[2024-01-24 15:26:55,051] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,054] [INFO] DQC Reference Directory: /var/lib/cwl/stg39288166-eab8-4097-9a7b-37e282852044/dqc_reference
[2024-01-24 15:26:56,517] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,518] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,518] [INFO] Running command: gunzip -c /var/lib/cwl/stgdced5ad1-749f-4119-a12e-71debb59a500/GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/cds.fna -a GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:08,713] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:08,713] [INFO] Task started: HMMsearch
[2024-01-24 15:27:08,714] [INFO] Running command: hmmsearch --tblout GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39288166-eab8-4097-9a7b-37e282852044/dqc_reference/reference_markers.hmm GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:08,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:08,964] [INFO] Found 6/6 markers.
[2024-01-24 15:27:08,999] [INFO] Query marker FASTA was written to GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:27:09,000] [INFO] Task started: Blastn
[2024-01-24 15:27:09,000] [INFO] Running command: blastn -query GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg39288166-eab8-4097-9a7b-37e282852044/dqc_reference/reference_markers.fasta -out GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:09,779] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:09,782] [INFO] Selected 11 target genomes.
[2024-01-24 15:27:09,782] [INFO] Target genome list was writen to GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:27:09,787] [INFO] Task started: fastANI
[2024-01-24 15:27:09,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgdced5ad1-749f-4119-a12e-71debb59a500/GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna.gz --refList GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:18,653] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:18,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39288166-eab8-4097-9a7b-37e282852044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:18,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39288166-eab8-4097-9a7b-37e282852044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:18,664] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:18,665] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:18,665] [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
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	100.0	1214	1214	95	conclusive
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	87.3818	962	1214	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	87.3464	1007	1214	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	84.4458	833	1214	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	84.1451	795	1214	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.4303	302	1214	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.4272	305	1214	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.2563	262	1214	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.9093	249	1214	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.8754	160	1214	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.7636	166	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:18,675] [INFO] DFAST Taxonomy check result was written to GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:27:18,675] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:18,676] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:18,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39288166-eab8-4097-9a7b-37e282852044/dqc_reference/checkm_data
[2024-01-24 15:27:18,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:18,716] [INFO] Task started: CheckM
[2024-01-24 15:27:18,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/checkm_input GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:27:57,134] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:57,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:57,153] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:57,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:57,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:27:57,154] [INFO] Task started: Blastn
[2024-01-24 15:27:57,154] [INFO] Running command: blastn -query GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg39288166-eab8-4097-9a7b-37e282852044/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:58,309] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:58,315] [INFO] Selected 7 target genomes.
[2024-01-24 15:27:58,315] [INFO] Target genome list was writen to GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:58,320] [INFO] Task started: fastANI
[2024-01-24 15:27:58,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgdced5ad1-749f-4119-a12e-71debb59a500/GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna.gz --refList GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:04,611] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:04,619] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:04,619] [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_900113435.1	s__Sulfitobacter dubius	100.0	1214	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	conclusive
GCF_003611275.1	s__Sulfitobacter sp001634775	89.6535	977	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCA_002703405.1	s__Sulfitobacter sp002703405	89.3543	833	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.87	96.48	0.79	0.78	3	-
GCF_017743885.1	s__Sulfitobacter sp001635605	87.8654	957	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_000172095.1	s__Sulfitobacter indolifex	87.3818	962	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102535.1	s__Sulfitobacter delicatus	84.4458	833	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346665.1	s__Sulfitobacter maritimus	84.1504	794	1214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:04,621] [INFO] GTDB search result was written to GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:04,622] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:04,626] [INFO] DFAST_QC result json was written to GCF_900113435.1_IMG-taxon_2616644813_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:28:04,626] [INFO] DFAST_QC completed!
[2024-01-24 15:28:04,626] [INFO] Total running time: 0h1m10s