[2024-01-24 12:23:50,691] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a8e4cca-00e9-432d-8a41-a8fbe55a7e74/dqc_reference
[2024-01-24 12:23:52,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,066] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,066] [INFO] Running command: gunzip -c /var/lib/cwl/stga5b2a160-384f-40ce-9225-bfa4b3b4e16e/GCF_014640075.1_ASM1464007v1_genomic.fna.gz | prodigal -d GCF_014640075.1_ASM1464007v1_genomic.fna/cds.fna -a GCF_014640075.1_ASM1464007v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:11,952] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:11,952] [INFO] Task started: HMMsearch
[2024-01-24 12:24:11,952] [INFO] Running command: hmmsearch --tblout GCF_014640075.1_ASM1464007v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a8e4cca-00e9-432d-8a41-a8fbe55a7e74/dqc_reference/reference_markers.hmm GCF_014640075.1_ASM1464007v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:12,278] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:12,279] [INFO] Found 6/6 markers.
[2024-01-24 12:24:12,345] [INFO] Query marker FASTA was written to GCF_014640075.1_ASM1464007v1_genomic.fna/markers.fasta
[2024-01-24 12:24:12,345] [INFO] Task started: Blastn
[2024-01-24 12:24:12,345] [INFO] Running command: blastn -query GCF_014640075.1_ASM1464007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a8e4cca-00e9-432d-8a41-a8fbe55a7e74/dqc_reference/reference_markers.fasta -out GCF_014640075.1_ASM1464007v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:13,274] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:13,278] [INFO] Selected 22 target genomes.
[2024-01-24 12:24:13,279] [INFO] Target genome list was writen to GCF_014640075.1_ASM1464007v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:13,286] [INFO] Task started: fastANI
[2024-01-24 12:24:13,287] [INFO] Running command: fastANI --query /var/lib/cwl/stga5b2a160-384f-40ce-9225-bfa4b3b4e16e/GCF_014640075.1_ASM1464007v1_genomic.fna.gz --refList GCF_014640075.1_ASM1464007v1_genomic.fna/target_genomes.txt --output GCF_014640075.1_ASM1464007v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:37,728] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:37,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a8e4cca-00e9-432d-8a41-a8fbe55a7e74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:37,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a8e4cca-00e9-432d-8a41-a8fbe55a7e74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:37,753] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:37,754] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:37,754] [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
Chelatococcus reniformis	strain=CGMCC 1.12919	GCA_014640075.1	1494448	1494448	type	True	100.0	2254	2254	95	conclusive
Camelimonas lactis	strain=DSM 22958	GCA_004342915.1	659006	659006	type	True	78.8567	553	2254	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	78.6397	567	2254	95	below_threshold
Camelimonas fluminis	strain=KCTC 42282	GCA_014656355.1	1576911	1576911	type	True	78.5893	565	2254	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	78.3742	446	2254	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	78.324	450	2254	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	77.6742	457	2254	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	77.6548	505	2254	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.6204	631	2254	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.5921	597	2254	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	77.5539	407	2254	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.5537	444	2254	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.5524	625	2254	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_003201475.1	28210	28210	type	True	77.5318	362	2254	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	77.524	430	2254	95	below_threshold
Methylobacterium aquaticum	strain=DSM 16371	GCA_001043915.1	270351	270351	type	True	77.519	538	2254	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	77.4943	552	2254	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.4828	618	2254	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.4308	565	2254	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	77.4228	396	2254	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	77.3602	529	2254	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	77.2735	483	2254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:37,757] [INFO] DFAST Taxonomy check result was written to GCF_014640075.1_ASM1464007v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:37,757] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:37,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:37,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a8e4cca-00e9-432d-8a41-a8fbe55a7e74/dqc_reference/checkm_data
[2024-01-24 12:24:37,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:37,826] [INFO] Task started: CheckM
[2024-01-24 12:24:37,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640075.1_ASM1464007v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640075.1_ASM1464007v1_genomic.fna/checkm_input GCF_014640075.1_ASM1464007v1_genomic.fna/checkm_result
[2024-01-24 12:25:36,427] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:36,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:36,454] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:36,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:36,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640075.1_ASM1464007v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:36,456] [INFO] Task started: Blastn
[2024-01-24 12:25:36,456] [INFO] Running command: blastn -query GCF_014640075.1_ASM1464007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a8e4cca-00e9-432d-8a41-a8fbe55a7e74/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640075.1_ASM1464007v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:38,058] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:38,062] [INFO] Selected 21 target genomes.
[2024-01-24 12:25:38,062] [INFO] Target genome list was writen to GCF_014640075.1_ASM1464007v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:38,074] [INFO] Task started: fastANI
[2024-01-24 12:25:38,074] [INFO] Running command: fastANI --query /var/lib/cwl/stga5b2a160-384f-40ce-9225-bfa4b3b4e16e/GCF_014640075.1_ASM1464007v1_genomic.fna.gz --refList GCF_014640075.1_ASM1464007v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640075.1_ASM1464007v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:00,738] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:00,760] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:00,761] [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_014640075.1	s__Camelimonas reniformis	100.0	2254	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Camelimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004342915.1	s__Camelimonas lactis	78.8405	555	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Camelimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196925.1	s__Chelatococcus_A caeni	78.6093	571	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_014656355.1	s__Camelimonas fluminis	78.5775	566	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Camelimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418005.1	s__Chelatococcus_A sambhunathii	78.3307	452	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.33	99.03	0.97	0.94	5	-
GCF_003173775.1	s__Methylobacterium sp003173775	77.6577	579	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_004004555.2	s__Methylobacterium sp004004555	77.5723	642	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008515.1	s__Phreatobacter cathodiphilus	77.5533	444	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003004785.1	s__Alsobacter soli	77.5376	409	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645695.1	s__Salinarimonas ramus	77.5208	429	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001043915.1	s__Methylobacterium aquaticum	77.5025	540	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201475.1	s__Chelatococcus asaccharovorans	77.4984	366	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014636935.1	s__Alsobacter metallidurans	77.4233	395	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112625.1	s__Methylobacterium sp900112625	77.4021	500	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_000019365.1	s__Methylobacterium sp000019365	77.3888	594	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
GCF_000022085.1	s__Methylobacterium nodulans	77.3792	524	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364445.2	s__Methylobacterium mesophilicum	77.3689	438	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009806555.1	s__Methylobacterium sp009806555	77.3642	460	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138435.1	s__Methylobacterium fujisawaense	77.3269	447	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.82	98.73	0.93	0.90	12	-
GCF_000429045.1	s__Salinarimonas rosea	77.2823	482	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903644085.1	s__Enterovirga sp903644085	77.2179	247	2254	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:00,762] [INFO] GTDB search result was written to GCF_014640075.1_ASM1464007v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:00,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:00,771] [INFO] DFAST_QC result json was written to GCF_014640075.1_ASM1464007v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:00,771] [INFO] DFAST_QC completed!
[2024-01-24 12:26:00,772] [INFO] Total running time: 0h2m10s