[2024-01-24 11:12:39,891] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,894] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fb63847-b820-44c5-8711-2f2c53a87420/dqc_reference
[2024-01-24 11:12:41,307] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,308] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,308] [INFO] Running command: gunzip -c /var/lib/cwl/stgd882bcbb-cd0a-473a-a5a1-c1b28e4593de/GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/cds.fna -a GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:47,722] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:47,723] [INFO] Task started: HMMsearch
[2024-01-24 11:12:47,723] [INFO] Running command: hmmsearch --tblout GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fb63847-b820-44c5-8711-2f2c53a87420/dqc_reference/reference_markers.hmm GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:48,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:48,038] [INFO] Found 6/6 markers.
[2024-01-24 11:12:48,076] [INFO] Query marker FASTA was written to GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:12:48,076] [INFO] Task started: Blastn
[2024-01-24 11:12:48,076] [INFO] Running command: blastn -query GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fb63847-b820-44c5-8711-2f2c53a87420/dqc_reference/reference_markers.fasta -out GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:48,679] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:48,682] [INFO] Selected 29 target genomes.
[2024-01-24 11:12:48,682] [INFO] Target genome list was writen to GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:12:48,701] [INFO] Task started: fastANI
[2024-01-24 11:12:48,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgd882bcbb-cd0a-473a-a5a1-c1b28e4593de/GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna.gz --refList GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:08,086] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:08,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fb63847-b820-44c5-8711-2f2c53a87420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:08,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fb63847-b820-44c5-8711-2f2c53a87420/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:08,105] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:08,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:08,106] [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 frigidicarnis	strain=DSM 12271	GCA_900111985.1	84698	84698	type	True	100.0	1385	1392	95	conclusive
Clostridium hydrogeniformans	strain=DSM 21757	GCA_000686705.1	349933	349933	type	True	78.3243	407	1392	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	77.4794	208	1392	95	below_threshold
Clostridium combesii	strain=DSM 20696	GCA_002749945.1	39481	39481	type	True	77.2549	256	1392	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.2328	251	1392	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	77.1292	200	1392	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	76.9738	231	1392	95	below_threshold
Clostridium algidicarnis	strain=DSM 15099	GCA_002934235.1	37659	37659	type	True	76.9362	177	1392	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.9071	247	1392	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	76.8491	209	1392	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	76.7636	224	1392	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.7426	220	1392	95	below_threshold
Clostridium ihumii	strain=AP5	GCA_000612845.1	1470356	1470356	type	True	76.7067	264	1392	95	below_threshold
Clostridium putrefaciens	strain=NCTC9836	GCA_900461105.1	99675	99675	type	True	76.6762	183	1392	95	below_threshold
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	76.6706	153	1392	95	below_threshold
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	76.6458	191	1392	95	below_threshold
Desnuesiella massiliensis	strain=mt10	GCA_001403615.1	1650662	1650662	type	True	76.6186	219	1392	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	76.6014	156	1392	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	76.5777	230	1392	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	76.491	208	1392	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	76.3419	206	1392	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.3331	197	1392	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.1837	165	1392	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	75.9716	152	1392	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.0129	68	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:08,108] [INFO] DFAST Taxonomy check result was written to GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:13:08,108] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:08,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:08,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fb63847-b820-44c5-8711-2f2c53a87420/dqc_reference/checkm_data
[2024-01-24 11:13:08,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:08,153] [INFO] Task started: CheckM
[2024-01-24 11:13:08,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/checkm_input GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:13:34,295] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:34,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:34,319] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:34,319] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:34,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:13:34,320] [INFO] Task started: Blastn
[2024-01-24 11:13:34,320] [INFO] Running command: blastn -query GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fb63847-b820-44c5-8711-2f2c53a87420/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:35,138] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:35,142] [INFO] Selected 30 target genomes.
[2024-01-24 11:13:35,143] [INFO] Target genome list was writen to GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:35,164] [INFO] Task started: fastANI
[2024-01-24 11:13:35,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgd882bcbb-cd0a-473a-a5a1-c1b28e4593de/GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna.gz --refList GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:55,231] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:55,258] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:55,259] [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_900111985.1	s__Clostridium_Z frigidicarnis	100.0	1385	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_Z	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000686705.1	s__Clostridium_Z hydrogeniformans	78.3362	402	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000753435.1	s__Clostridium_L amazonitimonense	77.686	199	1392	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_900112485.1	s__Clostridium uliginosum	77.2093	254	1392	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_001276215.1	s__Clostridium_F sp001276215	77.0832	233	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_001276985.1	s__Clostridium_F botulinum	77.0418	251	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
GCF_000424205.1	s__Clostridium_X cadaveris	77.0366	203	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	99.52	99.40	0.92	0.82	7	-
GCF_002934235.1	s__Clostridium_L algidicarnis	76.9492	176	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	97.66	96.15	0.89	0.86	14	-
GCF_900129365.1	s__Clostridium_AH fallax	76.8858	240	1392	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_018332455.1	s__Clostridium_AR polyendosporum	76.785	147	1392	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_001038625.1	s__Clostridium_AM carboxidivorans	76.7845	222	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_000612845.1	s__Clostridium_J ihumii	76.7231	262	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001403615.1	s__Desnuesiella massiliensis	76.6088	220	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Desnuesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004015185.1	s__Clostridium_AR sp004015185	76.6037	156	1392	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_017873235.1	s__Clostridium moniliforme	76.5959	228	1392	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_009928445.1	s__Clostridium_AR sp009928445	76.5934	164	1392	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_000633595.2	s__Clostridium_AM drakei	76.5667	219	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
GCA_900539375.1	s__Clostridium sp900539375	76.5508	162	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.09	99.02	0.89	0.86	4	-
GCF_016595795.1	s__Clostridium_AR sp016595795	76.5334	182	1392	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_000013285.1	s__Clostridium_P perfringens	76.5001	207	1392	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	-
GCA_015058525.1	s__Clostridium butyricum_A	76.4969	115	1392	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	76.4364	186	1392	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_004353185.1	s__Clostridium cuniculi	76.3281	204	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCA_900766315.1	s__Clostridium sp900766315	76.3185	196	1392	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_902785295.1	s__Clostridium sp902785295	75.9834	169	1392	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_900167505.1	s__F0540 sp900167505	75.9409	157	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCF_016765695.1	s__Sporosalibacterium faouarense	75.0129	68	1392	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__VENL01;g__Sporosalibacterium	95.0	99.35	99.35	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:55,261] [INFO] GTDB search result was written to GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:55,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:55,266] [INFO] DFAST_QC result json was written to GCF_900111985.1_IMG-taxon_2634166358_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:13:55,267] [INFO] DFAST_QC completed!
[2024-01-24 11:13:55,267] [INFO] Total running time: 0h1m15s