[2024-01-24 14:19:37,585] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:37,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:37,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg0232a7f4-bff1-4df5-ab57-208cf74d43f7/dqc_reference
[2024-01-24 14:19:41,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:41,063] [INFO] Task started: Prodigal
[2024-01-24 14:19:41,063] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd77bc55-20a6-4297-832a-b3bfb1aaf4b0/GCF_004005855.1_ASM400585v1_genomic.fna.gz | prodigal -d GCF_004005855.1_ASM400585v1_genomic.fna/cds.fna -a GCF_004005855.1_ASM400585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:58,883] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:58,884] [INFO] Task started: HMMsearch
[2024-01-24 14:19:58,884] [INFO] Running command: hmmsearch --tblout GCF_004005855.1_ASM400585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0232a7f4-bff1-4df5-ab57-208cf74d43f7/dqc_reference/reference_markers.hmm GCF_004005855.1_ASM400585v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:59,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:59,356] [INFO] Found 6/6 markers.
[2024-01-24 14:19:59,409] [INFO] Query marker FASTA was written to GCF_004005855.1_ASM400585v1_genomic.fna/markers.fasta
[2024-01-24 14:19:59,410] [INFO] Task started: Blastn
[2024-01-24 14:19:59,410] [INFO] Running command: blastn -query GCF_004005855.1_ASM400585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0232a7f4-bff1-4df5-ab57-208cf74d43f7/dqc_reference/reference_markers.fasta -out GCF_004005855.1_ASM400585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:02,678] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:02,682] [INFO] Selected 21 target genomes.
[2024-01-24 14:20:02,682] [INFO] Target genome list was writen to GCF_004005855.1_ASM400585v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:02,700] [INFO] Task started: fastANI
[2024-01-24 14:20:02,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd77bc55-20a6-4297-832a-b3bfb1aaf4b0/GCF_004005855.1_ASM400585v1_genomic.fna.gz --refList GCF_004005855.1_ASM400585v1_genomic.fna/target_genomes.txt --output GCF_004005855.1_ASM400585v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:29,230] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:29,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0232a7f4-bff1-4df5-ab57-208cf74d43f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:29,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0232a7f4-bff1-4df5-ab57-208cf74d43f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:29,331] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:29,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:29,332] [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
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	100.0	1738	1742	95	conclusive
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	87.3597	1204	1742	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	79.2577	720	1742	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	79.0311	714	1742	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	78.6966	628	1742	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	78.6321	545	1742	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	78.6065	548	1742	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.4396	548	1742	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	78.3795	609	1742	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.3615	543	1742	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	78.3579	634	1742	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	78.3141	550	1742	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	78.2376	550	1742	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.2318	609	1742	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	78.2316	556	1742	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	78.2039	584	1742	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	77.9324	638	1742	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	75.242	147	1742	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	75.1832	152	1742	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	75.1483	61	1742	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.7733	164	1742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:29,334] [INFO] DFAST Taxonomy check result was written to GCF_004005855.1_ASM400585v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:29,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:29,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:29,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0232a7f4-bff1-4df5-ab57-208cf74d43f7/dqc_reference/checkm_data
[2024-01-24 14:20:29,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:29,408] [INFO] Task started: CheckM
[2024-01-24 14:20:29,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005855.1_ASM400585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005855.1_ASM400585v1_genomic.fna/checkm_input GCF_004005855.1_ASM400585v1_genomic.fna/checkm_result
[2024-01-24 14:21:39,138] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:39,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:39,166] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:39,167] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:39,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005855.1_ASM400585v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:39,168] [INFO] Task started: Blastn
[2024-01-24 14:21:39,168] [INFO] Running command: blastn -query GCF_004005855.1_ASM400585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0232a7f4-bff1-4df5-ab57-208cf74d43f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005855.1_ASM400585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:42,159] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:42,162] [INFO] Selected 22 target genomes.
[2024-01-24 14:21:42,163] [INFO] Target genome list was writen to GCF_004005855.1_ASM400585v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:42,183] [INFO] Task started: fastANI
[2024-01-24 14:21:42,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd77bc55-20a6-4297-832a-b3bfb1aaf4b0/GCF_004005855.1_ASM400585v1_genomic.fna.gz --refList GCF_004005855.1_ASM400585v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005855.1_ASM400585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:05,688] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:05,757] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:05,757] [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_004005855.1	s__Rhodovarius sp004005855	100.0	1738	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009900765.1	s__Rhodovarius lipocyclicus	87.3813	1201	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129145.1	s__Roseococcus sp007129145	79.2647	349	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018413645.1	s__Roseococcus sp018413645	79.0223	716	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336745.1	s__Roseococcus sp004336745	78.911	707	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376425.1	s__Rhodovarius sp014376425	78.8096	528	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129065.1	s__Roseomonas_B soli	78.6677	617	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490445.1	s__Roseomonas ludipueritiae	78.5948	550	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355885.1	s__Roseococcus sp017355885	78.5818	614	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386565.1	s__Roseomonas oryzae	78.5777	553	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298245.1	s__Rhodovarius sp013298245	78.5027	516	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018129005.1	s__Roseomonas_B eburnea	78.497	692	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	78.455	607	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	78.3333	639	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_001941945.1	s__Roseomonas gilardii	78.2747	572	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	96.77	95.72	0.89	0.83	6	-
GCF_017355405.1	s__Roseomonas sp017355405	78.2505	607	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000622225.1	s__Roseomonas mucosa	78.225	558	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.41	98.67	0.95	0.89	8	-
GCF_011040385.1	s__Roseomonas_A sp011040385	78.1466	754	1742	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765735.1	s__Variovorax sp009765735	75.3135	333	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241895.1	s__Rubrivivax sp018241895	75.2487	193	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003100395.1	s__Aquabacterium olei	75.2416	147	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241265.1	s__JAFEEF01 sp018241265	75.0401	188	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAFEEF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:05,759] [INFO] GTDB search result was written to GCF_004005855.1_ASM400585v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:05,760] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:05,765] [INFO] DFAST_QC result json was written to GCF_004005855.1_ASM400585v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:05,765] [INFO] DFAST_QC completed!
[2024-01-24 14:22:05,765] [INFO] Total running time: 0h2m28s