Cafe5 hanging with no output

[ryvan1021]

Similar to the issue posted in #58. I have tried removing any orthogroups where a gene only occurs in one species, and I've also tried a more extreme case where I removed a group if any species did not have an ortholog.

stdout for both cases basically looks like this:

(base) bash-4.2$ CAFE5/bin/cafe5 -i orthogroups_no_zeros.tsv -t SpeciesTree_rooted.txt

Command line: CAFE5/bin/cafe5 -i orthogroups_no_zeros.tsv -t SpeciesTree_rooted.txt

Filtering families not present at the root from: 4425 to 4425

No root family size distribution specified, using uniform distribution

Optimizer strategy: Nelder-Mead with similarity cutoff
Iterations: 300
Expansion: 2
Reflection: 1

Starting Search for Initial Parameter Values
Lambda: 0.88360296837672

The results dir is also empty.
I'm running this on a cluster with 48 cores/96 threads.

My orthogroups file contains 25 species:

Desc    Orthogroup      aquilegia       arabidopsis     buxus   carica  corydalis       glycine gossypium       grevillea       lupinus macadamia       maize   marchantia      medicago        nelumbo oryza   paspalum        physcomitrium   populus protea  selaginella     setaria solanum telopea tetracentron    theobroma       Total
(null)  OG0000000       71      126     48      71      66      298     395     72      165     88      184     19      154     98      110     133     57      169     101     39      153     126     93      75      98      3009
(null)  OG0000001       65      128     98      77      66      257     360     103     153     107     180     12      128     115     80      99      42      163     111     24      99      102     122     131     125     2947
(null)  OG0000002       43      52      15      29      34      91      135     30      69      40      63      4       65      45      65      73      24      58      52      37      68      49      37      22      66      1266
(null)  OG0000004       27      45      21      21      21      101     156     28      61      33      74      2       43      45      32      43      59      62      40      26      37      32      47      26      35      1117
(null)  OG0000009       50      30      34      23      15      36      75      45      11      28      33      5       58      17      39      37      6       53      43      64      46      29      34      27      33      871
(null)  OG0000012       26      30      14      22      19      86      102     17      50      24      49      2       27      29      28      43      12      52      29      3       41      27      28      17      32      809
(null)  OG0000014       25      37      8       20      28      107     117     5       38      7       15      3       89      39      8       8       25      35      7       15      12      49      12      20      35      764
(null)  OG0000015       18      40      21      14      11      51      88      27      28      24      53      1       32      26      18      33      46      53      20      5       29      20      30      31      27      746
(null)  OG0000016       17      21      40      14      16      68      59      18      31      26      42      7       54      30      36      38      8       26      24      27      43      29      27      18      23      742
(null)  OG0000017       21      25      21      82      17      48      71      22      42      26      32      1       58      17      17      16      4       50      33      9       13      23      32      19      29      728
(null)  OG0000019       23      37      20      17      19      45      69      24      39      27      30      21      24      27      15      22      35      40      22      13      18      19      29      31      23      689
(null)  OG0000022       16      40      17      13      8       73      106     17      35      15      42      4       12      27      20      22      20      51      16      5       21      20      27      28      27      682
(null)  OG0000023       28      34      44      22      4       30      64      4       10      10      40      20      23      10      34      56      35      40      6       29      33      12      6       58      27      679
(null)  OG0000024       38      11      13      16      8       62      69      15      22      25      39      15      37      18      23      33      38      29      5       26      19      25      32      19      39      676
(null)  OG0000025       21      28      27      13      18      44      48      38      23      35      21      36      29      22      10      16      27      31      39      14      13      25      40      30      28      676

Any ideas on what I should do? Should I try removing the Total column? Also, what is the typical runtime for an analysis?

Thanks!

[ryvan1021]

Okay, it looks like I was able to resolve the issue by removing the total column and reinstalling gcc and linking to my bashrc file in my personal directory on the cluster I'm using.

Not sure why it was so complicated for me, but yeah. I think the issue is resolved now. It's calculating new Lambdas instead of hanging.

