[2024-01-24 13:40:35,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,075] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdeb0d58-93d1-4ee5-87cf-c7ca2c19a5f1/dqc_reference
[2024-01-24 13:40:36,555] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,556] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,556] [INFO] Running command: gunzip -c /var/lib/cwl/stgda897233-f3c6-4cf8-9484-4a22839b3c28/GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/cds.fna -a GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,896] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,896] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,896] [INFO] Running command: hmmsearch --tblout GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdeb0d58-93d1-4ee5-87cf-c7ca2c19a5f1/dqc_reference/reference_markers.hmm GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,222] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,258] [INFO] Query marker FASTA was written to GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:49,259] [INFO] Task started: Blastn
[2024-01-24 13:40:49,259] [INFO] Running command: blastn -query GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdeb0d58-93d1-4ee5-87cf-c7ca2c19a5f1/dqc_reference/reference_markers.fasta -out GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,332] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,336] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:50,336] [INFO] Target genome list was writen to GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,344] [INFO] Task started: fastANI
[2024-01-24 13:40:50,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgda897233-f3c6-4cf8-9484-4a22839b3c28/GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna.gz --refList GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:04,324] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:04,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdeb0d58-93d1-4ee5-87cf-c7ca2c19a5f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:04,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdeb0d58-93d1-4ee5-87cf-c7ca2c19a5f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:04,340] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:04,340] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:04,340] [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
Jannaschia aquimarina	strain=DSM 28248	GCA_900188045.1	935700	935700	type	True	100.0	1352	1352	95	conclusive
Jannaschia aquimarina	strain=GSW-M26	GCA_000877395.1	935700	935700	type	True	99.9636	1307	1352	95	conclusive
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	79.5462	617	1352	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	79.0181	517	1352	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	79.0178	517	1352	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	78.7559	526	1352	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	78.6706	446	1352	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	78.6474	440	1352	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	78.4647	451	1352	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.1259	304	1352	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.0697	380	1352	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	78.0412	313	1352	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.7901	320	1352	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	77.7335	286	1352	95	below_threshold
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	77.536	257	1352	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.4942	300	1352	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.4936	249	1352	95	below_threshold
Paracoccus contaminans	strain=RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	GCA_002105555.1	1945662	1945662	type	True	77.1502	217	1352	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.0627	240	1352	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:04,343] [INFO] DFAST Taxonomy check result was written to GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:04,343] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:04,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:04,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdeb0d58-93d1-4ee5-87cf-c7ca2c19a5f1/dqc_reference/checkm_data
[2024-01-24 13:41:04,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:04,390] [INFO] Task started: CheckM
[2024-01-24 13:41:04,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/checkm_input GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:41:43,385] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:43,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:43,406] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:43,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:43,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:41:43,407] [INFO] Task started: Blastn
[2024-01-24 13:41:43,407] [INFO] Running command: blastn -query GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdeb0d58-93d1-4ee5-87cf-c7ca2c19a5f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:45,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:45,362] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:45,363] [INFO] Target genome list was writen to GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:45,393] [INFO] Task started: fastANI
[2024-01-24 13:41:45,394] [INFO] Running command: fastANI --query /var/lib/cwl/stgda897233-f3c6-4cf8-9484-4a22839b3c28/GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna.gz --refList GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:00,348] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:00,365] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:00,365] [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_000877395.1	s__Jannaschia aquimarina	99.9636	1307	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003340555.1	s__Jannaschia formosa	79.5295	619	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820245.1	s__Jannaschia sp016820245	79.0304	529	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116765.1	s__Jannaschia seohaensis	79.0092	518	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013404595.1	s__Jannaschia marina	78.7828	525	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001408515.1	s__Jannaschia seosinensis	78.7419	399	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	78.6614	447	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900113875.1	s__Jannaschia pohangensis	78.4554	452	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	78.1424	404	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	78.1379	357	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	78.1092	283	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_900107235.1	s__Citreimonas salinaria	78.08	360	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	78.0524	312	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	77.9254	328	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCA_002720475.1	s__Roseovarius sp002720475	77.9042	210	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCF_000379485.1	s__Wenxinia marina	77.9012	373	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002814095.1	s__Sagittula sp002814095	77.7549	351	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	77.725	346	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106665.1	s__Paracoccus sanguinis	77.7191	288	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.10	96.00	0.89	0.81	6	-
GCA_003255745.1	s__Paracoccus saliphilus_A	76.9742	199	1352	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:00,367] [INFO] GTDB search result was written to GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:00,368] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:00,374] [INFO] DFAST_QC result json was written to GCF_900188045.1_IMG-taxon_2681813552_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:00,374] [INFO] DFAST_QC completed!
[2024-01-24 13:42:00,374] [INFO] Total running time: 0h1m25s