[2024-01-24 12:29:28,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ebeeb21-e58c-4b04-8109-57db6cc16b46/dqc_reference
[2024-01-24 12:29:30,433] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,440] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,440] [INFO] Running command: gunzip -c /var/lib/cwl/stg23cfd579-2397-4248-8807-5665c4b08c19/GCF_003664205.1_ASM366420v1_genomic.fna.gz | prodigal -d GCF_003664205.1_ASM366420v1_genomic.fna/cds.fna -a GCF_003664205.1_ASM366420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:44,578] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:44,579] [INFO] Task started: HMMsearch
[2024-01-24 12:29:44,579] [INFO] Running command: hmmsearch --tblout GCF_003664205.1_ASM366420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ebeeb21-e58c-4b04-8109-57db6cc16b46/dqc_reference/reference_markers.hmm GCF_003664205.1_ASM366420v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:44,934] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:44,935] [INFO] Found 6/6 markers.
[2024-01-24 12:29:44,976] [INFO] Query marker FASTA was written to GCF_003664205.1_ASM366420v1_genomic.fna/markers.fasta
[2024-01-24 12:29:44,977] [INFO] Task started: Blastn
[2024-01-24 12:29:44,977] [INFO] Running command: blastn -query GCF_003664205.1_ASM366420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ebeeb21-e58c-4b04-8109-57db6cc16b46/dqc_reference/reference_markers.fasta -out GCF_003664205.1_ASM366420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:45,795] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:45,799] [INFO] Selected 16 target genomes.
[2024-01-24 12:29:45,799] [INFO] Target genome list was writen to GCF_003664205.1_ASM366420v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:45,809] [INFO] Task started: fastANI
[2024-01-24 12:29:45,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg23cfd579-2397-4248-8807-5665c4b08c19/GCF_003664205.1_ASM366420v1_genomic.fna.gz --refList GCF_003664205.1_ASM366420v1_genomic.fna/target_genomes.txt --output GCF_003664205.1_ASM366420v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:59,905] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:59,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ebeeb21-e58c-4b04-8109-57db6cc16b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:59,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ebeeb21-e58c-4b04-8109-57db6cc16b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:59,922] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:29:59,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:59,923] [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
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	100.0	1491	1494	95	conclusive
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	99.9832	1480	1494	95	conclusive
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	83.1147	972	1494	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	81.4425	743	1494	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	81.0883	678	1494	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	81.006	737	1494	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	80.5342	700	1494	95	below_threshold
Ruegeria haliotis	strain=B1Z28	GCA_013377785.1	2747601	2747601	type	True	80.3962	683	1494	95	below_threshold
Ruegeria profundi	strain=ZGT108	GCA_001507545.1	1685378	1685378	type	True	79.9468	597	1494	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.9422	635	1494	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.4396	493	1494	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.4729	250	1494	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.1824	140	1494	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.0314	186	1494	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9021	169	1494	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.6961	179	1494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:59,925] [INFO] DFAST Taxonomy check result was written to GCF_003664205.1_ASM366420v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:59,926] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:59,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:59,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ebeeb21-e58c-4b04-8109-57db6cc16b46/dqc_reference/checkm_data
[2024-01-24 12:29:59,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:59,972] [INFO] Task started: CheckM
[2024-01-24 12:29:59,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003664205.1_ASM366420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003664205.1_ASM366420v1_genomic.fna/checkm_input GCF_003664205.1_ASM366420v1_genomic.fna/checkm_result
[2024-01-24 12:30:46,516] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:46,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:46,538] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:46,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:46,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003664205.1_ASM366420v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:46,540] [INFO] Task started: Blastn
[2024-01-24 12:30:46,540] [INFO] Running command: blastn -query GCF_003664205.1_ASM366420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ebeeb21-e58c-4b04-8109-57db6cc16b46/dqc_reference/reference_markers_gtdb.fasta -out GCF_003664205.1_ASM366420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:47,808] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:47,812] [INFO] Selected 18 target genomes.
[2024-01-24 12:30:47,812] [INFO] Target genome list was writen to GCF_003664205.1_ASM366420v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:47,831] [INFO] Task started: fastANI
[2024-01-24 12:30:47,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg23cfd579-2397-4248-8807-5665c4b08c19/GCF_003664205.1_ASM366420v1_genomic.fna.gz --refList GCF_003664205.1_ASM366420v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003664205.1_ASM366420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:05,415] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:05,432] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:05,432] [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_000192475.1	s__Ruegeria conchae	99.9832	1480	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000813985.1	s__Ruegeria sp000813985	83.993	948	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106805.1	s__Ruegeria halocynthiae	83.1147	972	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	82.1283	814	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032445.1	s__Ruegeria arenilitoris_F	81.5456	774	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	81.4935	761	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_013032005.1	s__Ruegeria atlantica_A	81.4828	732	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.11	97.00	0.94	0.90	12	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	81.3019	762	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_013035315.1	s__Ruegeria arenilitoris_D	81.251	728	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.80	95.80	0.90	0.90	2	-
GCF_017743995.1	s__Ruegeria sp017743995	81.2308	711	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013033355.1	s__Ruegeria lacuscaerulensis_A	81.225	694	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.80	95.61	0.96	0.93	5	-
GCF_013112245.1	s__Ruegeria sp013112245	81.1772	722	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.18	96.94	0.93	0.89	11	-
GCF_013032095.1	s__Ruegeria atlantica_E	81.079	702	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013034685.1	s__Ruegeria lacuscaerulensis_B	81.0225	728	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.87	97.79	0.94	0.94	3	-
GCF_013032455.1	s__Ruegeria atlantica_B	80.8413	681	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.37	96.74	0.95	0.90	3	-
GCF_017743975.1	s__Ruegeria sp017743975	80.7904	701	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903914075.1	s__Ruegeria sp903914075	80.7887	634	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.16	95.09	0.87	0.84	7	-
GCF_013031405.1	s__Ruegeria sp013031405	79.8526	637	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:05,438] [INFO] GTDB search result was written to GCF_003664205.1_ASM366420v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:05,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:05,447] [INFO] DFAST_QC result json was written to GCF_003664205.1_ASM366420v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:05,447] [INFO] DFAST_QC completed!
[2024-01-24 12:31:05,447] [INFO] Total running time: 0h1m36s