[2023-06-13 15:45:09,676] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:45:09,680] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:45:09,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg525f56ea-c658-411c-b228-84d3e8d8228b/dqc_reference
[2023-06-13 15:45:11,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:45:11,211] [INFO] Task started: Prodigal
[2023-06-13 15:45:11,211] [INFO] Running command: gunzip -c /var/lib/cwl/stg564d54b0-3c00-4017-9216-6b29c6bfbf24/GCA_022828065.1_ASM2282806v1_genomic.fna.gz | prodigal -d GCA_022828065.1_ASM2282806v1_genomic.fna/cds.fna -a GCA_022828065.1_ASM2282806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:45:23,054] [INFO] Task succeeded: Prodigal
[2023-06-13 15:45:23,054] [INFO] Task started: HMMsearch
[2023-06-13 15:45:23,054] [INFO] Running command: hmmsearch --tblout GCA_022828065.1_ASM2282806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg525f56ea-c658-411c-b228-84d3e8d8228b/dqc_reference/reference_markers.hmm GCA_022828065.1_ASM2282806v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:45:23,353] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:45:23,354] [INFO] Found 6/6 markers.
[2023-06-13 15:45:23,391] [INFO] Query marker FASTA was written to GCA_022828065.1_ASM2282806v1_genomic.fna/markers.fasta
[2023-06-13 15:45:23,392] [INFO] Task started: Blastn
[2023-06-13 15:45:23,392] [INFO] Running command: blastn -query GCA_022828065.1_ASM2282806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg525f56ea-c658-411c-b228-84d3e8d8228b/dqc_reference/reference_markers.fasta -out GCA_022828065.1_ASM2282806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:24,242] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:24,263] [INFO] Selected 29 target genomes.
[2023-06-13 15:45:24,263] [INFO] Target genome list was writen to GCA_022828065.1_ASM2282806v1_genomic.fna/target_genomes.txt
[2023-06-13 15:45:24,272] [INFO] Task started: fastANI
[2023-06-13 15:45:24,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg564d54b0-3c00-4017-9216-6b29c6bfbf24/GCA_022828065.1_ASM2282806v1_genomic.fna.gz --refList GCA_022828065.1_ASM2282806v1_genomic.fna/target_genomes.txt --output GCA_022828065.1_ASM2282806v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:44,023] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:44,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg525f56ea-c658-411c-b228-84d3e8d8228b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:44,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg525f56ea-c658-411c-b228-84d3e8d8228b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:44,047] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:45:44,047] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:45:44,048] [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
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	76.7561	153	1207	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	76.7407	154	1207	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.6928	153	1207	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.6522	81	1207	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	76.6301	111	1207	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.6294	86	1207	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.5581	85	1207	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.5237	107	1207	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	76.3538	82	1207	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	76.339	101	1207	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.2902	97	1207	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	76.261	103	1207	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	76.2421	130	1207	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	76.2421	130	1207	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	76.2351	114	1207	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	76.2338	95	1207	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	76.2119	86	1207	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	76.1667	105	1207	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	76.1648	106	1207	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.1586	97	1207	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	76.1581	91	1207	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	76.1578	75	1207	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	76.1265	101	1207	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.0998	92	1207	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	75.9684	107	1207	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.3137	50	1207	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:45:44,051] [INFO] DFAST Taxonomy check result was written to GCA_022828065.1_ASM2282806v1_genomic.fna/tc_result.tsv
[2023-06-13 15:45:44,052] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:44,052] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:44,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg525f56ea-c658-411c-b228-84d3e8d8228b/dqc_reference/checkm_data
[2023-06-13 15:45:44,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:44,098] [INFO] Task started: CheckM
[2023-06-13 15:45:44,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022828065.1_ASM2282806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022828065.1_ASM2282806v1_genomic.fna/checkm_input GCA_022828065.1_ASM2282806v1_genomic.fna/checkm_result
[2023-06-13 15:46:23,810] [INFO] Task succeeded: CheckM
[2023-06-13 15:46:23,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 15:46:23,839] [INFO] ===== Completeness check finished =====
[2023-06-13 15:46:23,839] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:46:23,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022828065.1_ASM2282806v1_genomic.fna/markers.fasta)
[2023-06-13 15:46:23,840] [INFO] Task started: Blastn
[2023-06-13 15:46:23,840] [INFO] Running command: blastn -query GCA_022828065.1_ASM2282806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg525f56ea-c658-411c-b228-84d3e8d8228b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022828065.1_ASM2282806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:46:25,149] [INFO] Task succeeded: Blastn
[2023-06-13 15:46:25,154] [INFO] Selected 20 target genomes.
[2023-06-13 15:46:25,154] [INFO] Target genome list was writen to GCA_022828065.1_ASM2282806v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:46:25,165] [INFO] Task started: fastANI
[2023-06-13 15:46:25,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg564d54b0-3c00-4017-9216-6b29c6bfbf24/GCA_022828065.1_ASM2282806v1_genomic.fna.gz --refList GCA_022828065.1_ASM2282806v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022828065.1_ASM2282806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:46:38,222] [INFO] Task succeeded: fastANI
[2023-06-13 15:46:38,249] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:46:38,250] [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
GCA_009838075.1	s__JABDJO01 sp009838075	88.648	862	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	99.86	99.86	0.89	0.89	2	-
GCA_009843725.1	s__JABDJO01 sp009843725	88.0056	665	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009839535.1	s__JABDJO01 sp009839535	87.0805	536	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	76.8853	118	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	76.741	154	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009830125.1	s__GH1-50 sp009830125	76.6928	153	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	76.6126	122	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	76.4417	103	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.4219	108	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	76.3805	108	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	76.3672	142	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789055.1	s__Oceanicola lentulus	76.2654	104	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280515.1	s__Albidovulum sp002280515	76.2174	108	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	76.174	114	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022265.1	s__Paenirhodobacter ferrireducens	76.1265	101	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	-
GCA_003241785.1	s__Amaricoccus sp003241785	76.095	97	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696705.1	s__RFGD01 sp003696705	76.0395	92	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__RFGD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959935.1	s__Falsirhodobacter xinxiangensis	75.9578	74	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002751875.1	s__Oceaniglobus indicus	75.9497	82	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131685.1	s__Rhodobaculum sp007131685	75.5924	69	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.44	99.41	0.86	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-13 15:46:38,252] [INFO] GTDB search result was written to GCA_022828065.1_ASM2282806v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:46:38,253] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:46:38,259] [INFO] DFAST_QC result json was written to GCA_022828065.1_ASM2282806v1_genomic.fna/dqc_result.json
[2023-06-13 15:46:38,259] [INFO] DFAST_QC completed!
[2023-06-13 15:46:38,259] [INFO] Total running time: 0h1m29s