[2024-01-24 13:37:15,359] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:15,360] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:15,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg0773196e-d945-4a77-9262-d2da07fac74b/dqc_reference
[2024-01-24 13:37:18,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:18,466] [INFO] Task started: Prodigal
[2024-01-24 13:37:18,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f5ac908-08a6-42a2-9685-2272a3613e03/GCF_000173075.1_ASM17307v1_genomic.fna.gz | prodigal -d GCF_000173075.1_ASM17307v1_genomic.fna/cds.fna -a GCF_000173075.1_ASM17307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:38:10,182] [INFO] Task succeeded: Prodigal
[2024-01-24 13:38:10,183] [INFO] Task started: HMMsearch
[2024-01-24 13:38:10,183] [INFO] Running command: hmmsearch --tblout GCF_000173075.1_ASM17307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0773196e-d945-4a77-9262-d2da07fac74b/dqc_reference/reference_markers.hmm GCF_000173075.1_ASM17307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:38:10,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:38:10,533] [INFO] Found 6/6 markers.
[2024-01-24 13:38:10,596] [INFO] Query marker FASTA was written to GCF_000173075.1_ASM17307v1_genomic.fna/markers.fasta
[2024-01-24 13:38:10,596] [INFO] Task started: Blastn
[2024-01-24 13:38:10,596] [INFO] Running command: blastn -query GCF_000173075.1_ASM17307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0773196e-d945-4a77-9262-d2da07fac74b/dqc_reference/reference_markers.fasta -out GCF_000173075.1_ASM17307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:11,199] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:11,203] [INFO] Selected 16 target genomes.
[2024-01-24 13:38:11,204] [INFO] Target genome list was writen to GCF_000173075.1_ASM17307v1_genomic.fna/target_genomes.txt
[2024-01-24 13:38:11,215] [INFO] Task started: fastANI
[2024-01-24 13:38:11,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f5ac908-08a6-42a2-9685-2272a3613e03/GCF_000173075.1_ASM17307v1_genomic.fna.gz --refList GCF_000173075.1_ASM17307v1_genomic.fna/target_genomes.txt --output GCF_000173075.1_ASM17307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:27,361] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:27,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0773196e-d945-4a77-9262-d2da07fac74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:27,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0773196e-d945-4a77-9262-d2da07fac74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:27,369] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:38:27,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:27,369] [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
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	100.0	2580	2583	95	conclusive
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	99.9533	2539	2583	95	conclusive
Terrimicrobium sacchariphilum	strain=NM-5	GCA_001613545.1	690879	690879	type	True	76.6045	97	2583	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	75.8724	101	2583	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	75.6902	108	2583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:27,371] [INFO] DFAST Taxonomy check result was written to GCF_000173075.1_ASM17307v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:27,371] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:27,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:27,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0773196e-d945-4a77-9262-d2da07fac74b/dqc_reference/checkm_data
[2024-01-24 13:38:27,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:27,449] [INFO] Task started: CheckM
[2024-01-24 13:38:27,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000173075.1_ASM17307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000173075.1_ASM17307v1_genomic.fna/checkm_input GCF_000173075.1_ASM17307v1_genomic.fna/checkm_result
[2024-01-24 13:40:39,011] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:39,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:39,039] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:39,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:39,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000173075.1_ASM17307v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:39,040] [INFO] Task started: Blastn
[2024-01-24 13:40:39,041] [INFO] Running command: blastn -query GCF_000173075.1_ASM17307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0773196e-d945-4a77-9262-d2da07fac74b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000173075.1_ASM17307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:40,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:40,702] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:40,702] [INFO] Target genome list was writen to GCF_000173075.1_ASM17307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:40,717] [INFO] Task started: fastANI
[2024-01-24 13:40:40,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f5ac908-08a6-42a2-9685-2272a3613e03/GCF_000173075.1_ASM17307v1_genomic.fna.gz --refList GCF_000173075.1_ASM17307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000173075.1_ASM17307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:55,671] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:55,687] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:55,687] [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_000173075.1	s__Chthoniobacter flavus	100.0	2580	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Chthoniobacter	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCA_903874975.1	s__Chthoniobacter sp903874975	77.6145	359	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Chthoniobacter	95.0	97.99	97.82	0.84	0.83	3	-
GCA_009885995.1	s__VFJQ01 sp009885995	77.0411	420	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__VFJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929475.1	s__SXWH01 sp903929475	76.7582	163	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	99.90	99.90	0.94	0.94	2	-
GCA_903882875.1	s__SXWH01 sp903882875	76.7342	298	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	99.98	99.97	0.98	0.98	3	-
GCA_014189875.1	s__SXWH01 sp014189875	76.6759	220	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__SXWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169975.1	s__Palsa-1392 sp003169975	76.6339	89	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Palsa-1392	95.0	99.97	99.95	0.98	0.97	5	-
GCA_903933715.1	s__UBA695 sp903933715	76.5676	86	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__UBA695	95.0	99.98	99.96	0.98	0.98	4	-
GCA_903859715.1	s__Opi-474 sp903859715	76.3404	67	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.98	99.96	0.98	0.96	7	-
GCA_002396485.1	s__UBA967 sp002396485	76.3275	54	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298145.1	s__UBA695 sp002298145	76.137	101	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__UBA695	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655545.1	s__JAATET01 sp015655545	76.1114	124	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__JAATET01;g__JAATET01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118375.1	s__Lacunisphaera lenta	76.0489	95	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169695.1	s__AV80 sp003169695	75.8279	57	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV80	95.0	99.90	99.87	0.97	0.96	4	-
GCA_903901425.1	s__CAIURC01 sp903901425	75.7766	102	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__CAIURC01	95.0	99.87	99.80	0.95	0.94	4	-
GCA_903825285.1	s__Opi-474 sp903825285	75.7325	79	2583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.78	99.55	0.96	0.94	12	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:55,690] [INFO] GTDB search result was written to GCF_000173075.1_ASM17307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:55,690] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:55,694] [INFO] DFAST_QC result json was written to GCF_000173075.1_ASM17307v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:55,695] [INFO] DFAST_QC completed!
[2024-01-24 13:40:55,695] [INFO] Total running time: 0h3m40s