[2024-01-25 17:36:20,457] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:20,459] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:20,459] [INFO] DQC Reference Directory: /var/lib/cwl/stg9338b1c5-bb09-4fda-b7c3-533955a30dc7/dqc_reference
[2024-01-25 17:36:21,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:21,666] [INFO] Task started: Prodigal
[2024-01-25 17:36:21,666] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8d786d5-f556-48ad-b77c-79c47319178c/GCF_009789075.1_ASM978907v1_genomic.fna.gz | prodigal -d GCF_009789075.1_ASM978907v1_genomic.fna/cds.fna -a GCF_009789075.1_ASM978907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:33,914] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:33,914] [INFO] Task started: HMMsearch
[2024-01-25 17:36:33,915] [INFO] Running command: hmmsearch --tblout GCF_009789075.1_ASM978907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9338b1c5-bb09-4fda-b7c3-533955a30dc7/dqc_reference/reference_markers.hmm GCF_009789075.1_ASM978907v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:34,141] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:34,143] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf8d786d5-f556-48ad-b77c-79c47319178c/GCF_009789075.1_ASM978907v1_genomic.fna.gz]
[2024-01-25 17:36:34,182] [INFO] Query marker FASTA was written to GCF_009789075.1_ASM978907v1_genomic.fna/markers.fasta
[2024-01-25 17:36:34,182] [INFO] Task started: Blastn
[2024-01-25 17:36:34,182] [INFO] Running command: blastn -query GCF_009789075.1_ASM978907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9338b1c5-bb09-4fda-b7c3-533955a30dc7/dqc_reference/reference_markers.fasta -out GCF_009789075.1_ASM978907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:34,973] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:34,977] [INFO] Selected 14 target genomes.
[2024-01-25 17:36:34,977] [INFO] Target genome list was writen to GCF_009789075.1_ASM978907v1_genomic.fna/target_genomes.txt
[2024-01-25 17:36:34,987] [INFO] Task started: fastANI
[2024-01-25 17:36:34,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d786d5-f556-48ad-b77c-79c47319178c/GCF_009789075.1_ASM978907v1_genomic.fna.gz --refList GCF_009789075.1_ASM978907v1_genomic.fna/target_genomes.txt --output GCF_009789075.1_ASM978907v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:46,509] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:46,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9338b1c5-bb09-4fda-b7c3-533955a30dc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:46,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9338b1c5-bb09-4fda-b7c3-533955a30dc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:46,519] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:36:46,519] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:36:46,519] [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 nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	82.3784	622	1284	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	82.3747	625	1284	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	80.0528	462	1284	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	80.0308	459	1284	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	80.0239	454	1284	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	79.9545	456	1284	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.9222	458	1284	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	79.9109	458	1284	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	79.4938	438	1284	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.4759	431	1284	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	79.4189	476	1284	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.2307	446	1284	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	79.2104	442	1284	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.7708	368	1284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:46,520] [INFO] DFAST Taxonomy check result was written to GCF_009789075.1_ASM978907v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:46,521] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:46,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:46,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9338b1c5-bb09-4fda-b7c3-533955a30dc7/dqc_reference/checkm_data
[2024-01-25 17:36:46,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:46,562] [INFO] Task started: CheckM
[2024-01-25 17:36:46,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009789075.1_ASM978907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009789075.1_ASM978907v1_genomic.fna/checkm_input GCF_009789075.1_ASM978907v1_genomic.fna/checkm_result
[2024-01-25 17:37:32,025] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:32,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:32,044] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:32,044] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:32,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009789075.1_ASM978907v1_genomic.fna/markers.fasta)
[2024-01-25 17:37:32,045] [INFO] Task started: Blastn
[2024-01-25 17:37:32,045] [INFO] Running command: blastn -query GCF_009789075.1_ASM978907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9338b1c5-bb09-4fda-b7c3-533955a30dc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_009789075.1_ASM978907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:33,325] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:33,328] [INFO] Selected 12 target genomes.
[2024-01-25 17:37:33,328] [INFO] Target genome list was writen to GCF_009789075.1_ASM978907v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:33,337] [INFO] Task started: fastANI
[2024-01-25 17:37:33,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d786d5-f556-48ad-b77c-79c47319178c/GCF_009789075.1_ASM978907v1_genomic.fna.gz --refList GCF_009789075.1_ASM978907v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009789075.1_ASM978907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:44,830] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:44,839] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:44,839] [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_009789075.1	s__Pseudooceanicola pacificus	100.0	1281	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002210105.1	s__Pseudooceanicola sp002210105	82.542	622	1284	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	82.4007	623	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	82.1403	566	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	80.0258	492	1284	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	79.977	464	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004959925.1	s__Pseudooceanicola onchidii	79.9311	458	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	79.7288	434	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	79.4569	482	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCA_006226775.1	s__Marinovum sp006226775	79.2329	424	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	79.1735	429	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_003111685.1	s__Salipiger pacificus_A	79.1059	408	1284	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:44,841] [INFO] GTDB search result was written to GCF_009789075.1_ASM978907v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:44,842] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:44,845] [INFO] DFAST_QC result json was written to GCF_009789075.1_ASM978907v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:44,845] [INFO] DFAST_QC completed!
[2024-01-25 17:37:44,845] [INFO] Total running time: 0h1m24s