIN, MH853358_1_CDS_0038_ENDOLYSIN, NODE38, MH853356_2_CDS_0024_ENDOLYSIN, NODE37, OQ633473_1_CDS_0060_ENDOLYSIN, NODE36, NODE8, MK448851_1_CDS_0065_ENDOLYSIN, NODE7, MK448669_1_CDS_0054_ENDOLYSIN, MK448971_1_CDS_0065_ENDOLYSIN, NODE44, NODE6, MK448956_1_CDS_0062_ENDOLYSIN, MK448796_1_CDS_0080_ENDOLYSIN, NODE47, NODE5, MK448952_1_CDS_0050_ENDOLYSIN, NODE4, MK448696_1_CDS_0052_ENDOLYSIN, NODE3, MK448766_1_CDS_0050_ENDOLYSIN, NODE2, MK448961_1_CDS_0048_ENDOLYSIN, NODE1, MK448775_1_CDS_0061_ENDOLYSIN, MK448953_1_CDS_0061_ENDOLYSIN` Selected 55 branches to include in the MEME analysis: `MK448824_1_CDS_0063_ENDOLYSIN, MK448712_1_CDS_0028_ENDOLYSIN, NODE13, DQ386162_1_CDS_0019_ENDOLYSIN, NODE12, MT430910_1_CDS_0024_ENDOLYSIN, NODE11, KR153145_1_CDS_0019_ENDOLYSIN, NODE10, MH892358_1_CDS_0022_ENDOLYSIN, NODE9, MH937482_1_CDS_0021_ENDOLYSIN, NODE8, NC_070693_1_CDS_0022_ENDOLYSIN, NODE7, NC_070664_1_CDS_0022_ENDOLYSIN, NODE6, NC_071075_1_CDS_0024_ENDOLYSIN, NODE5, MK448933_1_CDS_0072_ENDOLYSIN, NODE4, MK448837_1_CDS_0053_ENDOLYSIN, MH853355_1_CDS_0038_ENDOLYSIN, MH853358_1_CDS_0038_ENDOLYSIN, NODE30, MK448956_1_CDS_0062_ENDOLYSIN, MH853356_2_CDS_0024_ENDOLYSIN, NODE33, NODE29, OQ633473_1_CDS_0060_ENDOLYSIN, NODE28, NODE26, JX409895_1_CDS_0041_ENDOLYSIN, NODE25, NODE3, JX409894_1_CDS_0017_ENDOLYSIN, MK448796_1_CDS_0080_ENDOLYSIN, NODE40, MK448669_1_CDS_0054_ENDOLYSIN, MK448971_1_CDS_0065_ENDOLYSIN, NODE43, NODE39, MK448851_1_CDS_0065_ENDOLYSIN, NODE38, NODE2, MK448775_1_CDS_0061_ENDOLYSIN, NODE1, MK448952_1_CDS_0050_ENDOLYSIN, MK448961_1_CDS_0048_ENDOLYSIN, NODE50, MK448696_1_CDS_0052_ENDOLYSIN, NODE49, MK448766_1_CDS_0050_ENDOLYSIN, NODE48, MK448953_1_CDS_0061_ENDOLYSIN` Selected 55 branches to include in the MEME analysis: `MK448824_1_CDS_0063_ENDOLYSIN, MK448712_1_CDS_0028_ENDOLYSIN, NODE13, DQ386162_1_CDS_0019_ENDOLYSIN, MT430910_1_CDS_0024_ENDOLYSIN, KR153145_1_CDS_0019_ENDOLYSIN, NODE19, NODE17, MH892358_1_CDS_0022_ENDOLYSIN, MH937482_1_CDS_0021_ENDOLYSIN, NODE24, NC_070693_1_CDS_0022_ENDOLYSIN, NC_070664_1_CDS_0022_ENDOLYSIN, NODE27, NODE23, NC_071075_1_CDS_0024_ENDOLYSIN, NODE22, NODE16, NODE12, MK448933_1_CDS_0072_ENDOLYSIN, NODE11, MK448837_1_CDS_0053_ENDOLYSIN, MH853355_1_CDS_0038_ENDOLYSIN, MH853358_1_CDS_0038_ENDOLYSIN, NODE35, NODE33, OQ633473_1_CDS_0060_ENDOLYSIN, NODE32, NODE10, JX409894_1_CDS_0017_ENDOLYSIN, JX409895_1_CDS_0041_ENDOLYSIN, NODE39, NODE9, MK448956_1_CDS_0062_ENDOLYSIN, MH853356_2_CDS_0024_ENDOLYSIN, NODE42, NODE8, MK448851_1_CDS_0065_ENDOLYSIN, NODE7, MK448669_1_CDS_0054_ENDOLYSIN, NODE6, MK448971_1_CDS_0065_ENDOLYSIN, NODE5, MK448796_1_CDS_0080_ENDOLYSIN, NODE4, MK448766_1_CDS_0050_ENDOLYSIN, NODE3, MK448775_1_CDS_0061_ENDOLYSIN, NODE2, MK448953_1_CDS_0061_ENDOLYSIN, NODE1, MK448952_1_CDS_0050_ENDOLYSIN, MK448696_1_CDS_0052_ENDOLYSIN, NODE52, MK448961_1_CDS_0048_ENDOLYSIN` Selected 