[2024-01-24 12:39:41,770] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg7292ddd3-f62c-4566-9ff5-5c8c228c5105/dqc_reference
[2024-01-24 12:39:43,094] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:43,095] [INFO] Task started: Prodigal
[2024-01-24 12:39:43,095] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0aa30d9-bb03-43b6-b098-24550cb3b64d/GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/cds.fna -a GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:55,238] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:55,239] [INFO] Task started: HMMsearch
[2024-01-24 12:39:55,239] [INFO] Running command: hmmsearch --tblout GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7292ddd3-f62c-4566-9ff5-5c8c228c5105/dqc_reference/reference_markers.hmm GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:55,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:55,562] [INFO] Found 6/6 markers.
[2024-01-24 12:39:55,604] [INFO] Query marker FASTA was written to GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:39:55,604] [INFO] Task started: Blastn
[2024-01-24 12:39:55,604] [INFO] Running command: blastn -query GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7292ddd3-f62c-4566-9ff5-5c8c228c5105/dqc_reference/reference_markers.fasta -out GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:56,324] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:56,331] [INFO] Selected 18 target genomes.
[2024-01-24 12:39:56,332] [INFO] Target genome list was writen to GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:39:56,339] [INFO] Task started: fastANI
[2024-01-24 12:39:56,339] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0aa30d9-bb03-43b6-b098-24550cb3b64d/GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna.gz --refList GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:10,864] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:10,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7292ddd3-f62c-4566-9ff5-5c8c228c5105/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:10,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7292ddd3-f62c-4566-9ff5-5c8c228c5105/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:10,876] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:40:10,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:10,877] [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
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	100.0	1478	1483	95	conclusive
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	99.986	1483	1483	95	conclusive
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	99.969	1461	1483	95	conclusive
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.825	55	1483	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.3864	94	1483	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	77.2904	96	1483	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.153	102	1483	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.1325	109	1483	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.1151	75	1483	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.9773	96	1483	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	76.4008	70	1483	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.3612	73	1483	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.3262	97	1483	95	below_threshold
Konateibacter massiliensis	strain=Marseille-P3773	GCA_900184995.1	2002841	2002841	type	True	76.3094	66	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:10,882] [INFO] DFAST Taxonomy check result was written to GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:40:10,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:10,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:10,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7292ddd3-f62c-4566-9ff5-5c8c228c5105/dqc_reference/checkm_data
[2024-01-24 12:40:10,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:10,936] [INFO] Task started: CheckM
[2024-01-24 12:40:10,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/checkm_input GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:40:47,852] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:47,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:47,875] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:47,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:47,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:40:47,877] [INFO] Task started: Blastn
[2024-01-24 12:40:47,877] [INFO] Running command: blastn -query GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7292ddd3-f62c-4566-9ff5-5c8c228c5105/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:49,044] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:49,048] [INFO] Selected 18 target genomes.
[2024-01-24 12:40:49,048] [INFO] Target genome list was writen to GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:49,081] [INFO] Task started: fastANI
[2024-01-24 12:40:49,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0aa30d9-bb03-43b6-b098-24550cb3b64d/GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna.gz --refList GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:59,243] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:59,260] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:59,260] [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_000173815.1	s__Marvinbryantia formatexigens	99.969	1461	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.98	99.98	0.99	0.99	3	conclusive
GCA_905201705.1	s__Marvinbryantia sp900550755	86.3173	815	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	99.85	99.71	0.93	0.91	3	-
GCA_905200565.1	s__CAG-56 sp905200565	84.5979	151	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002473385.1	s__Marvinbryantia sp002473385	82.896	602	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297895.1	s__Marvinbryantia sp016297895	77.3331	123	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612585.1	s__Choladousia sp003612585	77.2891	120	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003463065.1	s__Limivivens sp900066135	76.9832	105	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.47	97.63	0.91	0.79	5	-
GCA_902363665.1	s__Choladousia sp902363665	76.9175	158	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	97.59	97.59	0.93	0.93	2	-
GCA_018713435.1	s__Merdiplasma excrementigallinarum	76.8282	87	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161355.1	s__Mediterraneibacter caccavium	76.7753	81	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.91	97.67	0.90	0.86	7	-
GCA_900551235.1	s__UMGS1375 sp900551235	76.7688	75	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223415.1	s__Copromonas sp900541255	76.5579	83	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	99.81	99.68	0.96	0.93	4	-
GCA_018712615.1	s__Egerieimonas_A faecigallinarum	76.5242	97	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Egerieimonas_A	95.0	99.76	99.76	0.85	0.85	2	-
GCF_018917935.1	s__CAG-194 sp018917935	76.4495	64	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491565.1	s__Choladousia sp002491565	76.4127	133	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715645.1	s__Merdisoma merdipullorum	76.3733	99	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	99.92	99.92	0.91	0.91	2	-
GCA_910587955.1	s__Merdisoma sp910587955	76.0797	91	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550285.1	s__Eisenbergiella sp900550285	76.0585	88	1483	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	99.00	98.94	0.88	0.81	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:59,263] [INFO] GTDB search result was written to GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:59,263] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:59,270] [INFO] DFAST_QC result json was written to GCF_900102475.1_IMG-taxon_2599185228_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:40:59,270] [INFO] DFAST_QC completed!
[2024-01-24 12:40:59,270] [INFO] Total running time: 0h1m18s