[2024-01-24 11:26:19,352] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:19,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:19,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg30a694fb-5754-4e95-bd1c-cadedcc5b8b1/dqc_reference
[2024-01-24 11:26:20,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:20,629] [INFO] Task started: Prodigal
[2024-01-24 11:26:20,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg525a6c57-d7eb-44a1-aa86-a52780008697/GCF_019754295.1_ASM1975429v1_genomic.fna.gz | prodigal -d GCF_019754295.1_ASM1975429v1_genomic.fna/cds.fna -a GCF_019754295.1_ASM1975429v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:33,612] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:33,612] [INFO] Task started: HMMsearch
[2024-01-24 11:26:33,613] [INFO] Running command: hmmsearch --tblout GCF_019754295.1_ASM1975429v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30a694fb-5754-4e95-bd1c-cadedcc5b8b1/dqc_reference/reference_markers.hmm GCF_019754295.1_ASM1975429v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:33,893] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:33,895] [INFO] Found 6/6 markers.
[2024-01-24 11:26:33,922] [INFO] Query marker FASTA was written to GCF_019754295.1_ASM1975429v1_genomic.fna/markers.fasta
[2024-01-24 11:26:33,922] [INFO] Task started: Blastn
[2024-01-24 11:26:33,923] [INFO] Running command: blastn -query GCF_019754295.1_ASM1975429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30a694fb-5754-4e95-bd1c-cadedcc5b8b1/dqc_reference/reference_markers.fasta -out GCF_019754295.1_ASM1975429v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:34,585] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:34,589] [INFO] Selected 27 target genomes.
[2024-01-24 11:26:34,590] [INFO] Target genome list was writen to GCF_019754295.1_ASM1975429v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:34,599] [INFO] Task started: fastANI
[2024-01-24 11:26:34,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg525a6c57-d7eb-44a1-aa86-a52780008697/GCF_019754295.1_ASM1975429v1_genomic.fna.gz --refList GCF_019754295.1_ASM1975429v1_genomic.fna/target_genomes.txt --output GCF_019754295.1_ASM1975429v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:47,700] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:47,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30a694fb-5754-4e95-bd1c-cadedcc5b8b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:47,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30a694fb-5754-4e95-bd1c-cadedcc5b8b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:47,719] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:47,719] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:47,720] [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
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	100.0	859	863	95	conclusive
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	79.0108	58	863	95	below_threshold
Sellimonas intestinalis	strain=BR72	GCA_001280875.1	1653434	1653434	type	True	78.7792	254	863	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	78.5921	75	863	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	78.3929	108	863	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.3544	121	863	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	78.2801	65	863	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.0845	121	863	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.071	85	863	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.0263	86	863	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	78.0181	86	863	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.8386	88	863	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.6623	98	863	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.646	118	863	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.0384	96	863	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	76.9358	97	863	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	76.8478	67	863	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.7754	68	863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:47,721] [INFO] DFAST Taxonomy check result was written to GCF_019754295.1_ASM1975429v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:47,722] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:47,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:47,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30a694fb-5754-4e95-bd1c-cadedcc5b8b1/dqc_reference/checkm_data
[2024-01-24 11:26:47,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:47,760] [INFO] Task started: CheckM
[2024-01-24 11:26:47,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019754295.1_ASM1975429v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019754295.1_ASM1975429v1_genomic.fna/checkm_input GCF_019754295.1_ASM1975429v1_genomic.fna/checkm_result
[2024-01-24 11:27:14,953] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:14,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:14,979] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:14,979] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:14,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019754295.1_ASM1975429v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:14,980] [INFO] Task started: Blastn
[2024-01-24 11:27:14,980] [INFO] Running command: blastn -query GCF_019754295.1_ASM1975429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30a694fb-5754-4e95-bd1c-cadedcc5b8b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_019754295.1_ASM1975429v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:16,071] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:16,076] [INFO] Selected 24 target genomes.
[2024-01-24 11:27:16,076] [INFO] Target genome list was writen to GCF_019754295.1_ASM1975429v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:16,109] [INFO] Task started: fastANI
[2024-01-24 11:27:16,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg525a6c57-d7eb-44a1-aa86-a52780008697/GCF_019754295.1_ASM1975429v1_genomic.fna.gz --refList GCF_019754295.1_ASM1975429v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019754295.1_ASM1975429v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:27,874] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:27,894] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:27,894] [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_002159995.1	s__Sellimonas sp002159995	98.8698	741	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sellimonas	95.0	99.10	98.94	0.88	0.83	3	conclusive
GCF_016900655.1	s__Sellimonas avistercoris	79.9026	326	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sellimonas	95.0	98.38	98.11	0.87	0.78	13	-
GCF_001280875.1	s__Sellimonas intestinalis	78.7792	254	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sellimonas	95.0	99.40	98.91	0.92	0.87	22	-
GCA_904393575.1	s__Sellimonas sp904393575	78.1862	222	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sellimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160325.1	s__An181 sp002160325	78.0566	119	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__An181	95.0	99.25	99.25	0.93	0.93	2	-
GCF_000155205.1	s__Mediterraneibacter lactaris	78.016	87	863	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_015560805.1	s__Schaedlerella glycyrrhizinilytica_A	77.7987	97	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.33	97.63	0.90	0.83	10	-
GCA_018365895.1	s__UBA9414 sp018365895	77.7213	96	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000155875.1	s__Bariatricus comes	77.6826	111	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCF_004345005.1	s__Extibacter muris	77.6448	75	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	95.70	95.67	0.77	0.77	4	-
GCA_004560705.1	s__Bariatricus sp004560705	77.5841	110	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.19	99.19	0.81	0.81	2	-
GCF_002160985.1	s__Lachnoclostridium_B stercoravium	77.5608	89	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.37	98.26	0.93	0.92	3	-
GCF_013300725.1	s__Bariatricus comes_A	77.3993	104	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCF_016901695.1	s__Lachnoclostridium_B massiliensis_A	77.3841	77	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003489085.1	s__UBA9414 sp003489085	77.315	66	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905197485.1	s__Faecalimonas sp900555395	77.0449	88	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	100.00	100.00	0.94	0.94	2	-
GCF_016908695.1	s__Blautia_A faecis	77.0264	56	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.52	97.01	0.80	0.69	30	-
GCA_900550865.1	s__Dorea_A sp900550865	77.0106	86	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008281175.1	s__Extibacter hylemonae	76.9371	96	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	99.20	98.44	0.97	0.93	5	-
GCA_019119675.1	s__Mediterraneibacter faecipullorum	76.6522	79	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120275.1	s__Mediterraneibacter excrementavium	76.2791	66	863	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:27,896] [INFO] GTDB search result was written to GCF_019754295.1_ASM1975429v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:27,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:27,900] [INFO] DFAST_QC result json was written to GCF_019754295.1_ASM1975429v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:27,901] [INFO] DFAST_QC completed!
[2024-01-24 11:27:27,901] [INFO] Total running time: 0h1m9s