[2024-01-24 12:47:05,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,312] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,312] [INFO] DQC Reference Directory: /var/lib/cwl/stge5cb9aec-cc65-4d34-bc6b-c5d493cd06f0/dqc_reference
[2024-01-24 12:47:06,511] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,512] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,512] [INFO] Running command: gunzip -c /var/lib/cwl/stg337d1b10-e507-4cb5-8e2f-f707005dd0b6/GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/cds.fna -a GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:14,084] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:14,085] [INFO] Task started: HMMsearch
[2024-01-24 12:47:14,085] [INFO] Running command: hmmsearch --tblout GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5cb9aec-cc65-4d34-bc6b-c5d493cd06f0/dqc_reference/reference_markers.hmm GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:14,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:14,300] [INFO] Found 6/6 markers.
[2024-01-24 12:47:14,324] [INFO] Query marker FASTA was written to GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:47:14,324] [INFO] Task started: Blastn
[2024-01-24 12:47:14,325] [INFO] Running command: blastn -query GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge5cb9aec-cc65-4d34-bc6b-c5d493cd06f0/dqc_reference/reference_markers.fasta -out GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:14,987] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:14,991] [INFO] Selected 16 target genomes.
[2024-01-24 12:47:14,991] [INFO] Target genome list was writen to GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:47:14,999] [INFO] Task started: fastANI
[2024-01-24 12:47:14,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg337d1b10-e507-4cb5-8e2f-f707005dd0b6/GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna.gz --refList GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:22,611] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:22,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5cb9aec-cc65-4d34-bc6b-c5d493cd06f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:22,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5cb9aec-cc65-4d34-bc6b-c5d493cd06f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:22,622] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:22,622] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:22,622] [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
Papillibacter cinnamivorans	strain=DSM 12816	GCA_900176335.1	100176	100176	type	True	100.0	954	955	95	conclusive
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	77.0975	76	955	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.7806	79	955	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.736	105	955	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.5324	74	955	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.5264	99	955	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.5062	75	955	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.4926	79	955	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.4474	78	955	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.3293	96	955	95	below_threshold
Sporobacter termitidis	strain=DSM 10068	GCA_900130065.1	44749	44749	type	True	75.9123	65	955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:22,624] [INFO] DFAST Taxonomy check result was written to GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:47:22,624] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:22,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:22,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5cb9aec-cc65-4d34-bc6b-c5d493cd06f0/dqc_reference/checkm_data
[2024-01-24 12:47:22,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:22,655] [INFO] Task started: CheckM
[2024-01-24 12:47:22,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/checkm_input GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:47:49,950] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:49,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:49,971] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:49,971] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:49,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:47:49,972] [INFO] Task started: Blastn
[2024-01-24 12:47:49,972] [INFO] Running command: blastn -query GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge5cb9aec-cc65-4d34-bc6b-c5d493cd06f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:51,071] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:51,078] [INFO] Selected 23 target genomes.
[2024-01-24 12:47:51,078] [INFO] Target genome list was writen to GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:51,106] [INFO] Task started: fastANI
[2024-01-24 12:47:51,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg337d1b10-e507-4cb5-8e2f-f707005dd0b6/GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna.gz --refList GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:01,516] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:01,532] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:01,532] [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_900176335.1	s__Papillibacter cinnamivorans	100.0	954	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Papillibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002161215.1	s__Flavonifractor avistercoris	77.3653	107	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_900626145.1	s__Intestinimonas timonensis	76.8527	99	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159175.1	s__An92 sp002159175	76.8028	102	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCF_000169255.2	s__Pseudoflavonifractor capillosus	76.7563	97	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	95.82	95.81	0.78	0.78	3	-
GCF_900169975.1	s__Marseille-P3106 sp900169975	76.6485	86	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Marseille-P3106	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901955.1	s__Flavonifractor phocaeensis_A	76.6023	88	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000239295.1	s__Flavonifractor plautii	76.5475	98	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.23	97.77	0.83	0.59	43	-
GCF_900199495.1	s__An92 sp900199495	76.4927	96	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.28	97.84	0.85	0.79	7	-
GCF_002159265.1	s__Flavonifractor sp002159265	76.4898	87	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018374635.1	s__An92 sp018374635	76.472	88	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017516065.1	s__RGIG5644 sp017516065	76.4373	65	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__RGIG5644	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811815.1	s__Flavonifractor sp017811815	76.3679	85	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	76.3627	88	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCA_017541995.1	s__Faecousia sp017541995	76.346	52	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118935.1	s__Dysosmobacter pullicola	76.2946	81	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_019119795.1	s__Intestinimonas pullistercoris	76.2659	74	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.29	99.15	0.85	0.82	4	-
GCA_019118505.1	s__Dysosmobacter excrementavium	76.2615	80	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588365.1	s__Pelethomonas sp910588365	76.2382	61	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713205.1	s__Avoscillospira stercorigallinarum	76.0116	51	955	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Avoscillospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:01,534] [INFO] GTDB search result was written to GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:01,534] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:01,538] [INFO] DFAST_QC result json was written to GCF_900176335.1_IMG-taxon_2588254267_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:48:01,538] [INFO] DFAST_QC completed!
[2024-01-24 12:48:01,538] [INFO] Total running time: 0h0m56s