[2024-01-24 15:26:33,267] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:33,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:33,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg27997c5f-bce8-41e8-84f9-118a7e1a03a8/dqc_reference
[2024-01-24 15:26:34,543] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:34,544] [INFO] Task started: Prodigal
[2024-01-24 15:26:34,544] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdd34ef5-50ca-473c-96d3-f5eb7fd875fd/GCF_009827095.1_ASM982709v1_genomic.fna.gz | prodigal -d GCF_009827095.1_ASM982709v1_genomic.fna/cds.fna -a GCF_009827095.1_ASM982709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:50,138] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:50,139] [INFO] Task started: HMMsearch
[2024-01-24 15:26:50,139] [INFO] Running command: hmmsearch --tblout GCF_009827095.1_ASM982709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27997c5f-bce8-41e8-84f9-118a7e1a03a8/dqc_reference/reference_markers.hmm GCF_009827095.1_ASM982709v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:50,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:50,502] [INFO] Found 6/6 markers.
[2024-01-24 15:26:50,561] [INFO] Query marker FASTA was written to GCF_009827095.1_ASM982709v1_genomic.fna/markers.fasta
[2024-01-24 15:26:50,561] [INFO] Task started: Blastn
[2024-01-24 15:26:50,561] [INFO] Running command: blastn -query GCF_009827095.1_ASM982709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27997c5f-bce8-41e8-84f9-118a7e1a03a8/dqc_reference/reference_markers.fasta -out GCF_009827095.1_ASM982709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:51,549] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:51,552] [INFO] Selected 19 target genomes.
[2024-01-24 15:26:51,553] [INFO] Target genome list was writen to GCF_009827095.1_ASM982709v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:51,561] [INFO] Task started: fastANI
[2024-01-24 15:26:51,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd34ef5-50ca-473c-96d3-f5eb7fd875fd/GCF_009827095.1_ASM982709v1_genomic.fna.gz --refList GCF_009827095.1_ASM982709v1_genomic.fna/target_genomes.txt --output GCF_009827095.1_ASM982709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:08,351] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:08,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27997c5f-bce8-41e8-84f9-118a7e1a03a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:08,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27997c5f-bce8-41e8-84f9-118a7e1a03a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:08,369] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:08,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:08,369] [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
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	99.9887	1695	1795	95	conclusive
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	81.6969	772	1795	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	81.6201	772	1795	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	81.3419	806	1795	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	81.3112	814	1795	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	79.8892	637	1795	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	79.8783	633	1795	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.5596	661	1795	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.4847	548	1795	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.8306	548	1795	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.6583	497	1795	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.3969	652	1795	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2056	466	1795	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.1957	579	1795	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	77.6561	397	1795	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.5241	379	1795	95	below_threshold
Thalassobius gelatinovorus	strain=CECT 4357	GCA_001458355.1	53501	53501	type	True	77.24	306	1795	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	77.2379	314	1795	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	77.1715	335	1795	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:08,371] [INFO] DFAST Taxonomy check result was written to GCF_009827095.1_ASM982709v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:08,371] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:08,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:08,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27997c5f-bce8-41e8-84f9-118a7e1a03a8/dqc_reference/checkm_data
[2024-01-24 15:27:08,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:08,422] [INFO] Task started: CheckM
[2024-01-24 15:27:08,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009827095.1_ASM982709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009827095.1_ASM982709v1_genomic.fna/checkm_input GCF_009827095.1_ASM982709v1_genomic.fna/checkm_result
[2024-01-24 15:28:06,961] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:06,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:06,985] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:06,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:06,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009827095.1_ASM982709v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:06,986] [INFO] Task started: Blastn
[2024-01-24 15:28:06,987] [INFO] Running command: blastn -query GCF_009827095.1_ASM982709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27997c5f-bce8-41e8-84f9-118a7e1a03a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_009827095.1_ASM982709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:08,728] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:08,733] [INFO] Selected 13 target genomes.
[2024-01-24 15:28:08,734] [INFO] Target genome list was writen to GCF_009827095.1_ASM982709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:08,747] [INFO] Task started: fastANI
[2024-01-24 15:28:08,747] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd34ef5-50ca-473c-96d3-f5eb7fd875fd/GCF_009827095.1_ASM982709v1_genomic.fna.gz --refList GCF_009827095.1_ASM982709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009827095.1_ASM982709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:23,262] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:23,275] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:23,275] [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_009827095.1	s__Pseudooceanicola sp009827095	100.0	1792	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	conclusive
GCF_000220565.1	s__Pseudooceanicola sp000220565	81.6324	727	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	81.6285	771	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	81.6053	809	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002786295.1	s__Pseudooceanicola marinus	81.3284	808	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011806405.1	s__Pseudooceanicola sp011806405	80.7345	751	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	80.1829	677	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	79.8649	635	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015223355.1	s__Salipiger pacificus_B	79.7859	725	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	79.602	655	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_009789075.1	s__Pseudooceanicola pacificus	79.5434	469	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	79.2779	614	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526275.1	s__Lutimaribacter sp000526275	77.8664	459	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:23,277] [INFO] GTDB search result was written to GCF_009827095.1_ASM982709v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:23,278] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:23,282] [INFO] DFAST_QC result json was written to GCF_009827095.1_ASM982709v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:23,282] [INFO] DFAST_QC completed!
[2024-01-24 15:28:23,282] [INFO] Total running time: 0h1m50s