55 branches to include in the MEME analysis: `MK448824_1_CDS_0063_ENDOLYSIN, MH892358_1_CDS_0022_ENDOLYSIN, MH937482_1_CDS_0021_ENDOLYSIN, NC_070693_1_CDS_0022_ENDOLYSIN, NODE17, NC_070664_1_CDS_0022_ENDOLYSIN, NODE16, NC_071075_1_CDS_0024_ENDOLYSIN, NODE15, NODE13, NODE11, MK448712_1_CDS_0028_ENDOLYSIN, NODE10, DQ386162_1_CDS_0019_ENDOLYSIN, KR153145_1_CDS_0019_ENDOLYSIN, NODE24, MT430910_1_CDS_0024_ENDOLYSIN, NODE23, NODE9, MK448933_1_CDS_0072_ENDOLYSIN, NODE8, JX409894_1_CDS_0017_ENDOLYSIN, JX409895_1_CDS_0041_ENDOLYSIN, NODE31, OQ633473_1_CDS_0060_ENDOLYSIN, NODE30, MH853355_1_CDS_0038_ENDOLYSIN, MH853358_1_CDS_0038_ENDOLYSIN, NODE35, NODE29, NODE7, MK448796_1_CDS_0080_ENDOLYSIN, NODE6, MK448837_1_CDS_0053_ENDOLYSIN, MK448956_1_CDS_0062_ENDOLYSIN, NODE39, NODE5, MK448669_1_CDS_0054_ENDOLYSIN, MK448971_1_CDS_0065_ENDOLYSIN, NODE42, NODE4, MH853356_2_CDS_0024_ENDOLYSIN, MK448851_1_CDS_0065_ENDOLYSIN, NODE45, NODE3, MK448952_1_CDS_0050_ENDOLYSIN, NODE2, MK448961_1_CDS_0048_ENDOLYSIN, NODE1, MK448696_1_CDS_0052_ENDOLYSIN, MK448766_1_CDS_0050_ENDOLYSIN, NODE50, MK448775_1_CDS_0061_ENDOLYSIN, MK448953_1_CDS_0061_ENDOLYSIN, NODE53` Selected 55 branches to include in the MEME analysis: `MK448824_1_CDS_0063_ENDOLYSIN, MK448712_1_CDS_0028_ENDOLYSIN, NODE11, DQ386162_1_CDS_0019_ENDOLYSIN, MT430910_1_CDS_0024_ENDOLYSIN, NODE15, KR153145_1_CDS_0019_ENDOLYSIN, NODE14, NODE10, MH892358_1_CDS_0022_ENDOLYSIN, MH937482_1_CDS_0021_ENDOLYSIN, NC_071075_1_CDS_0024_ENDOLYSIN, NODE22, NC_070693_1_CDS_0022_ENDOLYSIN, NC_070664_1_CDS_0022_ENDOLYSIN, NODE25, NODE21, NODE19, NODE9, MK448933_1_CDS_0072_ENDOLYSIN, NODE8, OQ633473_1_CDS_0060_ENDOLYSIN, MK448796_1_CDS_0080_ENDOLYSIN, NODE29, NODE7, JX409894_1_CDS_0017_ENDOLYSIN, JX409895_1_CDS_0041_ENDOLYSIN, NODE35, MH853355_1_CDS_0038_ENDOLYSIN, NODE34, MH853358_1_CDS_0038_ENDOLYSIN, NODE33, MK448851_1_CDS_0065_ENDOLYSIN, NODE32, NODE6, MK448837_1_CDS_0053_ENDOLYSIN, MH853356_2_CDS_0024_ENDOLYSIN, NODE44, MK448956_1_CDS_0062_ENDOLYSIN, NODE43, MK448669_1_CDS_0054_ENDOLYSIN, NODE42, MK448971_1_CDS_0065_ENDOLYSIN, NODE41, NODE5, MK448766_1_CDS_0050_ENDOLYSIN, NODE4, MK448952_1_CDS_0050_ENDOLYSIN, NODE3, MK448696_1_CDS_0052_ENDOLYSIN, NODE2, MK448775_1_CDS_0061_ENDOLYSIN, NODE1, MK448953_1_CDS_0061_ENDOLYSIN, MK448961_1_CDS_0048_ENDOLYSIN` Selected 