[2024-01-24 13:33:41,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:41,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:41,301] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfff4487-12b4-4730-8f6b-cd68d055c21d/dqc_reference
[2024-01-24 13:33:42,490] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,491] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,491] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4e29870-6f55-403b-a5b8-3239ec00af37/GCF_900461065.1_51485_E02_genomic.fna.gz | prodigal -d GCF_900461065.1_51485_E02_genomic.fna/cds.fna -a GCF_900461065.1_51485_E02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:46,397] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:46,397] [INFO] Task started: HMMsearch
[2024-01-24 13:33:46,398] [INFO] Running command: hmmsearch --tblout GCF_900461065.1_51485_E02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfff4487-12b4-4730-8f6b-cd68d055c21d/dqc_reference/reference_markers.hmm GCF_900461065.1_51485_E02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:46,679] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:46,680] [INFO] Found 6/6 markers.
[2024-01-24 13:33:46,707] [INFO] Query marker FASTA was written to GCF_900461065.1_51485_E02_genomic.fna/markers.fasta
[2024-01-24 13:33:46,707] [INFO] Task started: Blastn
[2024-01-24 13:33:46,707] [INFO] Running command: blastn -query GCF_900461065.1_51485_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfff4487-12b4-4730-8f6b-cd68d055c21d/dqc_reference/reference_markers.fasta -out GCF_900461065.1_51485_E02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:47,318] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:47,322] [INFO] Selected 26 target genomes.
[2024-01-24 13:33:47,322] [INFO] Target genome list was writen to GCF_900461065.1_51485_E02_genomic.fna/target_genomes.txt
[2024-01-24 13:33:47,488] [INFO] Task started: fastANI
[2024-01-24 13:33:47,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e29870-6f55-403b-a5b8-3239ec00af37/GCF_900461065.1_51485_E02_genomic.fna.gz --refList GCF_900461065.1_51485_E02_genomic.fna/target_genomes.txt --output GCF_900461065.1_51485_E02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:04,460] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:04,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfff4487-12b4-4730-8f6b-cd68d055c21d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:04,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfff4487-12b4-4730-8f6b-cd68d055c21d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:04,485] [INFO] Found 26 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:34:04,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:34:04,485] [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 fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	100.0	943	944	95	conclusive
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	99.9242	879	944	95	conclusive
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	78.7543	279	944	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	78.5299	274	944	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.4786	283	944	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	78.3701	216	944	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	77.9595	275	944	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	77.9401	234	944	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	77.771	193	944	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	77.7628	263	944	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	77.646	213	944	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	77.5908	237	944	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	77.46	227	944	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	77.3867	295	944	95	below_threshold
Clostridium intestinale	strain=DSM 6191	GCA_900130055.1	36845	36845	type	True	77.3254	215	944	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	77.3099	223	944	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.2806	217	944	95	below_threshold
Clostridium zeae	strain=CSC2	GCA_017312485.1	2759022	2759022	type	True	77.2333	240	944	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	77.2175	282	944	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.131	249	944	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.0586	259	944	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.7839	204	944	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.4103	207	944	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	76.2725	218	944	95	below_threshold
Fusobacterium necrogenes	strain=NCTC10723	GCA_900450765.1	858	858	type	True	75.8442	72	944	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	75.0064	75	944	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:04,487] [INFO] DFAST Taxonomy check result was written to GCF_900461065.1_51485_E02_genomic.fna/tc_result.tsv
[2024-01-24 13:34:04,488] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:04,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:04,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfff4487-12b4-4730-8f6b-cd68d055c21d/dqc_reference/checkm_data
[2024-01-24 13:34:04,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:04,519] [INFO] Task started: CheckM
[2024-01-24 13:34:04,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900461065.1_51485_E02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900461065.1_51485_E02_genomic.fna/checkm_input GCF_900461065.1_51485_E02_genomic.fna/checkm_result
[2024-01-24 13:34:23,801] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:23,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:23,823] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:23,823] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:23,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900461065.1_51485_E02_genomic.fna/markers.fasta)
[2024-01-24 13:34:23,824] [INFO] Task started: Blastn
[2024-01-24 13:34:23,824] [INFO] Running command: blastn -query GCF_900461065.1_51485_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfff4487-12b4-4730-8f6b-cd68d055c21d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900461065.1_51485_E02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:24,630] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:24,633] [INFO] Selected 30 target genomes.
