[2024-01-24 13:01:19,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:19,373] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:19,373] [INFO] DQC Reference Directory: /var/lib/cwl/stg7073a2da-8415-4329-ac23-1dcb9f0a2186/dqc_reference
[2024-01-24 13:01:20,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,626] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg8508db86-f5b8-401c-816e-96dd77ca79eb/GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/cds.fna -a GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:33,508] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:33,509] [INFO] Task started: HMMsearch
[2024-01-24 13:01:33,509] [INFO] Running command: hmmsearch --tblout GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7073a2da-8415-4329-ac23-1dcb9f0a2186/dqc_reference/reference_markers.hmm GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:33,759] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:33,760] [INFO] Found 6/6 markers.
[2024-01-24 13:01:33,801] [INFO] Query marker FASTA was written to GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:33,801] [INFO] Task started: Blastn
[2024-01-24 13:01:33,801] [INFO] Running command: blastn -query GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7073a2da-8415-4329-ac23-1dcb9f0a2186/dqc_reference/reference_markers.fasta -out GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:34,703] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:34,709] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:34,709] [INFO] Target genome list was writen to GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:34,728] [INFO] Task started: fastANI
[2024-01-24 13:01:34,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg8508db86-f5b8-401c-816e-96dd77ca79eb/GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna.gz --refList GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:49,477] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:49,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7073a2da-8415-4329-ac23-1dcb9f0a2186/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:49,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7073a2da-8415-4329-ac23-1dcb9f0a2186/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:49,499] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:49,499] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:49,500] [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 litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	100.0	1296	1296	95	conclusive
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	82.451	769	1296	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	82.4277	769	1296	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	81.7535	718	1296	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	81.7137	724	1296	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	79.9501	572	1296	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	79.8178	603	1296	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	79.7466	638	1296	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	79.5825	599	1296	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	79.539	555	1296	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.1404	525	1296	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.6007	419	1296	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.5561	398	1296	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.5403	400	1296	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	78.4786	413	1296	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.3148	398	1296	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.2015	382	1296	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.0795	380	1296	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.0744	296	1296	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:49,502] [INFO] DFAST Taxonomy check result was written to GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:01:49,502] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:49,503] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:49,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7073a2da-8415-4329-ac23-1dcb9f0a2186/dqc_reference/checkm_data
[2024-01-24 13:01:49,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:49,549] [INFO] Task started: CheckM
[2024-01-24 13:01:49,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/checkm_input GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:33,098] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:33,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:33,121] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:33,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:33,122] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:33,123] [INFO] Task started: Blastn
[2024-01-24 13:02:33,123] [INFO] Running command: blastn -query GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7073a2da-8415-4329-ac23-1dcb9f0a2186/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:34,624] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:34,629] [INFO] Selected 18 target genomes.
[2024-01-24 13:02:34,629] [INFO] Target genome list was writen to GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:34,652] [INFO] Task started: fastANI
[2024-01-24 13:02:34,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg8508db86-f5b8-401c-816e-96dd77ca79eb/GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna.gz --refList GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:49,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:49,486] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:49,487] [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_900142765.1	s__Roseovarius litoreus	100.0	1296	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	conclusive
GCF_900172255.1	s__Roseovarius halotolerans	82.4514	769	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142665.1	s__Roseovarius pacificus	81.7535	718	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_009669325.1	s__Roseovarius bejariae	79.9598	571	1296	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	79.9279	552	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008728195.1	s__Roseovarius indicus	79.9044	650	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_011601345.1	s__Roseovarius gahaiensis	79.8216	603	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	79.7518	637	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_001441615.1	s__Roseovarius atlanticus	79.6042	597	1296	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	79.5046	600	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_003260265.1	s__Roseovarius sp003260265	79.2554	520	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761875.1	s__Roseovarius aestuariivivens	79.1926	520	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.148	525	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	78.9426	499	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	78.8022	326	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	78.6499	429	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	78.5671	397	1296	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900172285.1	s__Roseovarius aestuarii	78.4644	414	1296	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 13:02:49,488] [INFO] GTDB search result was written to GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:49,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:49,495] [INFO] DFAST_QC result json was written to GCF_900142765.1_IMG-taxon_2700988728_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:49,495] [INFO] DFAST_QC completed!
[2024-01-24 13:02:49,495] [INFO] Total running time: 0h1m30s