[2023-06-28 18:01:37,975] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:01:37,986] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:01:37,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d1437f8-1d95-46c0-bfb4-613bcc6f2f4f/dqc_reference
[2023-06-28 18:01:39,353] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:01:39,354] [INFO] Task started: Prodigal
[2023-06-28 18:01:39,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg93308ec2-f054-4e0f-a0b2-07cf3a9f4041/GCA_020629175.1_ASM2062917v1_genomic.fna.gz | prodigal -d GCA_020629175.1_ASM2062917v1_genomic.fna/cds.fna -a GCA_020629175.1_ASM2062917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:01:49,503] [INFO] Task succeeded: Prodigal
[2023-06-28 18:01:49,504] [INFO] Task started: HMMsearch
[2023-06-28 18:01:49,504] [INFO] Running command: hmmsearch --tblout GCA_020629175.1_ASM2062917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d1437f8-1d95-46c0-bfb4-613bcc6f2f4f/dqc_reference/reference_markers.hmm GCA_020629175.1_ASM2062917v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:01:49,793] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:01:49,795] [INFO] Found 6/6 markers.
[2023-06-28 18:01:49,836] [INFO] Query marker FASTA was written to GCA_020629175.1_ASM2062917v1_genomic.fna/markers.fasta
[2023-06-28 18:01:49,837] [INFO] Task started: Blastn
[2023-06-28 18:01:49,837] [INFO] Running command: blastn -query GCA_020629175.1_ASM2062917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d1437f8-1d95-46c0-bfb4-613bcc6f2f4f/dqc_reference/reference_markers.fasta -out GCA_020629175.1_ASM2062917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:01:50,707] [INFO] Task succeeded: Blastn
[2023-06-28 18:01:50,710] [INFO] Selected 32 target genomes.
[2023-06-28 18:01:50,711] [INFO] Target genome list was writen to GCA_020629175.1_ASM2062917v1_genomic.fna/target_genomes.txt
[2023-06-28 18:01:50,717] [INFO] Task started: fastANI
[2023-06-28 18:01:50,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg93308ec2-f054-4e0f-a0b2-07cf3a9f4041/GCA_020629175.1_ASM2062917v1_genomic.fna.gz --refList GCA_020629175.1_ASM2062917v1_genomic.fna/target_genomes.txt --output GCA_020629175.1_ASM2062917v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:02:16,860] [INFO] Task succeeded: fastANI
[2023-06-28 18:02:16,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d1437f8-1d95-46c0-bfb4-613bcc6f2f4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:02:16,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d1437f8-1d95-46c0-bfb4-613bcc6f2f4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:02:16,892] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:02:16,892] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:02:16,892] [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
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	77.3492	152	1009	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	77.3376	233	1009	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.1883	154	1009	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	77.1472	184	1009	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.0878	192	1009	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.9202	129	1009	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	76.8826	198	1009	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.8653	142	1009	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	76.8216	127	1009	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	76.8109	126	1009	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	76.8014	128	1009	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	76.7823	176	1009	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	76.7539	176	1009	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.7507	188	1009	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.712	190	1009	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	76.7106	110	1009	95	below_threshold
Qingshengfaniella alkalisoli	strain=LN3S51	GCA_007855645.1	2599296	2599296	type	True	76.6955	81	1009	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.6732	151	1009	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	76.668	160	1009	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	76.6121	148	1009	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	76.6064	147	1009	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.5974	141	1009	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	76.5564	163	1009	95	below_threshold
Pelagovum pacificum	strain=SM1903	GCA_016134045.1	2588711	2588711	type	True	76.553	134	1009	95	below_threshold
Pelagovum pacificum	strain=SM1903	GCA_006363825.1	2588711	2588711	type	True	76.5381	136	1009	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	76.5333	138	1009	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.4185	110	1009	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.3945	120	1009	95	below_threshold
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	76.3686	131	1009	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	76.3035	157	1009	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.2747	123	1009	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.183	102	1009	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:02:16,896] [INFO] DFAST Taxonomy check result was written to GCA_020629175.1_ASM2062917v1_genomic.fna/tc_result.tsv
