[2024-01-24 11:59:09,262] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:09,264] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:09,264] [INFO] DQC Reference Directory: /var/lib/cwl/stg089e96f6-5104-4030-b8f8-20f77dcdf2ca/dqc_reference
[2024-01-24 11:59:10,545] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:10,546] [INFO] Task started: Prodigal
[2024-01-24 11:59:10,547] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d068765-dc94-452b-9cfd-496e85fe5131/GCF_011601345.1_ASM1160134v1_genomic.fna.gz | prodigal -d GCF_011601345.1_ASM1160134v1_genomic.fna/cds.fna -a GCF_011601345.1_ASM1160134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:22,339] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:22,339] [INFO] Task started: HMMsearch
[2024-01-24 11:59:22,339] [INFO] Running command: hmmsearch --tblout GCF_011601345.1_ASM1160134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg089e96f6-5104-4030-b8f8-20f77dcdf2ca/dqc_reference/reference_markers.hmm GCF_011601345.1_ASM1160134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:22,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:22,668] [INFO] Found 6/6 markers.
[2024-01-24 11:59:22,722] [INFO] Query marker FASTA was written to GCF_011601345.1_ASM1160134v1_genomic.fna/markers.fasta
[2024-01-24 11:59:22,722] [INFO] Task started: Blastn
[2024-01-24 11:59:22,723] [INFO] Running command: blastn -query GCF_011601345.1_ASM1160134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg089e96f6-5104-4030-b8f8-20f77dcdf2ca/dqc_reference/reference_markers.fasta -out GCF_011601345.1_ASM1160134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:23,470] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:23,473] [INFO] Selected 18 target genomes.
[2024-01-24 11:59:23,473] [INFO] Target genome list was writen to GCF_011601345.1_ASM1160134v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:23,493] [INFO] Task started: fastANI
[2024-01-24 11:59:23,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d068765-dc94-452b-9cfd-496e85fe5131/GCF_011601345.1_ASM1160134v1_genomic.fna.gz --refList GCF_011601345.1_ASM1160134v1_genomic.fna/target_genomes.txt --output GCF_011601345.1_ASM1160134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:37,992] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:37,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg089e96f6-5104-4030-b8f8-20f77dcdf2ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:37,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg089e96f6-5104-4030-b8f8-20f77dcdf2ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:38,008] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:38,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:38,009] [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 gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	100.0	1086	1089	95	conclusive
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	82.3116	710	1089	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	82.2327	707	1089	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.7155	565	1089	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	79.691	567	1089	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	79.5953	544	1089	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.2485	414	1089	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.235	420	1089	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.6286	297	1089	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.5034	337	1089	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.404	268	1089	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3774	220	1089	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.3378	280	1089	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	77.2442	233	1089	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.1698	258	1089	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.1024	245	1089	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.0966	245	1089	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.6839	205	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:38,011] [INFO] DFAST Taxonomy check result was written to GCF_011601345.1_ASM1160134v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:38,014] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:38,015] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:38,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg089e96f6-5104-4030-b8f8-20f77dcdf2ca/dqc_reference/checkm_data
[2024-01-24 11:59:38,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:38,065] [INFO] Task started: CheckM
[2024-01-24 11:59:38,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011601345.1_ASM1160134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011601345.1_ASM1160134v1_genomic.fna/checkm_input GCF_011601345.1_ASM1160134v1_genomic.fna/checkm_result
[2024-01-24 12:00:16,487] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:16,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:16,515] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:16,515] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:16,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011601345.1_ASM1160134v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:16,516] [INFO] Task started: Blastn
[2024-01-24 12:00:16,516] [INFO] Running command: blastn -query GCF_011601345.1_ASM1160134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg089e96f6-5104-4030-b8f8-20f77dcdf2ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_011601345.1_ASM1160134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:18,493] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:18,499] [INFO] Selected 14 target genomes.
[2024-01-24 12:00:18,499] [INFO] Target genome list was writen to GCF_011601345.1_ASM1160134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:18,510] [INFO] Task started: fastANI
[2024-01-24 12:00:18,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d068765-dc94-452b-9cfd-496e85fe5131/GCF_011601345.1_ASM1160134v1_genomic.fna.gz --refList GCF_011601345.1_ASM1160134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011601345.1_ASM1160134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:28,921] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:28,938] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:28,938] [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_011601345.1	s__Roseovarius gahaiensis	100.0	1086	1089	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_900142665.1	s__Roseovarius pacificus	82.3006	711	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_900142765.1	s__Roseovarius litoreus	79.8999	600	1089	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	79.7079	566	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009669325.1	s__Roseovarius bejariae	79.5956	543	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.5144	421	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	78.2864	369	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	78.2347	420	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_003072125.1	s__Roseovarius sediminicola	78.1959	373	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	77.9103	324	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002094885.1	s__Salibaculum halophilum	77.4149	267	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	77.3592	247	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_001975705.1	s__Salipiger abyssi	77.2698	324	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	77.1605	259	1089	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:28,940] [INFO] GTDB search result was written to GCF_011601345.1_ASM1160134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:28,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:28,947] [INFO] DFAST_QC result json was written to GCF_011601345.1_ASM1160134v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:28,947] [INFO] DFAST_QC completed!
[2024-01-24 12:00:28,947] [INFO] Total running time: 0h1m20s