[2024-01-24 10:47:09,788] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg5484b2e3-2bef-4300-bef2-9ab0c17d0f30/dqc_reference
[2024-01-24 10:47:12,074] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,076] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg1db7b945-a248-4190-ae7e-3708287d6d17/GCF_003129485.1_ASM312948v1_genomic.fna.gz | prodigal -d GCF_003129485.1_ASM312948v1_genomic.fna/cds.fna -a GCF_003129485.1_ASM312948v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,863] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,863] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,863] [INFO] Running command: hmmsearch --tblout GCF_003129485.1_ASM312948v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5484b2e3-2bef-4300-bef2-9ab0c17d0f30/dqc_reference/reference_markers.hmm GCF_003129485.1_ASM312948v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,182] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,213] [INFO] Query marker FASTA was written to GCF_003129485.1_ASM312948v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,213] [INFO] Task started: Blastn
[2024-01-24 10:47:22,213] [INFO] Running command: blastn -query GCF_003129485.1_ASM312948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5484b2e3-2bef-4300-bef2-9ab0c17d0f30/dqc_reference/reference_markers.fasta -out GCF_003129485.1_ASM312948v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,939] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,943] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:22,944] [INFO] Target genome list was writen to GCF_003129485.1_ASM312948v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,296] [INFO] Task started: fastANI
[2024-01-24 10:47:23,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db7b945-a248-4190-ae7e-3708287d6d17/GCF_003129485.1_ASM312948v1_genomic.fna.gz --refList GCF_003129485.1_ASM312948v1_genomic.fna/target_genomes.txt --output GCF_003129485.1_ASM312948v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:36,569] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:36,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5484b2e3-2bef-4300-bef2-9ab0c17d0f30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:36,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5484b2e3-2bef-4300-bef2-9ab0c17d0f30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:36,584] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:36,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:36,584] [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 aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	100.0	1114	1114	95	conclusive
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	81.7681	756	1114	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.6454	648	1114	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	80.4875	657	1114	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	80.4263	579	1114	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	80.3388	598	1114	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	80.3108	609	1114	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	80.3103	596	1114	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.0121	605	1114	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	79.9665	603	1114	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	79.8802	544	1114	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	79.8323	547	1114	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	79.8106	549	1114	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.739	582	1114	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.6993	574	1114	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	79.5503	543	1114	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	79.4841	560	1114	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	79.2737	536	1114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:36,586] [INFO] DFAST Taxonomy check result was written to GCF_003129485.1_ASM312948v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:36,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:36,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:36,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5484b2e3-2bef-4300-bef2-9ab0c17d0f30/dqc_reference/checkm_data
[2024-01-24 10:47:36,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:36,660] [INFO] Task started: CheckM
[2024-01-24 10:47:36,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003129485.1_ASM312948v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003129485.1_ASM312948v1_genomic.fna/checkm_input GCF_003129485.1_ASM312948v1_genomic.fna/checkm_result
[2024-01-24 10:48:10,231] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:10,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:10,252] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:10,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:10,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003129485.1_ASM312948v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:10,253] [INFO] Task started: Blastn
[2024-01-24 10:48:10,254] [INFO] Running command: blastn -query GCF_003129485.1_ASM312948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5484b2e3-2bef-4300-bef2-9ab0c17d0f30/dqc_reference/reference_markers_gtdb.fasta -out GCF_003129485.1_ASM312948v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:11,209] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:11,213] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:11,213] [INFO] Target genome list was writen to GCF_003129485.1_ASM312948v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:11,656] [INFO] Task started: fastANI
[2024-01-24 10:48:11,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg1db7b945-a248-4190-ae7e-3708287d6d17/GCF_003129485.1_ASM312948v1_genomic.fna.gz --refList GCF_003129485.1_ASM312948v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003129485.1_ASM312948v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:25,504] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:25,525] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:25,525] [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_003129485.1	s__Polaribacter sp003129485	100.0	1114	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009832745.1	s__Polaribacter sp009832745	81.7746	755	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	81.2672	698	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335085.1	s__Polaribacter sp003335085	81.0261	646	1114	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	80.9349	650	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_002954605.1	s__Polaribacter butkevichii	80.4913	657	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861005.1	s__Polaribacter vadi_A	80.4471	660	1114	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	80.3945	634	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	80.339	606	1114	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	80.1751	586	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	80.0346	602	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001280865.1	s__Polaribacter dokdonensis	79.8264	547	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000152945.2	s__Polaribacter sp000152945	79.772	513	1114	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	79.7564	581	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	79.5753	434	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954665.1	s__Polaribacter glomeratus	79.5016	558	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002943715.1	s__Polaribacter filamentus	79.2727	537	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	79.0389	480	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:25,527] [INFO] GTDB search result was written to GCF_003129485.1_ASM312948v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:25,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:25,531] [INFO] DFAST_QC result json was written to GCF_003129485.1_ASM312948v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:25,532] [INFO] DFAST_QC completed!
[2024-01-24 10:48:25,532] [INFO] Total running time: 0h1m16s