[2024-01-24 12:21:57,478] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b694606-0d34-4897-a62d-cca809741e86/dqc_reference
[2024-01-24 12:21:58,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,881] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg56a54004-c517-441f-bd31-3da879366781/GCF_022478115.1_ASM2247811v1_genomic.fna.gz | prodigal -d GCF_022478115.1_ASM2247811v1_genomic.fna/cds.fna -a GCF_022478115.1_ASM2247811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:07,144] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:07,144] [INFO] Task started: HMMsearch
[2024-01-24 12:22:07,144] [INFO] Running command: hmmsearch --tblout GCF_022478115.1_ASM2247811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b694606-0d34-4897-a62d-cca809741e86/dqc_reference/reference_markers.hmm GCF_022478115.1_ASM2247811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:07,401] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:07,402] [INFO] Found 6/6 markers.
[2024-01-24 12:22:07,428] [INFO] Query marker FASTA was written to GCF_022478115.1_ASM2247811v1_genomic.fna/markers.fasta
[2024-01-24 12:22:07,429] [INFO] Task started: Blastn
[2024-01-24 12:22:07,429] [INFO] Running command: blastn -query GCF_022478115.1_ASM2247811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b694606-0d34-4897-a62d-cca809741e86/dqc_reference/reference_markers.fasta -out GCF_022478115.1_ASM2247811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:08,069] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:08,072] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:08,073] [INFO] Target genome list was writen to GCF_022478115.1_ASM2247811v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:08,081] [INFO] Task started: fastANI
[2024-01-24 12:22:08,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg56a54004-c517-441f-bd31-3da879366781/GCF_022478115.1_ASM2247811v1_genomic.fna.gz --refList GCF_022478115.1_ASM2247811v1_genomic.fna/target_genomes.txt --output GCF_022478115.1_ASM2247811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:21,542] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:21,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b694606-0d34-4897-a62d-cca809741e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:21,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b694606-0d34-4897-a62d-cca809741e86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:21,558] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:21,559] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:21,559] [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
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	100.0	937	937	95	conclusive
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	91.3731	799	937	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.2112	568	937	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	80.1373	504	937	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	80.0383	521	937	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	79.9416	546	937	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	79.8614	541	937	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	79.7904	468	937	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	79.7739	495	937	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	79.7163	507	937	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	79.6841	520	937	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	79.6243	480	937	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.5598	493	937	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	79.3538	484	937	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	79.31	484	937	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	79.1877	436	937	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	79.1208	441	937	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	78.2703	364	937	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	78.1713	350	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:21,570] [INFO] DFAST Taxonomy check result was written to GCF_022478115.1_ASM2247811v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:21,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:21,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:21,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b694606-0d34-4897-a62d-cca809741e86/dqc_reference/checkm_data
[2024-01-24 12:22:21,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:21,606] [INFO] Task started: CheckM
[2024-01-24 12:22:21,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022478115.1_ASM2247811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022478115.1_ASM2247811v1_genomic.fna/checkm_input GCF_022478115.1_ASM2247811v1_genomic.fna/checkm_result
[2024-01-24 12:22:49,391] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:49,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:49,420] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:49,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:49,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022478115.1_ASM2247811v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:49,421] [INFO] Task started: Blastn
[2024-01-24 12:22:49,421] [INFO] Running command: blastn -query GCF_022478115.1_ASM2247811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b694606-0d34-4897-a62d-cca809741e86/dqc_reference/reference_markers_gtdb.fasta -out GCF_022478115.1_ASM2247811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:50,398] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:50,401] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:50,401] [INFO] Target genome list was writen to GCF_022478115.1_ASM2247811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:50,414] [INFO] Task started: fastANI
[2024-01-24 12:22:50,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg56a54004-c517-441f-bd31-3da879366781/GCF_022478115.1_ASM2247811v1_genomic.fna.gz --refList GCF_022478115.1_ASM2247811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022478115.1_ASM2247811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:03,663] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:03,683] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:03,683] [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_001889045.1	s__Tenacibaculum_A todarodis	91.3731	799	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	80.6527	563	937	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	80.224	566	937	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	80.199	509	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	80.0931	483	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	80.0577	523	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002954605.1	s__Polaribacter butkevichii	80.0033	524	937	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	79.9414	546	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009796785.1	s__Polaribacter sp009796785	79.8638	538	937	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	79.7667	455	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	79.7003	509	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001693415.1	s__Tenacibaculum soleae	79.559	439	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687935.1	s__Polaribacter sp000687935	79.3969	495	937	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	79.3428	481	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014062345.1	s__Tenacibaculum pelagium	79.1039	442	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	79.0804	366	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	78.9935	356	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCA_004762155.1	s__Tenacibaculum sp004762155	78.8206	455	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610735.1	s__Tenacibaculum lutimaris	78.2703	364	937	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:03,685] [INFO] GTDB search result was written to GCF_022478115.1_ASM2247811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:03,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:03,691] [INFO] DFAST_QC result json was written to GCF_022478115.1_ASM2247811v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:03,692] [INFO] DFAST_QC completed!
[2024-01-24 12:23:03,692] [INFO] Total running time: 0h1m6s