[2024-01-24 13:16:58,891] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:58,893] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:58,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg23d41d18-3640-4454-a3c6-3723f05fead8/dqc_reference
[2024-01-24 13:17:00,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:00,073] [INFO] Task started: Prodigal
[2024-01-24 13:17:00,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e209ab9-9b6f-4149-a7f2-36b3b858b714/GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/cds.fna -a GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:09,731] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:09,731] [INFO] Task started: HMMsearch
[2024-01-24 13:17:09,731] [INFO] Running command: hmmsearch --tblout GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23d41d18-3640-4454-a3c6-3723f05fead8/dqc_reference/reference_markers.hmm GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:09,976] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:09,977] [INFO] Found 6/6 markers.
[2024-01-24 13:17:10,006] [INFO] Query marker FASTA was written to GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:17:10,006] [INFO] Task started: Blastn
[2024-01-24 13:17:10,006] [INFO] Running command: blastn -query GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg23d41d18-3640-4454-a3c6-3723f05fead8/dqc_reference/reference_markers.fasta -out GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:10,837] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:10,841] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:10,841] [INFO] Target genome list was writen to GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:17:10,847] [INFO] Task started: fastANI
[2024-01-24 13:17:10,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e209ab9-9b6f-4149-a7f2-36b3b858b714/GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna.gz --refList GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:21,693] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:21,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23d41d18-3640-4454-a3c6-3723f05fead8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:21,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23d41d18-3640-4454-a3c6-3723f05fead8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:21,708] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:21,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:21,709] [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
Salinibacterium xinjiangense	strain=CGMCC 1.05381	GCA_900230175.1	386302	386302	type	True	100.0	1003	1004	95	conclusive
Salinibacterium xinjiangense	strain=CGMCC 1.5381	GCA_014645015.1	386302	386302	type	True	99.9919	1001	1004	95	conclusive
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	78.4604	327	1004	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	78.1314	290	1004	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	78.0249	299	1004	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	77.9991	290	1004	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	77.9958	259	1004	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	77.9922	292	1004	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=LMG 3663	GCA_002240565.1	33014	28447	type	True	77.9182	217	1004	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	77.8858	217	1004	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	77.8749	203	1004	95	below_threshold
Okibacterium fritillariae	strain=VKM Ac-2059	GCA_900167575.1	123320	123320	type	True	77.8581	187	1004	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	77.7958	228	1004	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	77.7944	214	1004	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	77.708	237	1004	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	77.5665	222	1004	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	77.5447	258	1004	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.3818	237	1004	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	77.2008	229	1004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:21,711] [INFO] DFAST Taxonomy check result was written to GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:17:21,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:21,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:21,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23d41d18-3640-4454-a3c6-3723f05fead8/dqc_reference/checkm_data
[2024-01-24 13:17:21,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:21,749] [INFO] Task started: CheckM
[2024-01-24 13:17:21,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/checkm_input GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:17:54,557] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:54,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:54,577] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:54,577] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:54,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:17:54,578] [INFO] Task started: Blastn
[2024-01-24 13:17:54,579] [INFO] Running command: blastn -query GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg23d41d18-3640-4454-a3c6-3723f05fead8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:55,823] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:55,828] [INFO] Selected 9 target genomes.
[2024-01-24 13:17:55,828] [INFO] Target genome list was writen to GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:55,838] [INFO] Task started: fastANI
[2024-01-24 13:17:55,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e209ab9-9b6f-4149-a7f2-36b3b858b714/GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna.gz --refList GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:01,637] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:01,646] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:01,646] [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_014645015.1	s__Rhodoglobus xinjiangensis	99.9919	1001	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_015752305.1	s__Rhodoglobus sp015752305	85.5537	741	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920435.1	s__Rhodoglobus sp903920435	79.1726	397	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.49	97.73	0.85	0.78	4	-
GCA_001725325.1	s__Rhodoglobus sp001725325	79.1474	424	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004310685.1	s__Conyzicola arctica	78.7875	336	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410945.1	s__Rhodoglobus sp013410945	78.3718	312	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449675.1	s__Glaciihabitans sp018449675	77.8109	253	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Glaciihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428745.1	s__Leifsonia sp001428745	77.5928	239	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003852775.1	s__Protaetiibacter sp003852775	77.3542	232	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:01,648] [INFO] GTDB search result was written to GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:01,649] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:01,655] [INFO] DFAST_QC result json was written to GCF_900230175.1_IMG-taxon_2721755902_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:18:01,656] [INFO] DFAST_QC completed!
[2024-01-24 13:18:01,656] [INFO] Total running time: 0h1m3s