[2024-01-24 14:11:49,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:49,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:49,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg202c2fb3-1b62-4e7f-abd1-fd9c1f60cbb3/dqc_reference
[2024-01-24 14:11:50,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:50,811] [INFO] Task started: Prodigal
[2024-01-24 14:11:50,811] [INFO] Running command: gunzip -c /var/lib/cwl/stgb35e8b49-cc9e-47d9-843a-1877ba50e65d/GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/cds.fna -a GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:03,388] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:03,389] [INFO] Task started: HMMsearch
[2024-01-24 14:12:03,389] [INFO] Running command: hmmsearch --tblout GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg202c2fb3-1b62-4e7f-abd1-fd9c1f60cbb3/dqc_reference/reference_markers.hmm GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:03,904] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:03,905] [INFO] Found 6/6 markers.
[2024-01-24 14:12:03,966] [INFO] Query marker FASTA was written to GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:12:03,967] [INFO] Task started: Blastn
[2024-01-24 14:12:03,967] [INFO] Running command: blastn -query GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg202c2fb3-1b62-4e7f-abd1-fd9c1f60cbb3/dqc_reference/reference_markers.fasta -out GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:05,440] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:05,444] [INFO] Selected 22 target genomes.
[2024-01-24 14:12:05,444] [INFO] Target genome list was writen to GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:12:05,463] [INFO] Task started: fastANI
[2024-01-24 14:12:05,463] [INFO] Running command: fastANI --query /var/lib/cwl/stgb35e8b49-cc9e-47d9-843a-1877ba50e65d/GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna.gz --refList GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:25,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:25,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg202c2fb3-1b62-4e7f-abd1-fd9c1f60cbb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:25,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg202c2fb3-1b62-4e7f-abd1-fd9c1f60cbb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:26,014] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:26,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:26,014] [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 tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	100.0	1232	1235	95	conclusive
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	82.3893	733	1235	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	81.5958	741	1235	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	81.1937	758	1235	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	80.0233	589	1235	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.8506	629	1235	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.773	589	1235	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.7684	589	1235	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	79.7638	674	1235	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	79.1367	552	1235	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	79.0196	479	1235	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	78.8908	493	1235	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.8469	523	1235	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.4086	491	1235	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.3948	442	1235	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.2639	428	1235	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.9992	364	1235	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	77.9371	398	1235	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.885	444	1235	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.68	331	1235	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6324	346	1235	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.3562	275	1235	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:26,016] [INFO] DFAST Taxonomy check result was written to GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:12:26,017] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:26,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:26,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg202c2fb3-1b62-4e7f-abd1-fd9c1f60cbb3/dqc_reference/checkm_data
[2024-01-24 14:12:26,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:26,059] [INFO] Task started: CheckM
[2024-01-24 14:12:26,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/checkm_input GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:13:06,800] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:06,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:06,824] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:06,825] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:06,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:13:06,826] [INFO] Task started: Blastn
[2024-01-24 14:13:06,826] [INFO] Running command: blastn -query GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg202c2fb3-1b62-4e7f-abd1-fd9c1f60cbb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:08,792] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:08,795] [INFO] Selected 13 target genomes.
[2024-01-24 14:13:08,796] [INFO] Target genome list was writen to GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:08,838] [INFO] Task started: fastANI
[2024-01-24 14:13:08,838] [INFO] Running command: fastANI --query /var/lib/cwl/stgb35e8b49-cc9e-47d9-843a-1877ba50e65d/GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna.gz --refList GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:19,761] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:19,775] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:19,775] [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_900109855.1	s__Roseovarius tolerans	100.0	1232	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	conclusive
GCF_002072155.1	s__Roseovarius sp002072155	88.5437	860	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	82.5568	581	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002925845.1	s__Roseovarius nitratireducens	82.3912	734	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCA_002842985.1	s__Roseovarius sp002842985	81.8074	740	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421985.1	s__Roseovarius sp002421985	81.6925	575	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109455.1	s__Roseovarius azorensis	81.605	741	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	81.5422	506	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCF_018069895.1	s__Roseovarius sp018069895	81.2934	688	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	-
GCA_014359765.1	s__Roseovarius sp014359765	81.2913	590	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744325.1	s__Roseovarius sp000744325	80.9217	721	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002080415.1	s__Roseovarius mucosus_A	80.6108	713	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	-
GCF_003651245.1	s__Roseovarius spongiae	79.2068	541	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:19,777] [INFO] GTDB search result was written to GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:19,778] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:19,785] [INFO] DFAST_QC result json was written to GCF_900109855.1_IMG-taxon_2619619026_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:13:19,786] [INFO] DFAST_QC completed!
[2024-01-24 14:13:19,786] [INFO] Total running time: 0h1m30s