diff --git a/PanACoTA/prepare_module/filter_genomes.py b/PanACoTA/prepare_module/filter_genomes.py index 28eff887c8a5412a2480554d2d78794d1e9f39e3..fe82ed97b9142a6395a9e20a26ea4f0856e0a6ca 100755 --- a/PanACoTA/prepare_module/filter_genomes.py +++ b/PanACoTA/prepare_module/filter_genomes.py @@ -163,6 +163,9 @@ def iterative_mash(sorted_genomes, genomes, outdir, species_linked, min_dist, ma # Compute pairwise distances compare_all(out_msh, matrix, mash_log, threads) + with open(matrix, "r") as mat: + for line in mat: + print(line) # Iteratively discard genomes # List of genomes to compare to the next ones until a limit value is reached. @@ -266,9 +269,6 @@ def sketch_all(genomes, sorted_genomes, outdir, list_reps, out_msh, mash_log, th f"{mash_log}") outf = open(mash_log, "w") - print("outf created") - print(utils.check_installed("mash")) - print(cmd_sketch) utils.run_cmd(cmd_sketch, error_sketch, eof=True, stdout=outf, stderr=outf, logger=logger) outf.close() return 0