55 branches to include in the MEME analysis: `MK448824_1_CDS_0063_ENDOLYSIN, MK448712_1_CDS_0028_ENDOLYSIN, NODE12, DQ386162_1_CDS_0019_ENDOLYSIN, MT430910_1_CDS_0024_ENDOLYSIN, KR153145_1_CDS_0019_ENDOLYSIN, NODE18, NODE16, MH892358_1_CDS_0022_ENDOLYSIN, MH937482_1_CDS_0021_ENDOLYSIN, NC_070664_1_CDS_0022_ENDOLYSIN, NODE25, NC_071075_1_CDS_0024_ENDOLYSIN, NODE24, NC_070693_1_CDS_0022_ENDOLYSIN, NODE23, NODE21, NODE15, NODE11, MK448933_1_CDS_0072_ENDOLYSIN, NODE10, OQ633473_1_CDS_0060_ENDOLYSIN, NODE9, MK448956_1_CDS_0062_ENDOLYSIN, NODE8, MK448837_1_CDS_0053_ENDOLYSIN, NODE7, JX409894_1_CDS_0017_ENDOLYSIN, JX409895_1_CDS_0041_ENDOLYSIN, NODE37, MH853358_1_CDS_0038_ENDOLYSIN, NODE36, MH853355_1_CDS_0038_ENDOLYSIN, NODE35, MK448851_1_CDS_0065_ENDOLYSIN, NODE34, NODE6, MK448796_1_CDS_0080_ENDOLYSIN, NODE5, MH853356_2_CDS_0024_ENDOLYSIN, MK448971_1_CDS_0065_ENDOLYSIN, NODE45, MK448669_1_CDS_0054_ENDOLYSIN, NODE44, NODE4, MK448952_1_CDS_0050_ENDOLYSIN, MK448696_1_CDS_0052_ENDOLYSIN, NODE49, NODE3, MK448766_1_CDS_0050_ENDOLYSIN, NODE2, MK448775_1_CDS_0061_ENDOLYSIN, NODE1, MK448953_1_CDS_0061_ENDOLYSIN, MK448961_1_CDS_0048_ENDOLYSIN` ### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model >kill-zero-lengths => Yes ### Deleted 8 zero-length internal branches: `NODE1, NODE2, NODE3, NODE36, NODE38, NODE4, NODE44, NODE47` Deleted 6 zero-length internal branches: `NODE1, NODE30, NODE33, NODE48, NODE49, NODE50` Deleted 6 zero-length internal branches: `NODE1, NODE2, NODE24, NODE3, NODE35, NODE52` Deleted 10 zero-length internal branches: `NODE1, NODE16, NODE17, NODE30, NODE31, NODE35, NODE39, NODE42, NODE50, NODE53` Deleted 8 zero-length internal branches: `NODE1, NODE2, NODE22, NODE3, NODE34, NODE35, NODE4, NODE6` Deleted 8 zero-length internal branches: `NODE1, NODE18, NODE2, NODE24, NODE25, NODE36, NODE37, NODE49` * Log(L) = -10700.46, AIC-c = 22082.12 (338 estimated parameters) * 6 partitions. Total tree length by partition (subs/site) 291.742, 108.306, 2.493, 2.251, 1.871, 4.516 ### Obtaining the global omega estimate based on relative GTR branch lengths and nucleotide substitution biases * Log(L) = -9765.53, AIC-c = 20141.44 (299 estimated parameters) * 6 partitions. Total tree length by partition (subs/site) 356.259, 136.711, 3.207, 3.113, 2.486, 7.277 * non-synonymous/synonymous rate ratio for *test* = 0.1350 >full-model => Yes Only analyze sites whose 1-based indices match the following list (null to skip) : >limit-to-sites => null For