hahnlab
Cafe5 hanging with no output
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!
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.
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.
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!
