[2024-01-25 20:17:50,787] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,788] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg11db15bf-af85-4aff-a503-367e335ba2e2/dqc_reference
[2024-01-25 20:17:52,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:52,028] [INFO] Task started: Prodigal
[2024-01-25 20:17:52,028] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdf3da75-cda3-46a6-a24a-075be4007eb6/GCF_001816145.1_ASM181614v1_genomic.fna.gz | prodigal -d GCF_001816145.1_ASM181614v1_genomic.fna/cds.fna -a GCF_001816145.1_ASM181614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:15,894] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:15,894] [INFO] Task started: HMMsearch
[2024-01-25 20:18:15,894] [INFO] Running command: hmmsearch --tblout GCF_001816145.1_ASM181614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11db15bf-af85-4aff-a503-367e335ba2e2/dqc_reference/reference_markers.hmm GCF_001816145.1_ASM181614v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:16,168] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:16,169] [INFO] Found 6/6 markers.
[2024-01-25 20:18:16,207] [INFO] Query marker FASTA was written to GCF_001816145.1_ASM181614v1_genomic.fna/markers.fasta
[2024-01-25 20:18:16,207] [INFO] Task started: Blastn
[2024-01-25 20:18:16,207] [INFO] Running command: blastn -query GCF_001816145.1_ASM181614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11db15bf-af85-4aff-a503-367e335ba2e2/dqc_reference/reference_markers.fasta -out GCF_001816145.1_ASM181614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:16,805] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:16,808] [INFO] Selected 19 target genomes.
[2024-01-25 20:18:16,808] [INFO] Target genome list was writen to GCF_001816145.1_ASM181614v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:16,829] [INFO] Task started: fastANI
[2024-01-25 20:18:16,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf3da75-cda3-46a6-a24a-075be4007eb6/GCF_001816145.1_ASM181614v1_genomic.fna.gz --refList GCF_001816145.1_ASM181614v1_genomic.fna/target_genomes.txt --output GCF_001816145.1_ASM181614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:40,392] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:40,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11db15bf-af85-4aff-a503-367e335ba2e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:40,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11db15bf-af85-4aff-a503-367e335ba2e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:40,405] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:18:40,405] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:18:40,405] [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
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	100.0	1478	1484	95	conclusive
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	90.8621	1169	1484	95	below_threshold
Hymenobacter sedentarius	strain=DG5B	GCA_001507645.1	1411621	1411621	type	True	84.0032	1034	1484	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	83.9937	1035	1484	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	83.8407	1056	1484	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	83.7417	1037	1484	95	below_threshold
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	83.564	1042	1484	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	83.5562	1032	1484	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	83.2179	995	1484	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	83.0469	968	1484	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	82.8147	1006	1484	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	81.4262	845	1484	95	below_threshold
Hymenobacter coccineus	strain=CCM 8649	GCA_001816125.1	1908235	1908235	type	True	80.8503	795	1484	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	79.1519	645	1484	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.7679	629	1484	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	74.8318	78	1484	95	below_threshold
Streptacidiphilus albus	strain=JL83	GCA_000744705.1	105425	105425	type	True	74.7451	79	1484	95	below_threshold
Streptacidiphilus albus	strain=NBRC 100918	GCA_000787755.1	105425	105425	type	True	74.7123	79	1484	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	74.5854	90	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:40,406] [INFO] DFAST Taxonomy check result was written to GCF_001816145.1_ASM181614v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:40,407] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:40,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:40,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11db15bf-af85-4aff-a503-367e335ba2e2/dqc_reference/checkm_data
[2024-01-25 20:18:40,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:40,455] [INFO] Task started: CheckM
[2024-01-25 20:18:40,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001816145.1_ASM181614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001816145.1_ASM181614v1_genomic.fna/checkm_input GCF_001816145.1_ASM181614v1_genomic.fna/checkm_result
[2024-01-25 20:19:41,643] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:41,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:41,665] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:41,666] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:41,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001816145.1_ASM181614v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:41,666] [INFO] Task started: Blastn
[2024-01-25 20:19:41,666] [INFO] Running command: blastn -query GCF_001816145.1_ASM181614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11db15bf-af85-4aff-a503-367e335ba2e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001816145.1_ASM181614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:42,563] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:42,566] [INFO] Selected 15 target genomes.
[2024-01-25 20:19:42,566] [INFO] Target genome list was writen to GCF_001816145.1_ASM181614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:42,583] [INFO] Task started: fastANI
[2024-01-25 20:19:42,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf3da75-cda3-46a6-a24a-075be4007eb6/GCF_001816145.1_ASM181614v1_genomic.fna.gz --refList GCF_001816145.1_ASM181614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001816145.1_ASM181614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:00,298] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:00,307] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:00,307] [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_001816145.1	s__Hymenobacter lapidarius	100.0	1478	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001816165.1	s__Hymenobacter glacialis	90.8481	1170	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	85.5952	1058	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694725.1	s__Hymenobacter jeongseonensis	84.012	1033	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507645.1	s__Hymenobacter sedentarius	84.0072	1034	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427455.1	s__Hymenobacter sp016427455	83.7711	1040	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	95.46	95.46	0.89	0.89	2	-
GCF_015694525.1	s__Hymenobacter ruricola	83.7468	1036	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275535.1	s__Hymenobacter artigasi	83.5659	1041	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115775.1	s__Hymenobacter arizonensis	83.3352	1069	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640435.1	s__Hymenobacter frigidus	83.2078	997	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734815.1	s__Hymenobacter rubidus	83.038	969	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816125.1	s__Hymenobacter coccineus	80.8684	792	1484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744705.1	s__Streptacidiphilus albus	74.7451	79	1484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_004799515.1	s__Phenylobacterium sp004799515	74.6161	56	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:00,309] [INFO] GTDB search result was written to GCF_001816145.1_ASM181614v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:00,309] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:00,312] [INFO] DFAST_QC result json was written to GCF_001816145.1_ASM181614v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:00,313] [INFO] DFAST_QC completed!
[2024-01-25 20:20:00,313] [INFO] Total running time: 0h2m10s