[2024-01-24 13:25:30,429] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg70c20499-cceb-45d8-a7b3-18d32ccbd782/dqc_reference
[2024-01-24 13:25:31,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,833] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf0daf61-5e97-4f88-82cb-7d4b3d9d4c03/GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/cds.fna -a GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:34,574] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:34,575] [INFO] Task started: HMMsearch
[2024-01-24 13:25:34,575] [INFO] Running command: hmmsearch --tblout GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70c20499-cceb-45d8-a7b3-18d32ccbd782/dqc_reference/reference_markers.hmm GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:34,830] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:34,832] [INFO] Found 6/6 markers.
[2024-01-24 13:25:34,852] [INFO] Query marker FASTA was written to GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:25:34,852] [INFO] Task started: Blastn
[2024-01-24 13:25:34,853] [INFO] Running command: blastn -query GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c20499-cceb-45d8-a7b3-18d32ccbd782/dqc_reference/reference_markers.fasta -out GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:35,496] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:35,500] [INFO] Selected 21 target genomes.
[2024-01-24 13:25:35,500] [INFO] Target genome list was writen to GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:25:35,520] [INFO] Task started: fastANI
[2024-01-24 13:25:35,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf0daf61-5e97-4f88-82cb-7d4b3d9d4c03/GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna.gz --refList GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:46,512] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:46,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70c20499-cceb-45d8-a7b3-18d32ccbd782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:46,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70c20499-cceb-45d8-a7b3-18d32ccbd782/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:46,528] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:46,529] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:46,529] [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
Caloramator fervidus	strain=DSM 5463	GCA_900108045.1	29344	29344	type	True	100.0	559	564	95	conclusive
Caloramator australicus	strain=RC3	GCA_000297115.1	515264	515264	type	True	80.1861	323	564	95	below_threshold
Caloramator mitchellensis	strain=VF08	GCA_001440545.1	908809	908809	type	True	77.6162	196	564	95	below_threshold
Fervidicella metallireducens	strain=AeB	GCA_000601455.1	655338	655338	type	True	76.6083	104	564	95	below_threshold
Fonticella tunisiensis	strain=DSM 24455	GCA_004364155.1	1096341	1096341	type	True	76.5549	69	564	95	below_threshold
Clostridium thermopalmarium	strain=DSM 5974	GCA_003097175.1	29373	29373	suspected-type	True	76.0713	50	564	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	75.9506	57	564	95	below_threshold
Clostridium rectalis	strain=Marseille-P4200	GCA_900626095.1	2040295	2040295	type	True	75.9208	63	564	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	75.8081	58	564	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	75.7862	59	564	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	75.7835	79	564	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	75.6627	71	564	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	75.6481	71	564	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	75.4971	51	564	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	75.4696	50	564	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	75.431	63	564	95	below_threshold
Clostridium gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	75.3767	53	564	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:46,531] [INFO] DFAST Taxonomy check result was written to GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:25:46,532] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:46,532] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:46,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70c20499-cceb-45d8-a7b3-18d32ccbd782/dqc_reference/checkm_data
[2024-01-24 13:25:46,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:46,557] [INFO] Task started: CheckM
[2024-01-24 13:25:46,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/checkm_input GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:26:03,842] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:03,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:03,866] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:03,867] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:03,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:26:03,868] [INFO] Task started: Blastn
[2024-01-24 13:26:03,868] [INFO] Running command: blastn -query GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg70c20499-cceb-45d8-a7b3-18d32ccbd782/dqc_reference/reference_markers_gtdb.fasta -out GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:04,853] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:04,857] [INFO] Selected 20 target genomes.
[2024-01-24 13:26:04,858] [INFO] Target genome list was writen to GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:04,877] [INFO] Task started: fastANI
[2024-01-24 13:26:04,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf0daf61-5e97-4f88-82cb-7d4b3d9d4c03/GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna.gz --refList GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:14,977] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:14,991] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:14,991] [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_900108045.1	s__Caloramator fervidus	100.0	559	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000297115.1	s__Caloramator australicus	80.1506	325	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440545.1	s__Caloramator mitchellensis	77.6162	196	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129265.1	s__Caloramator_A proteoclasticus	77.5595	128	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_A	95.0	98.54	98.54	0.90	0.90	2	-
GCF_000430995.1	s__Thermobrachium celere	77.4071	168	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Thermobrachium	95.0	98.16	98.16	0.91	0.91	2	-
GCF_006016075.1	s__Caloramator_B sp006016075	76.8879	141	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167605.1	s__Caloramator_B quimbayensis	76.8577	125	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918055.1	s__Clostridium sp018918055	76.1785	54	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400085.1	s__UBA4839 sp002400085	76.0368	76	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__UBA4839	95.0	99.41	99.11	0.85	0.82	15	-
GCF_002285495.1	s__Clostridium isatidis	75.9506	57	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.19	99.19	0.81	0.81	2	-
GCA_000753435.1	s__Clostridium_L amazonitimonense	75.4989	61	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	99.33	97.98	0.97	0.93	4	-
GCF_000340885.1	s__Clostridium saccharoperbutylacetonicum	75.4971	51	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.35	98.00	0.96	0.89	7	-
GCF_000619945.1	s__Clostridium_AO lundense	75.4836	64	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270375.1	s__Clostridium_S sp001270375	75.45	50	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539375.1	s__Clostridium sp900539375	75.4189	51	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.09	99.02	0.89	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:14,993] [INFO] GTDB search result was written to GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:14,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:15,001] [INFO] DFAST_QC result json was written to GCF_900108045.1_IMG-taxon_2599185232_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:26:15,002] [INFO] DFAST_QC completed!
[2024-01-24 13:26:15,002] [INFO] Total running time: 0h0m45s