[2024-01-25 20:08:05,492] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:08:05,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:08:05,493] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6454bfc-661b-47bb-88e9-1cfb40ecfb7d/dqc_reference
[2024-01-25 20:08:06,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:08:06,613] [INFO] Task started: Prodigal
[2024-01-25 20:08:06,613] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf6e6f21-04d4-493c-bfbe-228909e3dbaa/GCF_018332455.1_ASM1833245v1_genomic.fna.gz | prodigal -d GCF_018332455.1_ASM1833245v1_genomic.fna/cds.fna -a GCF_018332455.1_ASM1833245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:11,515] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:11,515] [INFO] Task started: HMMsearch
[2024-01-25 20:08:11,515] [INFO] Running command: hmmsearch --tblout GCF_018332455.1_ASM1833245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6454bfc-661b-47bb-88e9-1cfb40ecfb7d/dqc_reference/reference_markers.hmm GCF_018332455.1_ASM1833245v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:11,751] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:11,752] [INFO] Found 6/6 markers.
[2024-01-25 20:08:11,779] [INFO] Query marker FASTA was written to GCF_018332455.1_ASM1833245v1_genomic.fna/markers.fasta
[2024-01-25 20:08:11,780] [INFO] Task started: Blastn
[2024-01-25 20:08:11,780] [INFO] Running command: blastn -query GCF_018332455.1_ASM1833245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6454bfc-661b-47bb-88e9-1cfb40ecfb7d/dqc_reference/reference_markers.fasta -out GCF_018332455.1_ASM1833245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:12,323] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:12,325] [INFO] Selected 21 target genomes.
[2024-01-25 20:08:12,326] [INFO] Target genome list was writen to GCF_018332455.1_ASM1833245v1_genomic.fna/target_genomes.txt
[2024-01-25 20:08:12,343] [INFO] Task started: fastANI
[2024-01-25 20:08:12,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf6e6f21-04d4-493c-bfbe-228909e3dbaa/GCF_018332455.1_ASM1833245v1_genomic.fna.gz --refList GCF_018332455.1_ASM1833245v1_genomic.fna/target_genomes.txt --output GCF_018332455.1_ASM1833245v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:26,741] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:26,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6454bfc-661b-47bb-88e9-1cfb40ecfb7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:26,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6454bfc-661b-47bb-88e9-1cfb40ecfb7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:26,755] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:08:26,755] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:26,755] [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 polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	100.0	1196	1204	95	conclusive
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	77.7813	206	1204	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.7744	214	1204	95	below_threshold
Clostridium fungisolvens	strain=TW1	GCA_014193895.1	1604897	1604897	type	True	77.657	250	1204	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	77.4733	236	1204	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	77.104	182	1204	95	below_threshold
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	77.038	177	1204	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.9219	228	1204	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	76.9106	145	1204	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.8963	156	1204	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	76.8792	178	1204	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	76.7864	171	1204	95	below_threshold
Clostridium hydrogeniformans	strain=DSM 21757	GCA_000686705.1	349933	349933	type	True	76.698	134	1204	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	76.691	141	1204	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	76.5562	144	1204	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.4284	196	1204	95	below_threshold
Clostridium rectalis	strain=Marseille-P4200	GCA_900626095.1	2040295	2040295	type	True	76.1536	100	1204	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	75.9838	118	1204	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	75.8796	118	1204	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	75.8734	118	1204	95	below_threshold
Caloramator australicus	strain=RC3	GCA_000297115.1	515264	515264	type	True	75.6182	51	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:26,756] [INFO] DFAST Taxonomy check result was written to GCF_018332455.1_ASM1833245v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:26,757] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:26,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:26,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6454bfc-661b-47bb-88e9-1cfb40ecfb7d/dqc_reference/checkm_data
[2024-01-25 20:08:26,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:26,796] [INFO] Task started: CheckM
[2024-01-25 20:08:26,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018332455.1_ASM1833245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018332455.1_ASM1833245v1_genomic.fna/checkm_input GCF_018332455.1_ASM1833245v1_genomic.fna/checkm_result
[2024-01-25 20:08:46,575] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:46,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:46,592] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:46,592] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:46,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018332455.1_ASM1833245v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:46,592] [INFO] Task started: Blastn
[2024-01-25 20:08:46,593] [INFO] Running command: blastn -query GCF_018332455.1_ASM1833245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6454bfc-661b-47bb-88e9-1cfb40ecfb7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018332455.1_ASM1833245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:47,331] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:47,334] [INFO] Selected 27 target genomes.
[2024-01-25 20:08:47,334] [INFO] Target genome list was writen to GCF_018332455.1_ASM1833245v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:47,370] [INFO] Task started: fastANI
[2024-01-25 20:08:47,370] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf6e6f21-04d4-493c-bfbe-228909e3dbaa/GCF_018332455.1_ASM1833245v1_genomic.fna.gz --refList GCF_018332455.1_ASM1833245v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018332455.1_ASM1833245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:09:04,326] [INFO] Task succeeded: fastANI
[2024-01-25 20:09:04,341] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:09:04,341] [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_018332455.1	s__Clostridium_AR polyendosporum	100.0	1196	1204	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	conclusive
GCF_900129365.1	s__Clostridium_AH fallax	77.7975	205	1204	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_014193895.1	s__Clostridium_AR fungisolvens	77.6695	249	1204	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_004015185.1	s__Clostridium_AR sp004015185	77.4644	236	1204	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_009928445.1	s__Clostridium_AR sp009928445	77.3889	228	1204	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_016595795.1	s__Clostridium_AR sp016595795	77.3529	250	1204	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_002327185.1	s__Clostridium chauvoei	77.0727	154	1204	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_009295725.1	s__Clostridium_P tarantellae	77.0671	183	1204	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_900111985.1	s__Clostridium_Z frigidicarnis	76.9449	139	1204	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	-
GCF_900456775.1	s__Clostridium_P ventriculi	76.8905	144	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.93	98.34	0.95	0.94	8	-
GCF_017873245.1	s__Clostridium tertium	76.8757	175	1204	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_002006345.1	s__Clostridium puniceum	76.8655	179	1204	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	76.8277	163	1204	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_900130055.1	s__Clostridium_T intestinale	76.7848	191	1204	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_004353185.1	s__Clostridium cuniculi	76.7559	158	1204	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_900112485.1	s__Clostridium uliginosum	76.755	171	1204	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_900539375.1	s__Clostridium sp900539375	76.7275	153	1204	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_900091705.1	s__Clostridium_P mediterraneense	76.7083	138	1204	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_016907995.1	s__Clostridium sardiniense	76.6812	151	1204	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_002050515.1	s__Clostridium thermobutyricum	76.6635	157	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	-
GCA_900547475.1	s__Clostridium sp900547475	76.6173	157	1204	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_018918325.1	s__Clostridium sp018918325	76.5999	117	1204	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	76.5562	144	1204	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_001276215.1	s__Clostridium_F sp001276215	76.3813	142	1204	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	-
GCA_018372555.1	s__Clostridium sp018372555	76.1332	123	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:09:04,343] [INFO] GTDB search result was written to GCF_018332455.1_ASM1833245v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:09:04,344] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:09:04,349] [INFO] DFAST_QC result json was written to GCF_018332455.1_ASM1833245v1_genomic.fna/dqc_result.json
[2024-01-25 20:09:04,350] [INFO] DFAST_QC completed!
[2024-01-25 20:09:04,350] [INFO] Total running time: 0h0m59s