[2024-01-24 11:35:08,241] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:08,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:08,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg11e6a98c-2e09-4d71-97f7-e0931a8f7b13/dqc_reference
[2024-01-24 11:35:09,453] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:09,454] [INFO] Task started: Prodigal
[2024-01-24 11:35:09,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg232efed4-48d5-4202-a870-0fbaace58356/GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/cds.fna -a GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:15,586] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:15,587] [INFO] Task started: HMMsearch
[2024-01-24 11:35:15,587] [INFO] Running command: hmmsearch --tblout GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11e6a98c-2e09-4d71-97f7-e0931a8f7b13/dqc_reference/reference_markers.hmm GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:15,906] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:15,907] [INFO] Found 6/6 markers.
[2024-01-24 11:35:15,942] [INFO] Query marker FASTA was written to GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:35:15,943] [INFO] Task started: Blastn
[2024-01-24 11:35:15,943] [INFO] Running command: blastn -query GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg11e6a98c-2e09-4d71-97f7-e0931a8f7b13/dqc_reference/reference_markers.fasta -out GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:16,554] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:16,557] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:16,557] [INFO] Target genome list was writen to GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:35:16,596] [INFO] Task started: fastANI
[2024-01-24 11:35:16,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg232efed4-48d5-4202-a870-0fbaace58356/GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna.gz --refList GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:28,210] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:28,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11e6a98c-2e09-4d71-97f7-e0931a8f7b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:28,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11e6a98c-2e09-4d71-97f7-e0931a8f7b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:28,224] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:28,224] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:28,225] [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 gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	100.0	1325	1328	95	conclusive
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	78.583	386	1328	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.5557	401	1328	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	78.521	387	1328	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	77.9895	381	1328	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.8143	351	1328	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.5073	311	1328	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.4467	263	1328	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	77.1598	318	1328	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	76.9659	284	1328	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	76.9622	236	1328	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008580445.1	223919	223919	suspected-type	True	76.848	233	1328	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.7886	226	1328	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	76.7601	226	1328	95	below_threshold
Clostridium beijerinckii	strain=NCTC13035	GCA_900447025.1	1520	1520	suspected-type	True	76.7418	240	1328	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	76.723	240	1328	95	below_threshold
Fervidicella metallireducens	strain=AeB	GCA_000601455.1	655338	655338	type	True	75.1997	55	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:28,226] [INFO] DFAST Taxonomy check result was written to GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:35:28,227] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:28,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:28,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11e6a98c-2e09-4d71-97f7-e0931a8f7b13/dqc_reference/checkm_data
[2024-01-24 11:35:28,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:28,269] [INFO] Task started: CheckM
[2024-01-24 11:35:28,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/checkm_input GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:35:53,140] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:53,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:53,162] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:53,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:53,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:35:53,163] [INFO] Task started: Blastn
[2024-01-24 11:35:53,163] [INFO] Running command: blastn -query GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg11e6a98c-2e09-4d71-97f7-e0931a8f7b13/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:53,982] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:53,986] [INFO] Selected 22 target genomes.
[2024-01-24 11:35:53,986] [INFO] Target genome list was writen to GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:54,008] [INFO] Task started: fastANI
[2024-01-24 11:35:54,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg232efed4-48d5-4202-a870-0fbaace58356/GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna.gz --refList GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:07,211] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:07,226] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:07,227] [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_900104115.1	s__Clostridium gasigenes	100.0	1325	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.21	97.55	0.90	0.87	10	conclusive
GCF_002327185.1	s__Clostridium chauvoei	78.5354	403	1328	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_003606265.1	s__Clostridium septicum	78.5092	393	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_017873245.1	s__Clostridium tertium	77.9967	381	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCF_015550425.1	s__Clostridium sp015550425	77.9004	390	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.01	99.01	0.93	0.93	2	-
GCA_017888565.1	s__Clostridium sp017888565	77.8802	394	1328	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_014836325.1	s__Clostridium sp014836325	77.8234	350	1328	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_000827935.1	s__Clostridium botulinum_A	77.6088	292	1328	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	77.5174	310	1328	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_017873235.1	s__Clostridium moniliforme	77.4694	261	1328	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_900543325.1	s__Clostridium sp900543325	77.3797	262	1328	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_900547475.1	s__Clostridium sp900547475	77.3342	285	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.47	95.30	0.88	0.84	3	-
GCF_001405015.1	s__Clostridium disporicum	77.3099	264	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCF_001735765.2	s__Clostridium taeniosporum	77.2317	295	1328	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_016907995.1	s__Clostridium sardiniense	77.209	288	1328	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_900540255.1	s__Clostridium sp900540255	77.0597	277	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	-
GCF_018223745.1	s__Clostridium beijerinckii	76.713	238	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	-
GCA_003539755.1	s__Clostridium sp003539755	76.5562	145	1328	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:07,229] [INFO] GTDB search result was written to GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:07,230] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:07,236] [INFO] DFAST_QC result json was written to GCF_900104115.1_IMG-taxon_2634166322_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:36:07,237] [INFO] DFAST_QC completed!
[2024-01-24 11:36:07,237] [INFO] Total running time: 0h0m59s