[2023-06-17 12:25:00,721] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:25:00,726] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:25:00,726] [INFO] DQC Reference Directory: /var/lib/cwl/stga2916e6e-bb9f-4d14-893f-06320848a58c/dqc_reference
[2023-06-17 12:25:02,075] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:25:02,076] [INFO] Task started: Prodigal
[2023-06-17 12:25:02,076] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7451902-ff46-42e3-9346-16b2d18c0d9a/GCA_003021375.1_ASM302137v1_genomic.fna.gz | prodigal -d GCA_003021375.1_ASM302137v1_genomic.fna/cds.fna -a GCA_003021375.1_ASM302137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:25:02,675] [INFO] Task succeeded: Prodigal
[2023-06-17 12:25:02,676] [INFO] Task started: HMMsearch
[2023-06-17 12:25:02,676] [INFO] Running command: hmmsearch --tblout GCA_003021375.1_ASM302137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2916e6e-bb9f-4d14-893f-06320848a58c/dqc_reference/reference_markers.hmm GCA_003021375.1_ASM302137v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:25:02,852] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:25:02,854] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgb7451902-ff46-42e3-9346-16b2d18c0d9a/GCA_003021375.1_ASM302137v1_genomic.fna.gz]
[2023-06-17 12:25:02,868] [INFO] Query marker FASTA was written to GCA_003021375.1_ASM302137v1_genomic.fna/markers.fasta
[2023-06-17 12:25:02,868] [INFO] Task started: Blastn
[2023-06-17 12:25:02,868] [INFO] Running command: blastn -query GCA_003021375.1_ASM302137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2916e6e-bb9f-4d14-893f-06320848a58c/dqc_reference/reference_markers.fasta -out GCA_003021375.1_ASM302137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:05,636] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:05,658] [INFO] Selected 0 target genomes.
[2023-06-17 12:25:05,659] [INFO] Target genome list was writen to GCA_003021375.1_ASM302137v1_genomic.fna/target_genomes.txt
[2023-06-17 12:25:05,659] [ERROR] File is empty. [GCA_003021375.1_ASM302137v1_genomic.fna/target_genomes.txt]
[2023-06-17 12:25:05,659] [ERROR] Task failed. No target genome found.
[2023-06-17 12:25:05,659] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:25:05,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2916e6e-bb9f-4d14-893f-06320848a58c/dqc_reference/checkm_data
[2023-06-17 12:25:05,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:25:05,669] [INFO] Task started: CheckM
[2023-06-17 12:25:05,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003021375.1_ASM302137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003021375.1_ASM302137v1_genomic.fna/checkm_input GCA_003021375.1_ASM302137v1_genomic.fna/checkm_result
[2023-06-17 12:25:18,548] [INFO] Task succeeded: CheckM
[2023-06-17 12:25:18,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:25:18,569] [INFO] ===== Completeness check finished =====
[2023-06-17 12:25:18,569] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:25:18,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003021375.1_ASM302137v1_genomic.fna/markers.fasta)
[2023-06-17 12:25:18,570] [INFO] Task started: Blastn
[2023-06-17 12:25:18,570] [INFO] Running command: blastn -query GCA_003021375.1_ASM302137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2916e6e-bb9f-4d14-893f-06320848a58c/dqc_reference/reference_markers_gtdb.fasta -out GCA_003021375.1_ASM302137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:18,983] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:18,987] [INFO] Selected 5 target genomes.
[2023-06-17 12:25:18,987] [INFO] Target genome list was writen to GCA_003021375.1_ASM302137v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:25:19,021] [INFO] Task started: fastANI
[2023-06-17 12:25:19,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7451902-ff46-42e3-9346-16b2d18c0d9a/GCA_003021375.1_ASM302137v1_genomic.fna.gz --refList GCA_003021375.1_ASM302137v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003021375.1_ASM302137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:25:22,960] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:22,963] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 12:25:22,964] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
--------------------------------------------------------------------------------
[2023-06-17 12:25:22,966] [INFO] GTDB search result was written to GCA_003021375.1_ASM302137v1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:25:22,967] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:25:22,970] [INFO] DFAST_QC result json was written to GCA_003021375.1_ASM302137v1_genomic.fna/dqc_result.json
[2023-06-17 12:25:22,971] [INFO] DFAST_QC completed!
[2023-06-17 12:25:22,971] [INFO] Total running time: 0h0m22s