[2024-01-24 15:18:35,618] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:35,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:35,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fed4460-9b7d-44d0-8813-e5fb568c875d/dqc_reference
[2024-01-24 15:18:38,358] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:38,362] [INFO] Task started: Prodigal
[2024-01-24 15:18:38,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg894ce7d2-dfc3-4fe4-a667-4af34f87a4cd/GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/cds.fna -a GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:45,745] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:45,746] [INFO] Task started: HMMsearch
[2024-01-24 15:18:45,746] [INFO] Running command: hmmsearch --tblout GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fed4460-9b7d-44d0-8813-e5fb568c875d/dqc_reference/reference_markers.hmm GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:46,206] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:46,207] [INFO] Found 6/6 markers.
[2024-01-24 15:18:46,247] [INFO] Query marker FASTA was written to GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:18:46,248] [INFO] Task started: Blastn
[2024-01-24 15:18:46,248] [INFO] Running command: blastn -query GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fed4460-9b7d-44d0-8813-e5fb568c875d/dqc_reference/reference_markers.fasta -out GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:49,194] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:49,197] [INFO] Selected 19 target genomes.
[2024-01-24 15:18:49,198] [INFO] Target genome list was writen to GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:18:49,224] [INFO] Task started: fastANI
[2024-01-24 15:18:49,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg894ce7d2-dfc3-4fe4-a667-4af34f87a4cd/GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna.gz --refList GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:05,309] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:05,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fed4460-9b7d-44d0-8813-e5fb568c875d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:05,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fed4460-9b7d-44d0-8813-e5fb568c875d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:05,324] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:05,325] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:05,325] [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
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	100.0	1411	1411	95	conclusive
Clostridium polynesiense	strain=MS1	GCA_000820705.1	1325933	1325933	type	True	78.6307	386	1411	95	below_threshold
Desnuesiella massiliensis	strain=mt10	GCA_001403615.1	1650662	1650662	type	True	78.1478	246	1411	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	77.9638	190	1411	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	77.3953	123	1411	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	76.7884	125	1411	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.7863	158	1411	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	76.7126	119	1411	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	76.6939	120	1411	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.6517	155	1411	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	76.5929	135	1411	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.5463	129	1411	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.5243	151	1411	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	76.4509	128	1411	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.3714	185	1411	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	75.7506	105	1411	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	74.9971	68	1411	95	below_threshold
Anaeromicrobium sediminis	strain=DY2726D	GCA_002270055.1	1478221	1478221	type	True	74.9471	60	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:05,327] [INFO] DFAST Taxonomy check result was written to GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:19:05,327] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:05,327] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:05,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fed4460-9b7d-44d0-8813-e5fb568c875d/dqc_reference/checkm_data
[2024-01-24 15:19:05,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:05,372] [INFO] Task started: CheckM
[2024-01-24 15:19:05,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/checkm_input GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:19:34,470] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:34,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:34,494] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:34,494] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:34,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:19:34,495] [INFO] Task started: Blastn
[2024-01-24 15:19:34,495] [INFO] Running command: blastn -query GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fed4460-9b7d-44d0-8813-e5fb568c875d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:35,292] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:35,295] [INFO] Selected 21 target genomes.
[2024-01-24 15:19:35,296] [INFO] Target genome list was writen to GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:35,305] [INFO] Task started: fastANI
[2024-01-24 15:19:35,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg894ce7d2-dfc3-4fe4-a667-4af34f87a4cd/GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna.gz --refList GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:48,715] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:48,738] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:48,739] [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_900142075.1	s__Clostridium_AA amylolyticum	100.0	1411	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AA	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000820705.1	s__Clostridium_AA polynesiense	78.6204	387	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AA	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001403615.1	s__Desnuesiella massiliensis	78.1187	246	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Desnuesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000753435.1	s__Clostridium_L amazonitimonense	77.8099	195	1411	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_000401215.1	s__Clostridium sartagoforme_A	77.0007	148	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCF_000013285.1	s__Clostridium_P perfringens	76.8223	108	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.05	95.74	0.91	0.81	315	-
GCF_002327185.1	s__Clostridium chauvoei	76.7869	125	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_900129365.1	s__Clostridium_AH fallax	76.6506	155	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009928445.1	s__Clostridium_AR sp009928445	76.4681	146	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827935.1	s__Clostridium botulinum_A	76.4579	123	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.05	97.92	0.91	0.85	31	-
GCF_900290265.1	s__Clostridium cagae	76.4352	126	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCF_900141845.1	s__Clostridium_AG cavendishii	76.3995	186	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766315.1	s__Clostridium sp900766315	76.3806	115	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015550425.1	s__Clostridium sp015550425	76.3785	133	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.01	99.01	0.93	0.93	2	-
GCF_900095445.1	s__UBA3947 sp900095445	76.3452	90	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__UBA3947	95.0	99.63	99.63	0.84	0.84	2	-
GCF_000498355.1	s__Clostridium sp000498355	76.3425	108	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004794105.1	s__Clostridium sartagoforme_B	76.3245	120	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCF_001758365.1	s__Clostridium_C acetireducens	76.1701	105	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000320405.1	s__Clostridium celatum	75.7506	105	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	-
GCA_902785295.1	s__Clostridium sp902785295	75.6043	91	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002270055.1	s__Anaeromicrobium sediminis	74.9471	60	1411	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Anaeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:48,740] [INFO] GTDB search result was written to GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:48,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:48,745] [INFO] DFAST_QC result json was written to GCF_900142075.1_IMG-taxon_2703719061_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:19:48,746] [INFO] DFAST_QC completed!
[2024-01-24 15:19:48,746] [INFO] Total running time: 0h1m13s