[2024-01-24 14:06:06,372] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg6543e4a8-3323-4294-ab6e-2435e4ed4341/dqc_reference
[2024-01-24 14:06:07,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,761] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,761] [INFO] Running command: gunzip -c /var/lib/cwl/stge4d03e72-1cb7-4495-b4f5-275bfe58ff88/GCF_009832745.1_ASM983274v1_genomic.fna.gz | prodigal -d GCF_009832745.1_ASM983274v1_genomic.fna/cds.fna -a GCF_009832745.1_ASM983274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:18,699] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:18,699] [INFO] Task started: HMMsearch
[2024-01-24 14:06:18,700] [INFO] Running command: hmmsearch --tblout GCF_009832745.1_ASM983274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6543e4a8-3323-4294-ab6e-2435e4ed4341/dqc_reference/reference_markers.hmm GCF_009832745.1_ASM983274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:18,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:18,992] [INFO] Found 6/6 markers.
[2024-01-24 14:06:19,022] [INFO] Query marker FASTA was written to GCF_009832745.1_ASM983274v1_genomic.fna/markers.fasta
[2024-01-24 14:06:19,023] [INFO] Task started: Blastn
[2024-01-24 14:06:19,023] [INFO] Running command: blastn -query GCF_009832745.1_ASM983274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6543e4a8-3323-4294-ab6e-2435e4ed4341/dqc_reference/reference_markers.fasta -out GCF_009832745.1_ASM983274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:19,742] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:19,746] [INFO] Selected 15 target genomes.
[2024-01-24 14:06:19,746] [INFO] Target genome list was writen to GCF_009832745.1_ASM983274v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:19,756] [INFO] Task started: fastANI
[2024-01-24 14:06:19,756] [INFO] Running command: fastANI --query /var/lib/cwl/stge4d03e72-1cb7-4495-b4f5-275bfe58ff88/GCF_009832745.1_ASM983274v1_genomic.fna.gz --refList GCF_009832745.1_ASM983274v1_genomic.fna/target_genomes.txt --output GCF_009832745.1_ASM983274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:31,579] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:31,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6543e4a8-3323-4294-ab6e-2435e4ed4341/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:31,580] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6543e4a8-3323-4294-ab6e-2435e4ed4341/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:31,594] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:31,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:31,595] [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 septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	100.0	1135	1135	95	conclusive
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	81.9139	756	1135	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.6728	652	1135	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	80.4999	588	1135	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	80.3982	671	1135	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	80.3837	622	1135	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	80.3675	607	1135	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	80.268	630	1135	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	80.2092	609	1135	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	80.1675	539	1135	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	80.1649	624	1135	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	80.1379	548	1135	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	80.0663	545	1135	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.8723	582	1135	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.7696	609	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:31,596] [INFO] DFAST Taxonomy check result was written to GCF_009832745.1_ASM983274v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:31,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:31,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:31,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6543e4a8-3323-4294-ab6e-2435e4ed4341/dqc_reference/checkm_data
[2024-01-24 14:06:31,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:31,636] [INFO] Task started: CheckM
[2024-01-24 14:06:31,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009832745.1_ASM983274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009832745.1_ASM983274v1_genomic.fna/checkm_input GCF_009832745.1_ASM983274v1_genomic.fna/checkm_result
[2024-01-24 14:07:08,719] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:08,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:08,739] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:08,739] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:08,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009832745.1_ASM983274v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:08,740] [INFO] Task started: Blastn
[2024-01-24 14:07:08,740] [INFO] Running command: blastn -query GCF_009832745.1_ASM983274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6543e4a8-3323-4294-ab6e-2435e4ed4341/dqc_reference/reference_markers_gtdb.fasta -out GCF_009832745.1_ASM983274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:09,721] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:09,726] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:09,726] [INFO] Target genome list was writen to GCF_009832745.1_ASM983274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:09,745] [INFO] Task started: fastANI
[2024-01-24 14:07:09,745] [INFO] Running command: fastANI --query /var/lib/cwl/stge4d03e72-1cb7-4495-b4f5-275bfe58ff88/GCF_009832745.1_ASM983274v1_genomic.fna.gz --refList GCF_009832745.1_ASM983274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009832745.1_ASM983274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:21,222] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:21,246] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:21,247] [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_009832745.1	s__Polaribacter sp009832745	100.0	1135	1135	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_003129485.1	s__Polaribacter sp003129485	81.9169	756	1135	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	81.2625	702	1135	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	81.2196	659	1135	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	81.1542	650	1135	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	80.8705	679	1135	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	80.7004	649	1135	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	80.3841	673	1135	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	80.362	623	1135	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002954685.1	s__Polaribacter porphyrae	80.3475	610	1135	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	80.2717	619	1135	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	80.2139	618	1135	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	80.1626	539	1135	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000687935.1	s__Polaribacter sp000687935	80.0874	605	1135	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	79.8836	539	1135	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 14:07:21,248] [INFO] GTDB search result was written to GCF_009832745.1_ASM983274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:21,249] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:21,254] [INFO] DFAST_QC result json was written to GCF_009832745.1_ASM983274v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:21,255] [INFO] DFAST_QC completed!
[2024-01-24 14:07:21,255] [INFO] Total running time: 0h1m15s