[2024-01-24 14:53:49,333] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:49,334] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:49,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c9e0f8c-1546-4ba2-a207-10526488841a/dqc_reference
[2024-01-24 14:53:50,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:50,568] [INFO] Task started: Prodigal
[2024-01-24 14:53:50,568] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7cceedf-dcef-4f5a-9443-dcdf39e47b73/GCF_003316635.1_ASM331663v1_genomic.fna.gz | prodigal -d GCF_003316635.1_ASM331663v1_genomic.fna/cds.fna -a GCF_003316635.1_ASM331663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:01,223] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:01,223] [INFO] Task started: HMMsearch
[2024-01-24 14:54:01,223] [INFO] Running command: hmmsearch --tblout GCF_003316635.1_ASM331663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c9e0f8c-1546-4ba2-a207-10526488841a/dqc_reference/reference_markers.hmm GCF_003316635.1_ASM331663v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:01,491] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:01,492] [INFO] Found 6/6 markers.
[2024-01-24 14:54:01,525] [INFO] Query marker FASTA was written to GCF_003316635.1_ASM331663v1_genomic.fna/markers.fasta
[2024-01-24 14:54:01,526] [INFO] Task started: Blastn
[2024-01-24 14:54:01,526] [INFO] Running command: blastn -query GCF_003316635.1_ASM331663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c9e0f8c-1546-4ba2-a207-10526488841a/dqc_reference/reference_markers.fasta -out GCF_003316635.1_ASM331663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:02,538] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:02,542] [INFO] Selected 24 target genomes.
[2024-01-24 14:54:02,542] [INFO] Target genome list was writen to GCF_003316635.1_ASM331663v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:02,600] [INFO] Task started: fastANI
[2024-01-24 14:54:02,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7cceedf-dcef-4f5a-9443-dcdf39e47b73/GCF_003316635.1_ASM331663v1_genomic.fna.gz --refList GCF_003316635.1_ASM331663v1_genomic.fna/target_genomes.txt --output GCF_003316635.1_ASM331663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:20,582] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:20,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c9e0f8c-1546-4ba2-a207-10526488841a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:20,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c9e0f8c-1546-4ba2-a207-10526488841a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:20,605] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:54:20,605] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:20,605] [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
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	100.0	1128	1132	95	conclusive
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	84.9201	828	1132	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.0806	468	1132	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.0056	472	1132	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.9549	433	1132	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.7773	433	1132	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.3688	403	1132	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.2926	398	1132	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.2912	433	1132	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.2611	407	1132	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.2179	279	1132	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	78.1786	399	1132	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.9404	387	1132	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.9175	293	1132	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.8059	317	1132	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7444	276	1132	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.7398	296	1132	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.6581	350	1132	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.5726	321	1132	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	77.5342	301	1132	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5071	292	1132	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	77.2518	271	1132	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	77.1736	274	1132	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8792	245	1132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:20,607] [INFO] DFAST Taxonomy check result was written to GCF_003316635.1_ASM331663v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:20,607] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:20,608] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:20,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c9e0f8c-1546-4ba2-a207-10526488841a/dqc_reference/checkm_data
[2024-01-24 14:54:20,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:20,649] [INFO] Task started: CheckM
[2024-01-24 14:54:20,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003316635.1_ASM331663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003316635.1_ASM331663v1_genomic.fna/checkm_input GCF_003316635.1_ASM331663v1_genomic.fna/checkm_result
[2024-01-24 14:54:55,284] [INFO] Task succeeded: CheckM
[2024-01-24 14:54:55,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:54:55,305] [INFO] ===== Completeness check finished =====
[2024-01-24 14:54:55,306] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:54:55,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003316635.1_ASM331663v1_genomic.fna/markers.fasta)
[2024-01-24 14:54:55,307] [INFO] Task started: Blastn
[2024-01-24 14:54:55,307] [INFO] Running command: blastn -query GCF_003316635.1_ASM331663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c9e0f8c-1546-4ba2-a207-10526488841a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003316635.1_ASM331663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:57,198] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:57,202] [INFO] Selected 10 target genomes.
[2024-01-24 14:54:57,203] [INFO] Target genome list was writen to GCF_003316635.1_ASM331663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:54:57,211] [INFO] Task started: fastANI
[2024-01-24 14:54:57,212] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7cceedf-dcef-4f5a-9443-dcdf39e47b73/GCF_003316635.1_ASM331663v1_genomic.fna.gz --refList GCF_003316635.1_ASM331663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003316635.1_ASM331663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:06,612] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:06,627] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:06,627] [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_003316635.1	s__Roseovarius dicentrarchi	100.0	1128	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003072125.1	s__Roseovarius sediminicola	84.8997	830	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156535.1	s__Roseovarius nanhaiticus	81.5463	701	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006125015.1	s__Roseovarius arcticus	80.1948	600	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	79.4447	549	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011040495.1	s__Roseovarius aestuariivivens_A	78.9375	427	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.6139	404	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	78.145	384	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.9317	388	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	77.6738	349	1132	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:06,629] [INFO] GTDB search result was written to GCF_003316635.1_ASM331663v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:06,630] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:06,635] [INFO] DFAST_QC result json was written to GCF_003316635.1_ASM331663v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:06,636] [INFO] DFAST_QC completed!
[2024-01-24 14:55:06,636] [INFO] Total running time: 0h1m17s