[2023-06-28 18:02:16,896] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:02:16,897] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:02:16,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d1437f8-1d95-46c0-bfb4-613bcc6f2f4f/dqc_reference/checkm_data
[2023-06-28 18:02:16,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:02:16,936] [INFO] Task started: CheckM
[2023-06-28 18:02:16,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020629175.1_ASM2062917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020629175.1_ASM2062917v1_genomic.fna/checkm_input GCA_020629175.1_ASM2062917v1_genomic.fna/checkm_result
[2023-06-28 18:02:50,987] [INFO] Task succeeded: CheckM
[2023-06-28 18:02:50,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:02:51,015] [INFO] ===== Completeness check finished =====
[2023-06-28 18:02:51,016] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:02:51,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020629175.1_ASM2062917v1_genomic.fna/markers.fasta)
[2023-06-28 18:02:51,017] [INFO] Task started: Blastn
[2023-06-28 18:02:51,017] [INFO] Running command: blastn -query GCA_020629175.1_ASM2062917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d1437f8-1d95-46c0-bfb4-613bcc6f2f4f/dqc_reference/reference_markers_gtdb.fasta -out GCA_020629175.1_ASM2062917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:02:52,548] [INFO] Task succeeded: Blastn
[2023-06-28 18:02:52,555] [INFO] Selected 31 target genomes.
[2023-06-28 18:02:52,555] [INFO] Target genome list was writen to GCA_020629175.1_ASM2062917v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:02:52,623] [INFO] Task started: fastANI
[2023-06-28 18:02:52,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg93308ec2-f054-4e0f-a0b2-07cf3a9f4041/GCA_020629175.1_ASM2062917v1_genomic.fna.gz --refList GCA_020629175.1_ASM2062917v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020629175.1_ASM2062917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:03:11,903] [INFO] Task succeeded: fastANI
[2023-06-28 18:03:11,933] [INFO] Found 31 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:03:11,933] [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_900184895.1	s__Flavimaricola marinus	77.326	234	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114675.1	s__Yoonia litorea	77.1883	154	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113435.1	s__Sulfitobacter dubius	77.0652	150	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_007995245.1	s__Tateyamaria sp007995245	77.0491	164	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814025.1	s__Tateyamaria sp000814025	77.0466	166	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920775.1	s__Marivivens sp009920775	76.9611	124	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420005.1	s__Loktanella sp001420005	76.9546	154	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	76.8936	184	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201935.1	s__Yoonia sp003201935	76.8619	203	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145405.1	s__Loktanella sp004145405	76.8576	158	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	76.8561	176	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.8005	187	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993005.1	s__JAACUH01 sp009993005	76.7886	203	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.7883	145	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_900128995.1	s__Loktanella atrilutea	76.7823	176	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054285.1	s__Litoreibacter ponti	76.7405	177	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	76.7351	138	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.712	190	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_900106805.1	s__Ruegeria halocynthiae	76.7106	110	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	76.6732	151	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002703405.1	s__Sulfitobacter sp002703405	76.6378	137	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.87	96.48	0.79	0.78	3	-
GCF_008065155.1	s__SW4 sp002732825	76.6331	202	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SW4	95.0	98.61	98.61	0.85	0.85	2	-
GCF_018263905.1	s__Loktanella sp018263905	76.6247	147	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	76.624	161	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	76.6006	131	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016134045.1	s__Oceanicola pacificus_A	76.553	134	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900141735.1	s__Wenxinia saemankumensis	76.5333	138	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003254465.1	s__Fluviibacterium sp003254465	76.4719	115	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879715.1	s__Nioella nitratireducens	76.407	152	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550095.1	s__Celeribacter ethanolicus	76.3686	131	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_003340565.1	s__HLUCCA09 sp003340565	76.2051	110	1009	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:03:11,936] [INFO] GTDB search result was written to GCA_020629175.1_ASM2062917v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:03:11,937] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:03:11,948] [INFO] DFAST_QC result json was written to GCA_020629175.1_ASM2062917v1_genomic.fna/dqc_result.json
[2023-06-28 18:03:11,948] [INFO] DFAST_QC completed!
[2023-06-28 18:03:11,949] [INFO] Total running time: 0h1m34s