diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 4fcb44f..0568f1a 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -17,12 +17,12 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest, macos-latest] + os: [ubuntu-latest, macos-12] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Setup Miniconda - uses: conda-incubator/setup-miniconda@v2.2.0 + uses: conda-incubator/setup-miniconda@v3 with: environment-file: ./lemur.yml activate-environment: lemur-env @@ -38,7 +38,7 @@ jobs: -d ./examples/example-db --tax-path ./examples/example-db/taxonomy.tsv -r species - --verbose > ./examples/example-output/example.log 2>&1; + --verbose; - name: Check that output was produced id: check_files diff --git a/lemur b/lemur index 9dbe27b..16054c9 100755 --- a/lemur +++ b/lemur @@ -670,7 +670,7 @@ class LemurRunEnv(): criteria has been met, stopping once it has.''' n_reads = len(set(self.P_rgs_df.reset_index()["Read_ID"])) if n_reads == 0: - self.log(f"No alignments available for EM algorithm.\nVerify SAM file, {self.self.args.output}P_rgs_df_raw.tsv, and consider lowering --min-aln-len-ratio or --fidelity flags., logging.ERROR) + self.log(f"No alignments available for EM algorithm.\nVerify SAM file, {self.self.args.output}P_rgs_df_raw.tsv, and consider lowering --min-aln-len-ratio or --fidelity flags.", logging.ERROR) exit(1) else: self.low_abundance_threshold = 1. / n_reads