[2024-01-25 18:33:20,690] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:33:20,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:33:20,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg06d06879-cd76-400b-a9ab-e4609b54e245/dqc_reference
[2024-01-25 18:33:21,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:33:21,868] [INFO] Task started: Prodigal
[2024-01-25 18:33:21,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg24477775-4ea6-4148-ae85-794675d181ea/GCF_003863335.1_ASM386333v1_genomic.fna.gz | prodigal -d GCF_003863335.1_ASM386333v1_genomic.fna/cds.fna -a GCF_003863335.1_ASM386333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:33:32,441] [INFO] Task succeeded: Prodigal
[2024-01-25 18:33:32,441] [INFO] Task started: HMMsearch
[2024-01-25 18:33:32,441] [INFO] Running command: hmmsearch --tblout GCF_003863335.1_ASM386333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06d06879-cd76-400b-a9ab-e4609b54e245/dqc_reference/reference_markers.hmm GCF_003863335.1_ASM386333v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:33:32,666] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:33:32,667] [INFO] Found 6/6 markers.
[2024-01-25 18:33:32,702] [INFO] Query marker FASTA was written to GCF_003863335.1_ASM386333v1_genomic.fna/markers.fasta
[2024-01-25 18:33:32,702] [INFO] Task started: Blastn
[2024-01-25 18:33:32,702] [INFO] Running command: blastn -query GCF_003863335.1_ASM386333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06d06879-cd76-400b-a9ab-e4609b54e245/dqc_reference/reference_markers.fasta -out GCF_003863335.1_ASM386333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:33:33,490] [INFO] Task succeeded: Blastn
[2024-01-25 18:33:33,493] [INFO] Selected 24 target genomes.
[2024-01-25 18:33:33,494] [INFO] Target genome list was writen to GCF_003863335.1_ASM386333v1_genomic.fna/target_genomes.txt
[2024-01-25 18:33:33,541] [INFO] Task started: fastANI
[2024-01-25 18:33:33,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg24477775-4ea6-4148-ae85-794675d181ea/GCF_003863335.1_ASM386333v1_genomic.fna.gz --refList GCF_003863335.1_ASM386333v1_genomic.fna/target_genomes.txt --output GCF_003863335.1_ASM386333v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:33:53,038] [INFO] Task succeeded: fastANI
[2024-01-25 18:33:53,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06d06879-cd76-400b-a9ab-e4609b54e245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:33:53,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06d06879-cd76-400b-a9ab-e4609b54e245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:33:53,053] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:33:53,053] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:33:53,053] [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
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.5788	525	1362	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	78.1749	359	1362	95	below_threshold
Gemmobacter megaterium	strain=CGMCC 1.11024	GCA_014636395.1	1086013	1086013	type	True	78.0123	409	1362	95	below_threshold
Gemmobacter megaterium	strain=DSM 26375	GCA_900156815.1	1086013	1086013	type	True	77.9827	410	1362	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.793	362	1362	95	below_threshold
Paracoccus sulfuroxidans	strain=CGMCC 1.5364	GCA_007830335.1	384678	384678	type	True	77.6827	296	1362	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	77.5513	357	1362	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	77.5236	382	1362	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.4526	301	1362	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	77.404	258	1362	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.3593	280	1362	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	77.3393	317	1362	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	77.3252	322	1362	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.3106	282	1362	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.2464	331	1362	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	77.2408	266	1362	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.1441	250	1362	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	77.0675	302	1362	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.0519	267	1362	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.9801	257	1362	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.9492	255	1362	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	76.9298	258	1362	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.7057	318	1362	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.594	235	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:33:53,054] [INFO] DFAST Taxonomy check result was written to GCF_003863335.1_ASM386333v1_genomic.fna/tc_result.tsv
[2024-01-25 18:33:53,055] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:33:53,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:33:53,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06d06879-cd76-400b-a9ab-e4609b54e245/dqc_reference/checkm_data
[2024-01-25 18:33:53,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:33:53,098] [INFO] Task started: CheckM
[2024-01-25 18:33:53,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003863335.1_ASM386333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003863335.1_ASM386333v1_genomic.fna/checkm_input GCF_003863335.1_ASM386333v1_genomic.fna/checkm_result
[2024-01-25 18:34:28,835] [INFO] Task succeeded: CheckM
[2024-01-25 18:34:28,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:34:28,871] [INFO] ===== Completeness check finished =====
[2024-01-25 18:34:28,871] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:34:28,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003863335.1_ASM386333v1_genomic.fna/markers.fasta)
[2024-01-25 18:34:28,872] [INFO] Task started: Blastn
[2024-01-25 18:34:28,872] [INFO] Running command: blastn -query GCF_003863335.1_ASM386333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06d06879-cd76-400b-a9ab-e4609b54e245/dqc_reference/reference_markers_gtdb.fasta -out GCF_003863335.1_ASM386333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:34:30,441] [INFO] Task succeeded: Blastn
[2024-01-25 18:34:30,445] [INFO] Selected 15 target genomes.
[2024-01-25 18:34:30,446] [INFO] Target genome list was writen to GCF_003863335.1_ASM386333v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:34:30,484] [INFO] Task started: fastANI
[2024-01-25 18:34:30,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg24477775-4ea6-4148-ae85-794675d181ea/GCF_003863335.1_ASM386333v1_genomic.fna.gz --refList GCF_003863335.1_ASM386333v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003863335.1_ASM386333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:34:43,232] [INFO] Task succeeded: fastANI
[2024-01-25 18:34:43,242] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:34:43,242] [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_003863335.1	s__Wagnerdoeblera faecalis	100.0	1359	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004054105.1	s__Wagnerdoeblera intermedia	87.6643	1003	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429765.1	s__Wagnerdoeblera nectariphila	78.5668	526	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156815.1	s__Wagnerdoeblera megaterium	77.9913	409	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013328815.1	s__UBA1943 sp013328815	77.7189	330	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	97.27	97.27	0.97	0.97	2	-
GCF_007830335.1	s__Paracoccus sulfuroxidans	77.7106	292	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001691415.1	s__Pararhodobacter sp001691415	77.587	283	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	77.5453	315	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCA_009925085.1	s__CYK-10 sp009925085	77.393	259	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CYK-10	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	77.2075	295	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
GCF_016765795.1	s__UBA1943 sp016765795	77.0846	268	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.0723	280	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900965.1	s__ETT8 sp002900965	77.0613	286	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011174775.1	s__Tabrizicola sp011174775	77.0418	268	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	76.9298	258	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:34:43,246] [INFO] GTDB search result was written to GCF_003863335.1_ASM386333v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:34:43,247] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:34:43,250] [INFO] DFAST_QC result json was written to GCF_003863335.1_ASM386333v1_genomic.fna/dqc_result.json
[2024-01-25 18:34:43,251] [INFO] DFAST_QC completed!
[2024-01-25 18:34:43,251] [INFO] Total running time: 0h1m23s