[2024-01-24 11:35:34,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a68ed14-596e-4f9a-a9f2-0c55ee35afe3/dqc_reference
[2024-01-24 11:35:35,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,513] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg92745606-7c82-499f-b226-a02def54ccb8/GCF_001680885.1_ASM168088v1_genomic.fna.gz | prodigal -d GCF_001680885.1_ASM168088v1_genomic.fna/cds.fna -a GCF_001680885.1_ASM168088v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:46,749] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:46,750] [INFO] Task started: HMMsearch
[2024-01-24 11:35:46,750] [INFO] Running command: hmmsearch --tblout GCF_001680885.1_ASM168088v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a68ed14-596e-4f9a-a9f2-0c55ee35afe3/dqc_reference/reference_markers.hmm GCF_001680885.1_ASM168088v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:47,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:47,053] [INFO] Found 6/6 markers.
[2024-01-24 11:35:47,087] [INFO] Query marker FASTA was written to GCF_001680885.1_ASM168088v1_genomic.fna/markers.fasta
[2024-01-24 11:35:47,087] [INFO] Task started: Blastn
[2024-01-24 11:35:47,088] [INFO] Running command: blastn -query GCF_001680885.1_ASM168088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a68ed14-596e-4f9a-a9f2-0c55ee35afe3/dqc_reference/reference_markers.fasta -out GCF_001680885.1_ASM168088v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:47,753] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:47,757] [INFO] Selected 15 target genomes.
[2024-01-24 11:35:47,757] [INFO] Target genome list was writen to GCF_001680885.1_ASM168088v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:47,775] [INFO] Task started: fastANI
[2024-01-24 11:35:47,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg92745606-7c82-499f-b226-a02def54ccb8/GCF_001680885.1_ASM168088v1_genomic.fna.gz --refList GCF_001680885.1_ASM168088v1_genomic.fna/target_genomes.txt --output GCF_001680885.1_ASM168088v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:59,882] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:59,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a68ed14-596e-4f9a-a9f2-0c55ee35afe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:59,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a68ed14-596e-4f9a-a9f2-0c55ee35afe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:59,900] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:59,900] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:59,900] [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
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	100.0	1253	1254	95	conclusive
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	99.995	1251	1254	95	conclusive
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	82.1728	765	1254	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	82.1664	774	1254	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	82.0982	793	1254	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	81.8403	717	1254	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	81.3806	712	1254	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	81.379	724	1254	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	81.1203	682	1254	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	80.9803	704	1254	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	80.8777	733	1254	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	80.8199	670	1254	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	80.6218	667	1254	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	80.5729	671	1254	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	80.414	648	1254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:59,902] [INFO] DFAST Taxonomy check result was written to GCF_001680885.1_ASM168088v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:59,903] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:59,903] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:59,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a68ed14-596e-4f9a-a9f2-0c55ee35afe3/dqc_reference/checkm_data
[2024-01-24 11:35:59,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:59,940] [INFO] Task started: CheckM
[2024-01-24 11:35:59,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001680885.1_ASM168088v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001680885.1_ASM168088v1_genomic.fna/checkm_input GCF_001680885.1_ASM168088v1_genomic.fna/checkm_result
[2024-01-24 11:36:35,861] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:35,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:35,881] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:35,881] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:35,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001680885.1_ASM168088v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:35,882] [INFO] Task started: Blastn
[2024-01-24 11:36:35,882] [INFO] Running command: blastn -query GCF_001680885.1_ASM168088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a68ed14-596e-4f9a-a9f2-0c55ee35afe3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001680885.1_ASM168088v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:36,787] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:36,791] [INFO] Selected 15 target genomes.
[2024-01-24 11:36:36,792] [INFO] Target genome list was writen to GCF_001680885.1_ASM168088v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:36,804] [INFO] Task started: fastANI
[2024-01-24 11:36:36,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg92745606-7c82-499f-b226-a02def54ccb8/GCF_001680885.1_ASM168088v1_genomic.fna.gz --refList GCF_001680885.1_ASM168088v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001680885.1_ASM168088v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:49,925] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:49,941] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:49,942] [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_001761365.1	s__Polaribacter vadi	99.995	1251	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000687935.1	s__Polaribacter sp000687935	88.7956	966	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	82.213	778	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_018861005.1	s__Polaribacter vadi_A	82.0585	768	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	81.853	714	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	81.7579	742	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	81.3798	723	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000766795.1	s__Polaribacter sp000766795	81.2335	661	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997085.1	s__Polaribacter sp007997085	81.099	737	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.89	99.89	0.97	0.97	2	-
GCF_002163675.1	s__Polaribacter sp002163675	80.9339	691	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569185.1	s__Polaribacter sp017569185	80.8105	671	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	80.7095	634	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943715.1	s__Polaribacter filamentus	80.617	667	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	80.5824	642	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	80.3811	652	1254	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:49,943] [INFO] GTDB search result was written to GCF_001680885.1_ASM168088v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:49,944] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:49,947] [INFO] DFAST_QC result json was written to GCF_001680885.1_ASM168088v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:49,947] [INFO] DFAST_QC completed!
[2024-01-24 11:36:49,948] [INFO] Total running time: 0h1m16s