[2024-01-24 13:13:23,760] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg81c54a0b-bc1f-4c6f-8ff2-0d4a45799503/dqc_reference
[2024-01-24 13:13:25,126] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:25,127] [INFO] Task started: Prodigal
[2024-01-24 13:13:25,127] [INFO] Running command: gunzip -c /var/lib/cwl/stge5d4fd6f-c32a-4bf6-a22e-4f738798ccbe/GCF_004761875.1_ASM476187v1_genomic.fna.gz | prodigal -d GCF_004761875.1_ASM476187v1_genomic.fna/cds.fna -a GCF_004761875.1_ASM476187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:37,754] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:37,754] [INFO] Task started: HMMsearch
[2024-01-24 13:13:37,754] [INFO] Running command: hmmsearch --tblout GCF_004761875.1_ASM476187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81c54a0b-bc1f-4c6f-8ff2-0d4a45799503/dqc_reference/reference_markers.hmm GCF_004761875.1_ASM476187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:38,271] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:38,272] [INFO] Found 6/6 markers.
[2024-01-24 13:13:38,326] [INFO] Query marker FASTA was written to GCF_004761875.1_ASM476187v1_genomic.fna/markers.fasta
[2024-01-24 13:13:38,326] [INFO] Task started: Blastn
[2024-01-24 13:13:38,326] [INFO] Running command: blastn -query GCF_004761875.1_ASM476187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c54a0b-bc1f-4c6f-8ff2-0d4a45799503/dqc_reference/reference_markers.fasta -out GCF_004761875.1_ASM476187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:39,354] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:39,357] [INFO] Selected 23 target genomes.
[2024-01-24 13:13:39,357] [INFO] Target genome list was writen to GCF_004761875.1_ASM476187v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:39,389] [INFO] Task started: fastANI
[2024-01-24 13:13:39,389] [INFO] Running command: fastANI --query /var/lib/cwl/stge5d4fd6f-c32a-4bf6-a22e-4f738798ccbe/GCF_004761875.1_ASM476187v1_genomic.fna.gz --refList GCF_004761875.1_ASM476187v1_genomic.fna/target_genomes.txt --output GCF_004761875.1_ASM476187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:57,170] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:57,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81c54a0b-bc1f-4c6f-8ff2-0d4a45799503/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:57,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81c54a0b-bc1f-4c6f-8ff2-0d4a45799503/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:57,189] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:57,189] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:57,190] [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
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	100.0	1293	1293	95	conclusive
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	80.0816	646	1293	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	80.0134	610	1293	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.1903	568	1293	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.113	532	1293	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	79.112	572	1293	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	79.0963	483	1293	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.0861	487	1293	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.8237	497	1293	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.8023	498	1293	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.7187	427	1293	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.5948	491	1293	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	78.4811	460	1293	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	78.0214	365	1293	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.9516	336	1293	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.8743	362	1293	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	77.8654	328	1293	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.8013	284	1293	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7234	309	1293	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.6672	341	1293	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.5673	309	1293	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	77.4359	288	1293	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.9939	219	1293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:57,192] [INFO] DFAST Taxonomy check result was written to GCF_004761875.1_ASM476187v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:57,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:57,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:57,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81c54a0b-bc1f-4c6f-8ff2-0d4a45799503/dqc_reference/checkm_data
[2024-01-24 13:13:57,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:57,237] [INFO] Task started: CheckM
[2024-01-24 13:13:57,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004761875.1_ASM476187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004761875.1_ASM476187v1_genomic.fna/checkm_input GCF_004761875.1_ASM476187v1_genomic.fna/checkm_result
[2024-01-24 13:14:36,921] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:36,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:36,942] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:36,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:36,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004761875.1_ASM476187v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:36,943] [INFO] Task started: Blastn
[2024-01-24 13:14:36,944] [INFO] Running command: blastn -query GCF_004761875.1_ASM476187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c54a0b-bc1f-4c6f-8ff2-0d4a45799503/dqc_reference/reference_markers_gtdb.fasta -out GCF_004761875.1_ASM476187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:38,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:38,573] [INFO] Selected 18 target genomes.
[2024-01-24 13:14:38,574] [INFO] Target genome list was writen to GCF_004761875.1_ASM476187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:38,594] [INFO] Task started: fastANI
[2024-01-24 13:14:38,594] [INFO] Running command: fastANI --query /var/lib/cwl/stge5d4fd6f-c32a-4bf6-a22e-4f738798ccbe/GCF_004761875.1_ASM476187v1_genomic.fna.gz --refList GCF_004761875.1_ASM476187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004761875.1_ASM476187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:53,661] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:53,680] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:53,680] [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_004761875.1	s__Roseovarius aestuariivivens	100.0	1293	1293	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_009363655.1	s__Roseovarius sp009363655	80.0868	633	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_001441615.1	s__Roseovarius atlanticus	80.0671	647	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	80.0064	610	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_009363715.1	s__Roseovarius sp009363715	79.8997	611	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142765.1	s__Roseovarius litoreus	79.117	531	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_900172255.1	s__Roseovarius halotolerans	79.0963	483	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142665.1	s__Roseovarius pacificus	78.841	496	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_009669325.1	s__Roseovarius bejariae	78.6698	427	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762325.1	s__Roseovarius faecimaris	78.5948	491	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109455.1	s__Roseovarius azorensis	78.4851	459	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	78.3247	405	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011601345.1	s__Roseovarius gahaiensis	78.0244	364	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	77.9853	336	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	77.9029	359	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_003116585.1	s__Albibacillus kandeliae	77.7896	347	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	77.5001	308	1293	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:53,682] [INFO] GTDB search result was written to GCF_004761875.1_ASM476187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:53,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:53,688] [INFO] DFAST_QC result json was written to GCF_004761875.1_ASM476187v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:53,688] [INFO] DFAST_QC completed!
[2024-01-24 13:14:53,689] [INFO] Total running time: 0h1m30s