[2024-01-24 13:34:24,633] [INFO] Target genome list was writen to GCF_900461065.1_51485_E02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:24,926] [INFO] Task started: fastANI
[2024-01-24 13:34:24,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e29870-6f55-403b-a5b8-3239ec00af37/GCF_900461065.1_51485_E02_genomic.fna.gz --refList GCF_900461065.1_51485_E02_genomic.fna/target_genomes_gtdb.txt --output GCF_900461065.1_51485_E02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:43,992] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:44,021] [INFO] Found 30 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:44,022] [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_900129365.1	s__Clostridium_AH fallax	99.9242	879	944	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	conclusive
GCF_000013285.1	s__Clostridium_P perfringens	78.4815	272	944	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_002285495.1	s__Clostridium isatidis	77.9161	191	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.19	99.19	0.81	0.81	2	-
GCF_001403635.1	s__Clostridium_P massiliamazoniense	77.7921	265	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900091705.1	s__Clostridium_P mediterraneense	77.6973	233	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018332455.1	s__Clostridium_AR polyendosporum	77.6762	211	944	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_015555905.1	s__Clostridium sp015555905	77.5973	209	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.95	98.95	0.73	0.73	2	-
GCA_000753455.2	s__Clostridium sp000753455	77.3878	228	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.13	99.13	0.91	0.91	2	-
GCF_900141845.1	s__Clostridium_AG cavendishii	77.3759	297	944	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_900547475.1	s__Clostridium sp900547475	77.3427	223	944	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_900130055.1	s__Clostridium_T intestinale	77.3336	213	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_T	95.0	95.87	95.52	0.87	0.83	4	-
GCF_009295725.1	s__Clostridium_P tarantellae	77.3074	274	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918325.1	s__Clostridium sp018918325	77.2908	162	944	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_017312485.1	s__Clostridium_AR sp017312485	77.2435	241	944	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_015670405.1	s__Clostridium sp015670405	77.2376	203	944	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_016765615.1	s__Clostridium_T sp016765615	77.1537	211	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836325.1	s__Clostridium sp014836325	77.148	249	944	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_004353185.1	s__Clostridium cuniculi	77.1106	239	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCF_004794105.1	s__Clostridium sartagoforme_B	77.099	221	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCA_015058475.1	s__Clostridium butyricum_B	77.0939	173	944	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_000320405.1	s__Clostridium celatum	76.9928	217	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	-
GCF_001458595.1	s__Clostridium neonatale	76.9815	228	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.07	98.42	0.91	0.80	11	-
GCF_000401215.1	s__Clostridium sartagoforme_A	76.9806	233	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCA_017888565.1	s__Clostridium sp017888565	76.9398	252	944	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_900759995.1	s__Clostridium sp900759995	76.933	219	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.46	98.18	0.80	0.79	3	-
GCA_900540255.1	s__Clostridium sp900540255	76.9118	217	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	-
GCA_012519845.1	s__Clostridium sp012519845	76.8624	170	944	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_009928485.1	s__Clostridium sp009928485	76.6825	236	944	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_002008345.1	s__Clostridium_F tepidum	76.4233	204	944	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_001276215.1	s__Clostridium_F sp001276215	76.2401	219	944	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:44,024] [INFO] GTDB search result was written to GCF_900461065.1_51485_E02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:44,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:44,030] [INFO] DFAST_QC result json was written to GCF_900461065.1_51485_E02_genomic.fna/dqc_result.json
[2024-01-24 13:34:44,030] [INFO] DFAST_QC completed!
[2024-01-24 13:34:44,030] [INFO] Total running time: 0h1m3s