[2024-01-24 13:57:13,492] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,495] [INFO] DQC Reference Directory: /var/lib/cwl/stg11a0ea33-3139-4537-b6af-f3a56fab4ca4/dqc_reference
[2024-01-24 13:57:14,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,796] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg07ce2eff-714d-498d-aad9-8281014ac8ef/GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/cds.fna -a GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:26,774] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:26,774] [INFO] Task started: HMMsearch
[2024-01-24 13:57:26,774] [INFO] Running command: hmmsearch --tblout GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11a0ea33-3139-4537-b6af-f3a56fab4ca4/dqc_reference/reference_markers.hmm GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:27,059] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:27,063] [INFO] Found 6/6 markers.
[2024-01-24 13:57:27,100] [INFO] Query marker FASTA was written to GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:27,100] [INFO] Task started: Blastn
[2024-01-24 13:57:27,100] [INFO] Running command: blastn -query GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg11a0ea33-3139-4537-b6af-f3a56fab4ca4/dqc_reference/reference_markers.fasta -out GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:28,102] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:28,106] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:28,107] [INFO] Target genome list was writen to GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:28,114] [INFO] Task started: fastANI
[2024-01-24 13:57:28,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ce2eff-714d-498d-aad9-8281014ac8ef/GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna.gz --refList GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:44,160] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:44,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11a0ea33-3139-4537-b6af-f3a56fab4ca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:44,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11a0ea33-3139-4537-b6af-f3a56fab4ca4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:44,176] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:44,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:44,176] [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 nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	100.0	1350	1351	95	conclusive
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	99.9749	1336	1351	95	conclusive
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	82.8478	865	1351	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.8971	617	1351	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.7654	627	1351	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	79.725	531	1351	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	79.4763	662	1351	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.4154	628	1351	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	79.3789	543	1351	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	79.3752	631	1351	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	78.6111	307	1351	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.4569	535	1351	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1437	416	1351	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9533	420	1351	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.8731	326	1351	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6518	352	1351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:44,178] [INFO] DFAST Taxonomy check result was written to GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:57:44,178] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:44,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:44,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11a0ea33-3139-4537-b6af-f3a56fab4ca4/dqc_reference/checkm_data
[2024-01-24 13:57:44,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:44,224] [INFO] Task started: CheckM
[2024-01-24 13:57:44,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/checkm_input GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:58:28,220] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:28,222] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:28,243] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:28,243] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:28,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:58:28,244] [INFO] Task started: Blastn
[2024-01-24 13:58:28,245] [INFO] Running command: blastn -query GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg11a0ea33-3139-4537-b6af-f3a56fab4ca4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:30,428] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:30,431] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:30,431] [INFO] Target genome list was writen to GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:30,447] [INFO] Task started: fastANI
[2024-01-24 13:58:30,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ce2eff-714d-498d-aad9-8281014ac8ef/GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna.gz --refList GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:41,621] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:41,632] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:41,632] [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_900109195.1	s__Pseudooceanicola nitratireducens	99.9749	1336	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	conclusive
GCF_004959925.1	s__Pseudooceanicola onchidii	82.8407	866	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	81.6985	865	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_000152725.1	s__Pseudooceanicola batsensis	81.611	818	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	81.3703	821	1351	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	79.9957	700	1351	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	79.6701	645	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	79.4757	664	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	79.3972	611	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCA_002709085.1	s__Pseudooceanicola sp002709085	79.3889	464	1351	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	79.3826	544	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	78.0999	401	1351	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:41,634] [INFO] GTDB search result was written to GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:41,634] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:41,638] [INFO] DFAST_QC result json was written to GCF_900112545.1_IMG-taxon_2687453758_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:58:41,638] [INFO] DFAST_QC completed!
[2024-01-24 13:58:41,638] [INFO] Total running time: 0h1m28s