[2024-01-24 13:31:31,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:31,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:31,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg6739d887-d1b2-4a87-9cd5-a5abf57acc48/dqc_reference
[2024-01-24 13:31:32,741] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:32,743] [INFO] Task started: Prodigal
[2024-01-24 13:31:32,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg166d2f96-40aa-4b59-9a8a-10f489add8a0/GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/cds.fna -a GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:47,581] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:47,581] [INFO] Task started: HMMsearch
[2024-01-24 13:31:47,581] [INFO] Running command: hmmsearch --tblout GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6739d887-d1b2-4a87-9cd5-a5abf57acc48/dqc_reference/reference_markers.hmm GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:47,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:47,879] [INFO] Found 6/6 markers.
[2024-01-24 13:31:47,928] [INFO] Query marker FASTA was written to GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:31:47,928] [INFO] Task started: Blastn
[2024-01-24 13:31:47,929] [INFO] Running command: blastn -query GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6739d887-d1b2-4a87-9cd5-a5abf57acc48/dqc_reference/reference_markers.fasta -out GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:48,939] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:48,944] [INFO] Selected 15 target genomes.
[2024-01-24 13:31:48,945] [INFO] Target genome list was writen to GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:31:48,954] [INFO] Task started: fastANI
[2024-01-24 13:31:48,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg166d2f96-40aa-4b59-9a8a-10f489add8a0/GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna.gz --refList GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:00,826] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:00,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6739d887-d1b2-4a87-9cd5-a5abf57acc48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:00,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6739d887-d1b2-4a87-9cd5-a5abf57acc48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:00,841] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:00,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:00,842] [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
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	100.0	1483	1488	95	conclusive
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	99.9981	1485	1488	95	conclusive
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	82.2937	766	1488	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	82.2894	759	1488	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	82.1345	711	1488	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	81.7988	722	1488	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	80.9906	653	1488	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.7519	499	1488	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.7166	435	1488	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.4025	359	1488	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.397	433	1488	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.0703	425	1488	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.9822	298	1488	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	77.8968	332	1488	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.8493	330	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:00,844] [INFO] DFAST Taxonomy check result was written to GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:32:00,845] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:00,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:00,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6739d887-d1b2-4a87-9cd5-a5abf57acc48/dqc_reference/checkm_data
[2024-01-24 13:32:00,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:00,898] [INFO] Task started: CheckM
[2024-01-24 13:32:00,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/checkm_input GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:32:47,656] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:47,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:47,682] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:47,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:47,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:32:47,683] [INFO] Task started: Blastn
[2024-01-24 13:32:47,683] [INFO] Running command: blastn -query GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6739d887-d1b2-4a87-9cd5-a5abf57acc48/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:49,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:49,419] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:49,420] [INFO] Target genome list was writen to GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:49,427] [INFO] Task started: fastANI
[2024-01-24 13:32:49,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg166d2f96-40aa-4b59-9a8a-10f489add8a0/GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna.gz --refList GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:00,661] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:00,680] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:00,681] [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_900142665.1	s__Roseovarius pacificus	100.0	1483	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	conclusive
GCF_900172255.1	s__Roseovarius halotolerans	82.3139	756	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011601345.1	s__Roseovarius gahaiensis	82.1238	712	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142765.1	s__Roseovarius litoreus	81.7988	722	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_009669325.1	s__Roseovarius bejariae	81.0107	651	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.9374	647	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003260265.1	s__Roseovarius sp003260265	79.9443	600	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	79.6301	619	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	79.2888	531	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	78.7683	446	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	78.7107	495	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.8493	330	1488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_014763045.1	s__Sulfitobacter aestuariivivens	76.9126	258	1488	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 13:33:00,686] [INFO] GTDB search result was written to GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:00,687] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:00,690] [INFO] DFAST_QC result json was written to GCF_900142665.1_IMG-taxon_2700988706_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:33:00,691] [INFO] DFAST_QC completed!
[2024-01-24 13:33:00,691] [INFO] Total running time: 0h1m29s