[2024-01-24 13:37:13,487] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:13,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:13,490] [INFO] DQC Reference Directory: /var/lib/cwl/stga2f90e0f-48d9-4b8a-8b95-01143ce9380e/dqc_reference
[2024-01-24 13:37:14,729] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:14,730] [INFO] Task started: Prodigal
[2024-01-24 13:37:14,731] [INFO] Running command: gunzip -c /var/lib/cwl/stg27a4a998-0e8e-4dbb-adf7-f09bd8ff91f1/GCF_018866245.1_ASM1886624v1_genomic.fna.gz | prodigal -d GCF_018866245.1_ASM1886624v1_genomic.fna/cds.fna -a GCF_018866245.1_ASM1886624v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:23,240] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:23,241] [INFO] Task started: HMMsearch
[2024-01-24 13:37:23,241] [INFO] Running command: hmmsearch --tblout GCF_018866245.1_ASM1886624v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2f90e0f-48d9-4b8a-8b95-01143ce9380e/dqc_reference/reference_markers.hmm GCF_018866245.1_ASM1886624v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:23,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:23,518] [INFO] Found 6/6 markers.
[2024-01-24 13:37:23,548] [INFO] Query marker FASTA was written to GCF_018866245.1_ASM1886624v1_genomic.fna/markers.fasta
[2024-01-24 13:37:23,548] [INFO] Task started: Blastn
[2024-01-24 13:37:23,548] [INFO] Running command: blastn -query GCF_018866245.1_ASM1886624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2f90e0f-48d9-4b8a-8b95-01143ce9380e/dqc_reference/reference_markers.fasta -out GCF_018866245.1_ASM1886624v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:24,230] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:24,234] [INFO] Selected 28 target genomes.
[2024-01-24 13:37:24,234] [INFO] Target genome list was writen to GCF_018866245.1_ASM1886624v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:24,254] [INFO] Task started: fastANI
[2024-01-24 13:37:24,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a4a998-0e8e-4dbb-adf7-f09bd8ff91f1/GCF_018866245.1_ASM1886624v1_genomic.fna.gz --refList GCF_018866245.1_ASM1886624v1_genomic.fna/target_genomes.txt --output GCF_018866245.1_ASM1886624v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:41,480] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:41,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2f90e0f-48d9-4b8a-8b95-01143ce9380e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:41,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2f90e0f-48d9-4b8a-8b95-01143ce9380e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:41,496] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:41,497] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:41,497] [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
Novisyntrophococcus fermenticellae	strain=JN500902	GCA_018866245.1	2068655	2068655	type	True	100.0	1140	1140	95	conclusive
Blautia liquoris	strain=LZLJ-3	GCA_015159595.1	2779518	2779518	type	True	80.9633	249	1140	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.124	57	1140	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	78.5438	54	1140	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.4555	76	1140	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.4468	52	1140	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	78.204	64	1140	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	78.068	59	1140	95	below_threshold
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	78.022	76	1140	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	77.938	82	1140	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.8016	60	1140	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	77.7823	82	1140	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.6213	96	1140	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	77.6143	82	1140	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	77.4364	63	1140	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	77.4326	76	1140	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	76.9946	62	1140	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_002915525.1	341220	341220	suspected-type	True	76.9566	54	1140	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.6715	62	1140	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.587	55	1140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:41,499] [INFO] DFAST Taxonomy check result was written to GCF_018866245.1_ASM1886624v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:41,499] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:41,499] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:41,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2f90e0f-48d9-4b8a-8b95-01143ce9380e/dqc_reference/checkm_data
[2024-01-24 13:37:41,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:41,537] [INFO] Task started: CheckM
[2024-01-24 13:37:41,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018866245.1_ASM1886624v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018866245.1_ASM1886624v1_genomic.fna/checkm_input GCF_018866245.1_ASM1886624v1_genomic.fna/checkm_result
[2024-01-24 13:38:13,109] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:13,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:13,135] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:13,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:13,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018866245.1_ASM1886624v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:13,136] [INFO] Task started: Blastn
[2024-01-24 13:38:13,136] [INFO] Running command: blastn -query GCF_018866245.1_ASM1886624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2f90e0f-48d9-4b8a-8b95-01143ce9380e/dqc_reference/reference_markers_gtdb.fasta -out GCF_018866245.1_ASM1886624v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:14,181] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:14,185] [INFO] Selected 24 target genomes.
[2024-01-24 13:38:14,185] [INFO] Target genome list was writen to GCF_018866245.1_ASM1886624v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:14,218] [INFO] Task started: fastANI
[2024-01-24 13:38:14,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg27a4a998-0e8e-4dbb-adf7-f09bd8ff91f1/GCF_018866245.1_ASM1886624v1_genomic.fna.gz --refList GCF_018866245.1_ASM1886624v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018866245.1_ASM1886624v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:27,104] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:27,130] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:27,131] [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
GCA_018866245.1	s__Pelethocola sp018866245	100.0	1140	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015159595.1	s__Pelethocola sp015159595	80.8735	248	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018714325.1	s__Pelethocola excrementipullorum	78.9257	290	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015557635.1	s__Fusicatenibacter saccharivorans	78.59	59	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fusicatenibacter	95.0	97.82	97.27	0.86	0.77	91	-
GCF_000155205.1	s__Mediterraneibacter lactaris	78.4978	51	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCF_003574295.1	s__Mediterraneibacter_A butyricigenes	78.2595	52	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter_A	95.0	98.15	98.07	0.82	0.80	5	-
GCA_900539175.1	s__Pelethocola sp900539175	78.1893	205	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	99.69	99.49	0.84	0.76	3	-
GCA_002409525.1	s__Pelethocola sp002409525	78.1485	147	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pelethocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524165.2	s__Muricomes sp012524165	77.825	58	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363515.1	s__Blautia sp000432195	77.7359	71	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.93	98.81	0.87	0.83	7	-
GCF_900129135.1	s__Lactonifactor longoviformis	77.4719	75	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lactonifactor	95.0	99.99	99.99	0.99	0.99	3	-
GCA_018374355.1	s__Oliverpabstia sp018374355	77.1228	75	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013304445.1	s__Blautia sp900541955	76.9229	70	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.45	99.32	0.89	0.85	6	-
GCA_902362715.1	s__Eubacterium_I sp900066595	76.8122	61	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018366495.1	s__JAGZHZ01 sp018366495	76.4492	50	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAGZHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713515.1	s__Scatomonas pullistercoris	76.1138	68	1140	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.97	99.97	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:27,132] [INFO] GTDB search result was written to GCF_018866245.1_ASM1886624v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:27,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:27,137] [INFO] DFAST_QC result json was written to GCF_018866245.1_ASM1886624v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:27,137] [INFO] DFAST_QC completed!
[2024-01-24 13:38:27,138] [INFO] Total running time: 0h1m14s