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LANL-Bioinformatics / PhaME

Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
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t1_all_snp_alignment.fna: No such file or directory #21

Closed mainguyenhuyen closed 9 months ago

mainguyenhuyen commented 1 year ago

Hi,

Thank you for your consideration. I ran into two problems when I installed and tested run PhaME. For some information, I am working on UPPMAX Rackham clusters. I have chosen to install PhaME like this: I installed dependencies by "module load" on Rackham server, then I clone the git by the time this issue was written. Then, I tested run by "test/TestAll.sh 1" in the correct PhaME directory. I ran into two problems as follows:

  1. Need nucmer --version >= 3.1 but you have 0 - please upgrade it. My nucmer version is 4.0.0rc1, so there is an error in checking version here.

  2. test/TestAll.sh: line 11: test/workdirs/t1_ebola_preads/results/alignments/t1_all_snp_alignment.fna: No such file or directory So inside folder t1_ebola_preads, there are 4 fastq files. Maybe you have upgraded the testing data set or the testing test run program and forget to change the corresponding files along with them?

Thank you.

mshakya commented 9 months ago

Hi, if this issue is still relevant, May i ask how are you installing the dependencies? You need to install them using conda (conda install phame) or separately. I recommend former option. Thanks.