[2024-01-25 18:37:35,678] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:35,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:35,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg309403f5-c5b0-4f91-ad01-04ef35021b8e/dqc_reference
[2024-01-25 18:37:36,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:36,848] [INFO] Task started: Prodigal
[2024-01-25 18:37:36,848] [INFO] Running command: gunzip -c /var/lib/cwl/stge060b7f1-2838-45b9-945c-a445701feccf/GCF_028368935.1_ASM2836893v1_genomic.fna.gz | prodigal -d GCF_028368935.1_ASM2836893v1_genomic.fna/cds.fna -a GCF_028368935.1_ASM2836893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:38:10,000] [INFO] Task succeeded: Prodigal
[2024-01-25 18:38:10,000] [INFO] Task started: HMMsearch
[2024-01-25 18:38:10,000] [INFO] Running command: hmmsearch --tblout GCF_028368935.1_ASM2836893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg309403f5-c5b0-4f91-ad01-04ef35021b8e/dqc_reference/reference_markers.hmm GCF_028368935.1_ASM2836893v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:38:10,409] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:38:10,410] [INFO] Found 6/6 markers.
[2024-01-25 18:38:10,496] [INFO] Query marker FASTA was written to GCF_028368935.1_ASM2836893v1_genomic.fna/markers.fasta
[2024-01-25 18:38:10,497] [INFO] Task started: Blastn
[2024-01-25 18:38:10,497] [INFO] Running command: blastn -query GCF_028368935.1_ASM2836893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309403f5-c5b0-4f91-ad01-04ef35021b8e/dqc_reference/reference_markers.fasta -out GCF_028368935.1_ASM2836893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:38:11,169] [INFO] Task succeeded: Blastn
[2024-01-25 18:38:11,172] [INFO] Selected 21 target genomes.
[2024-01-25 18:38:11,173] [INFO] Target genome list was writen to GCF_028368935.1_ASM2836893v1_genomic.fna/target_genomes.txt
[2024-01-25 18:38:11,195] [INFO] Task started: fastANI
[2024-01-25 18:38:11,195] [INFO] Running command: fastANI --query /var/lib/cwl/stge060b7f1-2838-45b9-945c-a445701feccf/GCF_028368935.1_ASM2836893v1_genomic.fna.gz --refList GCF_028368935.1_ASM2836893v1_genomic.fna/target_genomes.txt --output GCF_028368935.1_ASM2836893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:38:38,319] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:38,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg309403f5-c5b0-4f91-ad01-04ef35021b8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:38:38,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg309403f5-c5b0-4f91-ad01-04ef35021b8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:38:38,334] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:38:38,335] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:38:38,335] [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
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	77.3758	1506	4487	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	77.3036	1428	4487	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	77.2894	1415	4487	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	77.0879	1118	4487	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.776	737	4487	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	75.4493	63	4487	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	75.1652	437	4487	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	75.0779	534	4487	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_010499425.1	63561	63561	type	True	75.0718	59	4487	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	75.0201	81	4487	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	74.967	461	4487	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.8697	352	4487	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	74.8557	202	4487	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	74.8377	176	4487	95	below_threshold
Elioraea thermophila	strain=YIM 72297	GCA_003336755.1	2185104	2185104	type	True	74.8318	271	4487	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	74.8169	98	4487	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	74.7909	394	4487	95	below_threshold
Alcanivorax dieselolei	strain=CGMCC 1.3690	GCA_014644575.1	285091	285091	type	True	74.7871	82	4487	95	below_threshold
Halovivax ruber	strain=XH-70	GCA_000328525.1	387341	387341	type	True	74.625	112	4487	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:38:38,339] [INFO] DFAST Taxonomy check result was written to GCF_028368935.1_ASM2836893v1_genomic.fna/tc_result.tsv
[2024-01-25 18:38:38,341] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:38:38,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:38:38,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg309403f5-c5b0-4f91-ad01-04ef35021b8e/dqc_reference/checkm_data
[2024-01-25 18:38:38,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:38:38,471] [INFO] Task started: CheckM
[2024-01-25 18:38:38,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028368935.1_ASM2836893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028368935.1_ASM2836893v1_genomic.fna/checkm_input GCF_028368935.1_ASM2836893v1_genomic.fna/checkm_result
[2024-01-25 18:40:53,333] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:53,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:53,360] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:53,360] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:53,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028368935.1_ASM2836893v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:53,361] [INFO] Task started: Blastn
[2024-01-25 18:40:53,361] [INFO] Running command: blastn -query GCF_028368935.1_ASM2836893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309403f5-c5b0-4f91-ad01-04ef35021b8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_028368935.1_ASM2836893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:54,519] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:54,522] [INFO] Selected 10 target genomes.
[2024-01-25 18:40:54,522] [INFO] Target genome list was writen to GCF_028368935.1_ASM2836893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:54,543] [INFO] Task started: fastANI
[2024-01-25 18:40:54,543] [INFO] Running command: fastANI --query /var/lib/cwl/stge060b7f1-2838-45b9-945c-a445701feccf/GCF_028368935.1_ASM2836893v1_genomic.fna.gz --refList GCF_028368935.1_ASM2836893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028368935.1_ASM2836893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:29,737] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:29,744] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:41:29,744] [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_000067165.1	s__Sorangium cellulosum_B	94.6446	3600	4487	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	88.7047	3369	4487	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCF_004135735.1	s__Sorangium cellulosum_F	86.4226	2761	4487	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002950945.1	s__Sorangium cellulosum_E	86.2603	3136	4487	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	77.3243	1481	4487	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649845.1	s__Polyangium spumosum	77.3034	1428	4487	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000601485.1	s__Chondromyces apiculatus	77.1685	1275	4487	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Chondromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001931535.1	s__Minicystis rosea	76.9991	1641	4487	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Minicystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994655.1	s__Corynebacterium sp002994655	74.7058	103	4487	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:29,747] [INFO] GTDB search result was written to GCF_028368935.1_ASM2836893v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:29,748] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:29,751] [INFO] DFAST_QC result json was written to GCF_028368935.1_ASM2836893v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:29,751] [INFO] DFAST_QC completed!
[2024-01-25 18:41:29,751] [INFO] Total running time: 0h3m54s