[2024-01-24 13:49:19,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg053fd84b-4bb4-4313-ab6e-318257509247/dqc_reference
[2024-01-24 13:49:20,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,753] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,754] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3e6905b-d221-4a57-8e63-0e786f6b5ad1/GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/cds.fna -a GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:25,573] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:25,573] [INFO] Task started: HMMsearch
[2024-01-24 13:49:25,573] [INFO] Running command: hmmsearch --tblout GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg053fd84b-4bb4-4313-ab6e-318257509247/dqc_reference/reference_markers.hmm GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:25,830] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:25,831] [INFO] Found 6/6 markers.
[2024-01-24 13:49:25,853] [INFO] Query marker FASTA was written to GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:25,853] [INFO] Task started: Blastn
[2024-01-24 13:49:25,853] [INFO] Running command: blastn -query GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg053fd84b-4bb4-4313-ab6e-318257509247/dqc_reference/reference_markers.fasta -out GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:26,515] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:26,519] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:26,519] [INFO] Target genome list was writen to GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:26,527] [INFO] Task started: fastANI
[2024-01-24 13:49:26,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3e6905b-d221-4a57-8e63-0e786f6b5ad1/GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna.gz --refList GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:37,716] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:37,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg053fd84b-4bb4-4313-ab6e-318257509247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:37,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg053fd84b-4bb4-4313-ab6e-318257509247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:37,721] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:37,721] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:37,721] [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
Eubacterium coprostanoligenes	strain=ATCC 51222	GCA_900167205.1	290054	290054	type	True	100.0	589	592	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:49:37,723] [INFO] DFAST Taxonomy check result was written to GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:49:37,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:37,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:37,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg053fd84b-4bb4-4313-ab6e-318257509247/dqc_reference/checkm_data
[2024-01-24 13:49:37,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:37,750] [INFO] Task started: CheckM
[2024-01-24 13:49:37,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/checkm_input GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:00,313] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:00,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,331] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:00,332] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:00,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:00,333] [INFO] Task started: Blastn
[2024-01-24 13:50:00,333] [INFO] Running command: blastn -query GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg053fd84b-4bb4-4313-ab6e-318257509247/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:01,440] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:01,443] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:01,444] [INFO] Target genome list was writen to GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:01,458] [INFO] Task started: fastANI
[2024-01-24 13:50:01,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3e6905b-d221-4a57-8e63-0e786f6b5ad1/GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna.gz --refList GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:04,840] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,853] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:04,853] [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
GCF_900167205.1	s__Eubacterium_R coprostanoligenes	100.0	589	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.02	97.98	0.90	0.89	4	conclusive
GCA_900539325.1	s__Eubacterium_R sp900539325	89.8363	480	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.44	97.34	0.90	0.87	4	-
GCA_900766895.1	s__Eubacterium_R sp900766895	81.1778	300	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539165.1	s__Eubacterium_R sp900539165	79.8692	268	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.98	99.98	0.94	0.94	2	-
GCA_900772705.1	s__Eubacterium_R sp900772705	79.5478	187	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542875.1	s__Eubacterium_R sp900542875	79.2228	240	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.37	97.10	0.91	0.86	6	-
GCA_003526845.1	s__Eubacterium_R sp003526845	78.7035	209	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.76	98.46	0.93	0.92	8	-
GCA_002494125.1	s__Eubacterium_R sp002494125	76.5443	72	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.97	97.69	0.80	0.75	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,855] [INFO] GTDB search result was written to GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:04,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:04,858] [INFO] DFAST_QC result json was written to GCF_900167205.1_IMG-taxon_2585428093_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:50:04,859] [INFO] DFAST_QC completed!
[2024-01-24 13:50:04,859] [INFO] Total running time: 0h0m46s