[2023-06-17 02:43:39,207] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:43:39,210] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:43:39,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b34e393-d3d0-4954-ba15-c6064cccd1ca/dqc_reference
[2023-06-17 02:43:40,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:43:40,636] [INFO] Task started: Prodigal
[2023-06-17 02:43:40,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fdf3669-eb80-476f-9b5a-7c8e56fe1bfe/GCA_028721985.1_ASM2872198v1_genomic.fna.gz | prodigal -d GCA_028721985.1_ASM2872198v1_genomic.fna/cds.fna -a GCA_028721985.1_ASM2872198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:43:43,816] [INFO] Task succeeded: Prodigal
[2023-06-17 02:43:43,816] [INFO] Task started: HMMsearch
[2023-06-17 02:43:43,816] [INFO] Running command: hmmsearch --tblout GCA_028721985.1_ASM2872198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b34e393-d3d0-4954-ba15-c6064cccd1ca/dqc_reference/reference_markers.hmm GCA_028721985.1_ASM2872198v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:43:44,032] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:43:44,033] [INFO] Found 6/6 markers.
[2023-06-17 02:43:44,055] [INFO] Query marker FASTA was written to GCA_028721985.1_ASM2872198v1_genomic.fna/markers.fasta
[2023-06-17 02:43:44,056] [INFO] Task started: Blastn
[2023-06-17 02:43:44,056] [INFO] Running command: blastn -query GCA_028721985.1_ASM2872198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b34e393-d3d0-4954-ba15-c6064cccd1ca/dqc_reference/reference_markers.fasta -out GCA_028721985.1_ASM2872198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:43:44,724] [INFO] Task succeeded: Blastn
[2023-06-17 02:43:44,728] [INFO] Selected 25 target genomes.
[2023-06-17 02:43:44,729] [INFO] Target genome list was writen to GCA_028721985.1_ASM2872198v1_genomic.fna/target_genomes.txt
[2023-06-17 02:43:44,734] [INFO] Task started: fastANI
[2023-06-17 02:43:44,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fdf3669-eb80-476f-9b5a-7c8e56fe1bfe/GCA_028721985.1_ASM2872198v1_genomic.fna.gz --refList GCA_028721985.1_ASM2872198v1_genomic.fna/target_genomes.txt --output GCA_028721985.1_ASM2872198v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:44:03,248] [INFO] Task succeeded: fastANI
[2023-06-17 02:44:03,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b34e393-d3d0-4954-ba15-c6064cccd1ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:44:03,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b34e393-d3d0-4954-ba15-c6064cccd1ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:44:03,251] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:44:03,251] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 02:44:03,251] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-17 02:44:03,253] [INFO] DFAST Taxonomy check result was written to GCA_028721985.1_ASM2872198v1_genomic.fna/tc_result.tsv
[2023-06-17 02:44:03,254] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:44:03,254] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:44:03,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b34e393-d3d0-4954-ba15-c6064cccd1ca/dqc_reference/checkm_data
[2023-06-17 02:44:03,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:44:03,275] [INFO] Task started: CheckM
[2023-06-17 02:44:03,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028721985.1_ASM2872198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028721985.1_ASM2872198v1_genomic.fna/checkm_input GCA_028721985.1_ASM2872198v1_genomic.fna/checkm_result
[2023-06-17 02:44:20,575] [INFO] Task succeeded: CheckM
[2023-06-17 02:44:20,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:44:20,600] [INFO] ===== Completeness check finished =====
[2023-06-17 02:44:20,600] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:44:20,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028721985.1_ASM2872198v1_genomic.fna/markers.fasta)
[2023-06-17 02:44:20,601] [INFO] Task started: Blastn
[2023-06-17 02:44:20,601] [INFO] Running command: blastn -query GCA_028721985.1_ASM2872198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b34e393-d3d0-4954-ba15-c6064cccd1ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_028721985.1_ASM2872198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:44:21,703] [INFO] Task succeeded: Blastn
[2023-06-17 02:44:21,707] [INFO] Selected 23 target genomes.
[2023-06-17 02:44:21,708] [INFO] Target genome list was writen to GCA_028721985.1_ASM2872198v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:44:21,729] [INFO] Task started: fastANI
[2023-06-17 02:44:21,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fdf3669-eb80-476f-9b5a-7c8e56fe1bfe/GCA_028721985.1_ASM2872198v1_genomic.fna.gz --refList GCA_028721985.1_ASM2872198v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028721985.1_ASM2872198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:44:28,046] [INFO] Task succeeded: fastANI
[2023-06-17 02:44:28,053] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:44:28,053] [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
GCA_003539515.1	s__CAG-349 sp003539515	98.0961	357	368	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-349	95.0	97.82	96.90	0.94	0.89	17	conclusive
GCA_001940895.1	s__CAG-349 sp001940895	78.89	126	368	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-349	95.0	98.38	97.95	0.83	0.78	4	-
--------------------------------------------------------------------------------
[2023-06-17 02:44:28,056] [INFO] GTDB search result was written to GCA_028721985.1_ASM2872198v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:44:28,056] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:44:28,058] [INFO] DFAST_QC result json was written to GCA_028721985.1_ASM2872198v1_genomic.fna/dqc_result.json
[2023-06-17 02:44:28,058] [INFO] DFAST_QC completed!
[2023-06-17 02:44:28,059] [INFO] Total running time: 0h0m49s