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thlee / SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data
http://chibba.pgml.uga.edu/snphylo/
GNU General Public License v2.0
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error message: phylip/exe/dnaml.app: is a directory #35

Open zuzmus opened 5 years ago

zuzmus commented 5 years ago

Dear all,

could anyone help me with this error message? After a whole day spent with updating, installing and re-installing of whatever is required by this software, I got to the point from which I can't get further.

I get the SNPhylo "succesfully installed", however, it is just able to load SNPs and then doesn't go further.

It gets stuck:

[running, running] . . . [1] 82820 [1] 83831 [1] 84841 Sat Nov 9 22:45:07 2019 Done. Hint: it is suggested to call snpgdsOpen' to open a SNP GDS file instead ofopenfn.gds'. SNP pruning based on LD: Excluding 0 SNP on non-autosomes Excluding 17,476 SNPs (monomorphic: TRUE, MAF: 0, missing rate: 1) Working space: 22 samples, 67,924 SNPs using 1 (CPU) core sliding window: 500,000 basepairs, Inf SNPs |LD| threshold: 1000 method: composite Chromosome 31965: 16.25%, 13,874/85,400 13,874 markers are selected in total. ./snphylo.sh: line 289: [: missing `]' ./snphylo.sh: line 296: /Users/zuza/SNPhylo/phylip/exe/dnaml.app: is a directory

I have tried the installation of several versions of Phylip, and the dnaml.app is working when I directly click on it. I also have installed phylip (several times) to different locations, nothing helps... I have just invested so much time in it that I feel pity to just give it up now... Thanks.

zuzmus commented 5 years ago

hey all, I have finally fixed this - I really had to replace the "}" by "]" on the line 289 in the running script snphylo.sh (there was a typo!!). I just don't get how this software could ever worked for someone if there are errors in the script... Ah, and yes, the dnaml.app really was a directory despite having an icon and .app in the name so I had to prolongate the path to its content (my mistake before). So I fixed these two issues. Anyway, it just moved me couple of lines below, to get further error messages:

. . . [1] 82820 [1] 83831 [1] 84841 Sun Nov 10 15:03:10 2019 Done. Hint: it is suggested to call snpgdsOpen' to open a SNP GDS file instead ofopenfn.gds'. SNP pruning based on LD: Excluding 0 SNP on non-autosomes Excluding 10,071 SNPs (monomorphic: TRUE, MAF: 0, missing rate: 1) Working space: 23 samples, 75,329 SNPs using 1 (CPU) core sliding window: 500,000 basepairs, Inf SNPs |LD| threshold: 1000 method: composite Chromosome 31965: 29.69%, 25,354/85,400 25,354 markers are selected in total. mv: rename outfile to snphylo.output.ml.txt: No such file or directory mv: rename outtree to snphylo.output.ml.tree: No such file or directory Newick file (snphylo.output.ml.tree) was not found! Usage: Rscript --vanilla draw_unrooted_tree.R -i Newick_file_name -p phylip_file_name [-n Number_of_BS_samples] [-o Prefix_of_output_files (output)] [-h]

So I'm finally giving up on this software, so far there has been an issue in every step. There will certainly be much smoother way how to calculate phylogenies.