[2024-01-24 11:05:27,617] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbd85ba4-cbc0-4a29-9462-ac4f8fd0e0e6/dqc_reference
[2024-01-24 11:05:28,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:28,962] [INFO] Task started: Prodigal
[2024-01-24 11:05:28,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ee1f0e3-34fa-4c8d-a539-857c9f36417c/GCF_016801985.1_ASM1680198v1_genomic.fna.gz | prodigal -d GCF_016801985.1_ASM1680198v1_genomic.fna/cds.fna -a GCF_016801985.1_ASM1680198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:56,225] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:56,226] [INFO] Task started: HMMsearch
[2024-01-24 11:05:56,226] [INFO] Running command: hmmsearch --tblout GCF_016801985.1_ASM1680198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbd85ba4-cbc0-4a29-9462-ac4f8fd0e0e6/dqc_reference/reference_markers.hmm GCF_016801985.1_ASM1680198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:56,695] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:56,696] [INFO] Found 6/6 markers.
[2024-01-24 11:05:56,755] [INFO] Query marker FASTA was written to GCF_016801985.1_ASM1680198v1_genomic.fna/markers.fasta
[2024-01-24 11:05:56,755] [INFO] Task started: Blastn
[2024-01-24 11:05:56,756] [INFO] Running command: blastn -query GCF_016801985.1_ASM1680198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbd85ba4-cbc0-4a29-9462-ac4f8fd0e0e6/dqc_reference/reference_markers.fasta -out GCF_016801985.1_ASM1680198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:57,744] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:57,748] [INFO] Selected 9 target genomes.
[2024-01-24 11:05:57,749] [INFO] Target genome list was writen to GCF_016801985.1_ASM1680198v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:57,752] [INFO] Task started: fastANI
[2024-01-24 11:05:57,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee1f0e3-34fa-4c8d-a539-857c9f36417c/GCF_016801985.1_ASM1680198v1_genomic.fna.gz --refList GCF_016801985.1_ASM1680198v1_genomic.fna/target_genomes.txt --output GCF_016801985.1_ASM1680198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:09,813] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:09,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbd85ba4-cbc0-4a29-9462-ac4f8fd0e0e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:09,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbd85ba4-cbc0-4a29-9462-ac4f8fd0e0e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:09,823] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:09,823] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:09,823] [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
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	100.0	2353	2353	95	conclusive
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	82.5076	1408	2353	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	82.3992	1313	2353	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	82.3775	1289	2353	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	82.3589	1393	2353	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.9696	124	2353	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.8548	121	2353	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.5454	153	2353	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.5413	153	2353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:09,825] [INFO] DFAST Taxonomy check result was written to GCF_016801985.1_ASM1680198v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:09,825] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:09,826] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:09,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbd85ba4-cbc0-4a29-9462-ac4f8fd0e0e6/dqc_reference/checkm_data
[2024-01-24 11:06:09,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:09,894] [INFO] Task started: CheckM
[2024-01-24 11:06:09,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016801985.1_ASM1680198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016801985.1_ASM1680198v1_genomic.fna/checkm_input GCF_016801985.1_ASM1680198v1_genomic.fna/checkm_result
[2024-01-24 11:07:26,662] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:26,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:26,689] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:26,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:26,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016801985.1_ASM1680198v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:26,691] [INFO] Task started: Blastn
[2024-01-24 11:07:26,691] [INFO] Running command: blastn -query GCF_016801985.1_ASM1680198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbd85ba4-cbc0-4a29-9462-ac4f8fd0e0e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016801985.1_ASM1680198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:28,475] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:28,482] [INFO] Selected 5 target genomes.
[2024-01-24 11:07:28,482] [INFO] Target genome list was writen to GCF_016801985.1_ASM1680198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:28,486] [INFO] Task started: fastANI
[2024-01-24 11:07:28,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee1f0e3-34fa-4c8d-a539-857c9f36417c/GCF_016801985.1_ASM1680198v1_genomic.fna.gz --refList GCF_016801985.1_ASM1680198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016801985.1_ASM1680198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:37,565] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:37,576] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:37,576] [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_016801985.1	s__Steroidobacter_A sp016801985	100.0	2353	2353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009932555.1	s__Steroidobacter_A agaridevorans	82.5059	1408	2353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	99.33	99.33	0.96	0.96	2	-
GCF_004138485.1	s__Steroidobacter_A soli	82.397	1313	2353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138335.1	s__Steroidobacter_A agariperforans	82.3589	1393	2353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790065.1	s__Steroidobacter_A sp016790065	81.9647	1026	2353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:37,578] [INFO] GTDB search result was written to GCF_016801985.1_ASM1680198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:37,578] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:37,581] [INFO] DFAST_QC result json was written to GCF_016801985.1_ASM1680198v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:37,581] [INFO] DFAST_QC completed!
[2024-01-24 11:07:37,581] [INFO] Total running time: 0h2m10s