[2024-01-24 13:21:55,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:55,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:55,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg1963742a-4bad-42d7-92f0-f72684b330c2/dqc_reference
[2024-01-24 13:21:57,023] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:57,024] [INFO] Task started: Prodigal
[2024-01-24 13:21:57,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg861d6660-63e0-4074-a48a-4498ab583625/GCF_000482785.1_ASM48278v1_genomic.fna.gz | prodigal -d GCF_000482785.1_ASM48278v1_genomic.fna/cds.fna -a GCF_000482785.1_ASM48278v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:13,625] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:13,625] [INFO] Task started: HMMsearch
[2024-01-24 13:22:13,626] [INFO] Running command: hmmsearch --tblout GCF_000482785.1_ASM48278v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1963742a-4bad-42d7-92f0-f72684b330c2/dqc_reference/reference_markers.hmm GCF_000482785.1_ASM48278v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:13,923] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:13,924] [INFO] Found 6/6 markers.
[2024-01-24 13:22:13,968] [INFO] Query marker FASTA was written to GCF_000482785.1_ASM48278v1_genomic.fna/markers.fasta
[2024-01-24 13:22:13,968] [INFO] Task started: Blastn
[2024-01-24 13:22:13,968] [INFO] Running command: blastn -query GCF_000482785.1_ASM48278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1963742a-4bad-42d7-92f0-f72684b330c2/dqc_reference/reference_markers.fasta -out GCF_000482785.1_ASM48278v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:14,850] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:14,854] [INFO] Selected 24 target genomes.
[2024-01-24 13:22:14,855] [INFO] Target genome list was writen to GCF_000482785.1_ASM48278v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:14,862] [INFO] Task started: fastANI
[2024-01-24 13:22:14,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg861d6660-63e0-4074-a48a-4498ab583625/GCF_000482785.1_ASM48278v1_genomic.fna.gz --refList GCF_000482785.1_ASM48278v1_genomic.fna/target_genomes.txt --output GCF_000482785.1_ASM48278v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:46,668] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:46,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1963742a-4bad-42d7-92f0-f72684b330c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:46,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1963742a-4bad-42d7-92f0-f72684b330c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:46,687] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:46,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:46,688] [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
Derxia gummosa	strain=DSM 723	GCA_000482785.1	203699	203699	type	True	100.0	1720	1721	95	conclusive
Derxia lacustris	strain=HL-12	GCA_002105195.1	764842	764842	type	True	86.9622	1334	1721	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	77.78	606	1721	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	77.7098	587	1721	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	77.6031	562	1721	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.5586	482	1721	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.5432	492	1721	95	below_threshold
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	77.5119	302	1721	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	77.3132	437	1721	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	77.2638	544	1721	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	77.2429	543	1721	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	77.2408	552	1721	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	77.2368	428	1721	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	77.2348	566	1721	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	77.0594	221	1721	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.9256	703	1721	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	76.8522	493	1721	95	below_threshold
Pandoraea pulmonicola	strain=DSM 16583	GCA_000815105.2	93221	93221	type	True	76.7274	357	1721	95	below_threshold
Pandoraea pulmonicola	strain=NCTC13159	GCA_900454575.1	93221	93221	type	True	76.7184	357	1721	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	76.6817	491	1721	95	below_threshold
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	76.5133	454	1721	95	below_threshold
Pandoraea commovens	strain=LMG 31010	GCA_902459615.1	2508289	2508289	type	True	76.5118	263	1721	95	below_threshold
Caballeronia cordobensis		GCA_001544575.2	1353886	1353886	type	True	76.3405	475	1721	95	below_threshold
Caballeronia cordobensis	strain=LMG 27620	GCA_001278535.1	1353886	1353886	type	True	76.2899	488	1721	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:46,690] [INFO] DFAST Taxonomy check result was written to GCF_000482785.1_ASM48278v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:46,690] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:46,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:46,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1963742a-4bad-42d7-92f0-f72684b330c2/dqc_reference/checkm_data
[2024-01-24 13:22:46,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:46,744] [INFO] Task started: CheckM
[2024-01-24 13:22:46,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000482785.1_ASM48278v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000482785.1_ASM48278v1_genomic.fna/checkm_input GCF_000482785.1_ASM48278v1_genomic.fna/checkm_result
[2024-01-24 13:24:00,457] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:00,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:00,477] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:00,478] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:00,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000482785.1_ASM48278v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:00,478] [INFO] Task started: Blastn
[2024-01-24 13:24:00,478] [INFO] Running command: blastn -query GCF_000482785.1_ASM48278v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1963742a-4bad-42d7-92f0-f72684b330c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000482785.1_ASM48278v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:01,872] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:01,876] [INFO] Selected 22 target genomes.
[2024-01-24 13:24:01,876] [INFO] Target genome list was writen to GCF_000482785.1_ASM48278v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:01,927] [INFO] Task started: fastANI
[2024-01-24 13:24:01,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg861d6660-63e0-4074-a48a-4498ab583625/GCF_000482785.1_ASM48278v1_genomic.fna.gz --refList GCF_000482785.1_ASM48278v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000482785.1_ASM48278v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:24,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:24,535] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:24,536] [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_000482785.1	s__Derxia gummosa	100.0	1720	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Derxia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002105195.1	s__Derxia lacustris	87.0111	1329	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Derxia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	77.5647	578	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCF_004310865.1	s__Aquabacterium lacunae	77.5514	298	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	77.523	326	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372525.1	s__Cupriavidus neocaledonicus	77.2481	543	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.97	99.97	0.99	0.98	3	-
GCF_000799605.1	s__Rhizobacter sp000799605	77.223	640	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142965.1	s__Rhizobacter sp900142965	77.2209	645	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635845.1	s__Oxalicibacterium solurbis	77.0729	218	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002902905.1	s__Achromobacter sp002902905	76.8891	506	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.15	96.15	0.87	0.87	2	-
GCA_016716275.1	s__JADJWR01 sp016716275	76.8577	444	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JADJWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183655.1	s__Azospira_A sp016183655	76.8476	383	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232985.1	s__JAFAMW01 sp019232985	76.8424	463	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFAMW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499135.1	s__Burkholderia dolosa	76.8167	517	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.52	98.66	0.97	0.91	15	-
GCA_016861185.1	s__DSNY01 sp016861185	76.7371	442	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__DSNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000815105.2	s__Pandoraea pulmonicola	76.733	356	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001571365.1	s__Achromobacter denitrificans	76.7262	418	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	-
GCF_003011895.2	s__Massilia glaciei	76.7196	481	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898725.1	s__UBA4615 sp903898725	76.7086	453	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261335.1	s__Bordetella sp002261335	76.6815	559	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	98.98	98.98	0.96	0.96	2	-
GCA_002428015.1	s__Massilia sp002428015	76.6506	455	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902459615.1	s__Pandoraea commovens	76.5183	262	1721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pandoraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:24,538] [INFO] GTDB search result was written to GCF_000482785.1_ASM48278v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:24,538] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:24,543] [INFO] DFAST_QC result json was written to GCF_000482785.1_ASM48278v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:24,543] [INFO] DFAST_QC completed!
[2024-01-24 13:24:24,543] [INFO] Total running time: 0h2m29s