sites whose 1-based indices match the following list, write out likelihood function snapshots (null string to skip) : >save-lf-for-sites => null ### Improving branch lengths, nucleotide substitution biases, and global dN/dS ratios under a full codon model * Log(L) = -9606.21 * Log(L) = -9606.21, AIC-c = 19822.81 (299 estimated parameters) * 6 partitions. Total tree length by partition (subs/site) 18.516, 18.868, 5.582, 4.809, 3.452, 14.027 * non-synonymous/synonymous rate ratio for *test* = 0.0614 Error: Master node received an error:<'constant' operation 'X'>, where 'X' is not a number. constant = 0 'X' = null While computing: meme.site_beta_nuisance*null Function call stack 1 : Tree meme.site_tree_fel = ((MK448953_1_CDS_0061_ENDOLYSIN,((((((((((((MK448824_1_CDS_0063_ENDOLYSIN,MK448712_1_CDS_0028_ENDOLYSIN)NODE13,DQ386162_1_CDS_0019_ENDOLYSIN)NODE12,MT430910_1_CDS_0024_ENDOLYSIN)NODE11,KR153145_1_CDS_0019_ENDOLYSIN)NODE10,MH892358_1_CDS_0022_ENDOLYSIN)NODE9,MH937482_1_CDS_0021_ENDOLYSIN)NODE8,NC_070693_1_CDS_0022_ENDOLYSIN)NODE7,NC_070664_1_CDS_0022_ENDOLYSIN)NODE6,NC_071075_1_CDS_0024_ENDOLYSIN)NODE5,MK448933_1_CDS_0072_ENDOLYSIN)NODE4,((MK448837_1_CDS_0053_ENDOLYSIN,((MH853355_1_CDS_0038_ENDOLYSIN,MH853358_1_CDS_0038_ENDOLYSIN,MK448956_1_CDS_0062_ENDOLYSIN,MH853356_2_CDS_0024_ENDOLYSIN)NODE29,OQ633473_1_CDS_0060_ENDOLYSIN)NODE28)NODE26,JX409895_1_CDS_0041_ENDOLYSIN)NODE25)NODE3,(((JX409894_1_CDS_0017_ENDOLYSIN,MK448796_1_CDS_0080_ENDOLYSIN)NODE40,(MK448669_1_CDS_0054_ENDOLYSIN,MK448971_1_CDS_0065_ENDOLYSIN)NODE43)NODE39,MK448851_1_CDS_0065_ENDOLYSIN)NODE38)NODE2,MK448775_1_CDS_0061_ENDOLYSIN,MK448766_1_CDS_0050_ENDOLYSIN,MK448696_1_CDS_0052_ENDOLYSIN,MK448952_1_CDS_0050_ENDOLYSIN,MK448961_1_CDS_0048_ENDOLYSIN)); Keyword arguments: { "tree":"/home/datamonkey/datamonkey-js-server/production/app/meme/output/65956336ba6f2072cc42574f.tre" } ------- 2 : ExecuteCommands("UseModel ("+model.ApplyModelToTree.modelID[terms.id]+"); Tree `id` = "+tree["string"]+"; ", /home/datamonkey/datamonkey-js-server/production/app/meme/../../.hyphy/res/TemplateBatchFiles/libv3/models/); Keyword arguments: { "tree":"/home/datamonkey/datamonkey-js-server/production/app/meme/output/65956336ba6f2072cc42574f.tre" } ------- 3 : model.ApplyModelToTree("meme.site_tree_fel",meme.trees[meme.partition_index],{terms.default:meme.site.background_fel},None); Keyword arguments: { "tree":"/home/datamonkey/datamonkey-js-server/production/app/meme/output/65956336ba6f2072cc42574f.tre" } -------

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