Closed kuzman1306 closed 3 years ago
Dear Nemanja, I'm embarrassed for not having answered before. The '/get_phylomarkers/bin/linux/.libs/lt-nw_reroot: error while loading shared libraries: libnw.so.0' that you report is solved in the new Docker image for GET_HOMOLOGUES+GET_PHYLOMARKERS released yesterday night , as well as in the new GET_PHYLOMARKERS image and latest GET_PHYLOMARKERS release on GitHub. With best regards, Pablo.
Dear Pablo,
I finally tried the new docker image and estimate_pangenome_phylogenies.sh v.1.2_16Sep21. I used the following command: estimate_pangenome_phylogenies.sh -c PARS -R 3 -i pangenome_matrix_t0.phylip -n 28 -b 25 -j 10 -t 1 , but I got the following error:
...
ERROR: missing ')' at line 677 near '(' WARNING: zero bipart count for ....................................................................................***........................ awk: program limit exceeded: maximum number of fields size=32767 FILENAME="pangenome_matrix_t0.tab" FNR=1 NR=1 the seq_key => seq_ID correspondences for aln pang_ID-Strain_corresp.tsv are: 0000000000 => ...
I wonder if you could help me here.
Best regards,
Nemanja
On Sun, Sep 19, 2021 at 8:53 PM Pablo Vinuesa @.***> wrote:
Closed #8 https://github.com/vinuesa/get_phylomarkers/issues/8.
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Hi @kuzman1306 , @vinuesa that looks like a file with too many columns for awk perhaps?
Hi @kuzman1306, v1.2_16Sep21 is a rather old version. If you look at the tags, the latest one is 20220618.
Could you please run 'docker pull vinuesa/get_phylomarkers:latest' to upgrade to v20220618?
As documented in the get_phylomarkers' DockerHub page, this version contains notable additions, most notably the addition of ASTRAL to compute a concatenation-independent species tree.
That version passes all tests, including a parsimony run with bootstrapping on a pangenome matrix with estimate_pangenome_phylogenies.sh.
Please let us know if you still encounter any problems.
Dear GET_PHYLOMARKERS team,
I am suing docker image "10032020-10Jan20" on Ubuntu 18.04 LTS. I successfully generated ML tree by using PGM as an input, but getting the following error with parsimony inference. Please see bellow the error.
I wonder if you could help me with this.
Cheers,
Nemanja