I do get this warning:

OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.

But the script is at least running now. Will update if program has an issue or something.

[benfulton]

We generally don't test with more than 16 cores (although with the size of machines these days we really should). With 25 species I would expect it to finish in a few minutes - if you were in the 1000 species range I would give it a few hours.

The OpenBLAS warning indicates that your OpenBLAS library doesn't support OpenMP. You might ask your cluster administrators to build you a version that does.

[xiongqian123456789]

Hello,

I have been met the same question with running cafe5 in the 64X Linux as follows:

cafe5 -i gene.counts.tab -t tree.withTime.nwk -p -o singlelambda --cores 30

My orthogroups file contains 33 species:
Desc Orthogroup A024 A026 A114 A116 A119 A128 D2005012428 D2010028359 D2010028360 D2010028364 D2010028368 D2010028373 D21050
null OG0000032 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 391 0 0 0
null OG0000281 0 120 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
null OG0000546 0 0 0 0 0 0 0 0 0 0 51 0 0 0 0 0 52 0 0
null OG0000555 0 0 0 0 0 0 0 0 0 0 0 0 81 0 0 0 0 0 0
null OG0001612 0 0 0 0 0 0 0 0 0 0 0 0 62 0 0 0 0 0 0
null OG0001850 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 59 0 0 0
null OG0001981 0 57 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
null OG0002057 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
null OG0002067 0 0 0 0 0 0 0 0 0 0 28 0 0 0 0 0 29 0 0
null OG0002944 0 0 0 0 0 0 0 0 25 0 0 0 0 0 0 0 0 24 0
null OG0003412 0 0 0 0 0 0 0 0 0 0 0 0 41 0 0 0 0 0 0
null OG0005307 0 0 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
null OG0005320 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
null OG0005321 0 0 0 0 0 0 0 0 0 0 19 0 0 0 0 0 20 0 0
null OG0005323 0 0 0 0 0 0 0 0 0 0 0 0 38 0 1 0 0 0 0
null OG0006093 0 0 1 0 0 36 0 0 0 0 0 0 0 0 0 0 0 0 0
null OG0006103 0 0 0 0 0 0 0 0 0 0 0 0 26 0 0 0 0 0 0
null OG0006531 0 0 0 1 0 0 0 0 0 0 0 0 35 0 0 0 0 0 0
null OG0006543 0 0 0 0 32 0 0 0 0 0 0 0 0 4 0 0 0 0 0
null OG0006545 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0
null OG0007399 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 17 0 0

The tree file is as following:
(D2105061946:30.941513,(D2010028360:30.074359,(D2203116313:26.336172,((D2105061943:0.236010,D2010028368:0.236010):23.611966,((GCA_014905635:16.532699,((A128:7.552227,(D2203116301:3.413674,D2105061942:3.413674):4.138553):6.167753,((A116:3.722526,D2210145207:3.722526):7.061285,((D2105061934:0.824385,A119:0.824385):6.393303,(GCA_014080715:4.926906,(D2010028359:3.659405,(D2105061941:1.738637,(GCA_030272055:1.327122,(D2005012428:0.942355,(GCA_030272155:0.514751,D2105061958:0.514751):0.427604):0.384767):0.411515):1.920768):1.267501):2.290783):3.566122):2.936170):2.812719):4.308440,((D2210145220:9.071671,((A024:0.196958,D2010028373:0.196958):5.203627,(D2105061930:2.509245,D2210145217:2.509245):2.891341):3.671086):8.465931,((A026:6.155852,A114:6.155852):8.562749,((GCA_000143455:6.002031,GCA_002284615:6.002031):5.997453,((D2010028364:4.552009,D2203116310:4.552009):3.552351,(GCA_003203535:4.863656,GCA_025201885:4.863656):3.240704):3.895123):2.719118):2.819000):3.303538):3.006837):2.488196):3.738187):0.867154);

And the task has been run over 24hs, the results is still empty with no output, and it also has no errors until now.

I aslo think there were no problems with the styles of the input files, the other task with 37 species has been running successfully.

Really appreciate for your help!