[2024-01-25 20:13:20,973] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:20,975] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:20,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg299b50f4-04a2-430b-833b-af478a9c3988/dqc_reference
[2024-01-25 20:13:22,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:22,096] [INFO] Task started: Prodigal
[2024-01-25 20:13:22,097] [INFO] Running command: gunzip -c /var/lib/cwl/stg50a70008-401b-4db5-9fa8-b8a0a487328b/GCF_001889045.1_ASM188904v1_genomic.fna.gz | prodigal -d GCF_001889045.1_ASM188904v1_genomic.fna/cds.fna -a GCF_001889045.1_ASM188904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:29,549] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:29,549] [INFO] Task started: HMMsearch
[2024-01-25 20:13:29,549] [INFO] Running command: hmmsearch --tblout GCF_001889045.1_ASM188904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg299b50f4-04a2-430b-833b-af478a9c3988/dqc_reference/reference_markers.hmm GCF_001889045.1_ASM188904v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:29,779] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:29,780] [INFO] Found 6/6 markers.
[2024-01-25 20:13:29,805] [INFO] Query marker FASTA was written to GCF_001889045.1_ASM188904v1_genomic.fna/markers.fasta
[2024-01-25 20:13:29,805] [INFO] Task started: Blastn
[2024-01-25 20:13:29,806] [INFO] Running command: blastn -query GCF_001889045.1_ASM188904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg299b50f4-04a2-430b-833b-af478a9c3988/dqc_reference/reference_markers.fasta -out GCF_001889045.1_ASM188904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:30,432] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:30,434] [INFO] Selected 18 target genomes.
[2024-01-25 20:13:30,435] [INFO] Target genome list was writen to GCF_001889045.1_ASM188904v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:30,448] [INFO] Task started: fastANI
[2024-01-25 20:13:30,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg50a70008-401b-4db5-9fa8-b8a0a487328b/GCF_001889045.1_ASM188904v1_genomic.fna.gz --refList GCF_001889045.1_ASM188904v1_genomic.fna/target_genomes.txt --output GCF_001889045.1_ASM188904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:44,190] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:44,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg299b50f4-04a2-430b-833b-af478a9c3988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:44,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg299b50f4-04a2-430b-833b-af478a9c3988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:44,202] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:13:44,203] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:44,203] [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 todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	100.0	1000	1006	95	conclusive
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	91.243	809	1006	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.3889	556	1006	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	80.0602	512	1006	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	80.0143	535	1006	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	79.9401	520	1006	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	79.8758	502	1006	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	79.7877	533	1006	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	79.7735	499	1006	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.5226	499	1006	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	79.5026	514	1006	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	79.4398	495	1006	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	79.2287	478	1006	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	79.2216	477	1006	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	79.146	435	1006	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	78.7588	458	1006	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	78.2697	377	1006	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	78.0622	360	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:44,205] [INFO] DFAST Taxonomy check result was written to GCF_001889045.1_ASM188904v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:44,207] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:44,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:44,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg299b50f4-04a2-430b-833b-af478a9c3988/dqc_reference/checkm_data
[2024-01-25 20:13:44,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:44,239] [INFO] Task started: CheckM
[2024-01-25 20:13:44,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001889045.1_ASM188904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001889045.1_ASM188904v1_genomic.fna/checkm_input GCF_001889045.1_ASM188904v1_genomic.fna/checkm_result
[2024-01-25 20:14:09,734] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:09,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:09,757] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:09,758] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:09,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001889045.1_ASM188904v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:09,759] [INFO] Task started: Blastn
[2024-01-25 20:14:09,759] [INFO] Running command: blastn -query GCF_001889045.1_ASM188904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg299b50f4-04a2-430b-833b-af478a9c3988/dqc_reference/reference_markers_gtdb.fasta -out GCF_001889045.1_ASM188904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:10,693] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:10,696] [INFO] Selected 22 target genomes.
[2024-01-25 20:14:10,696] [INFO] Target genome list was writen to GCF_001889045.1_ASM188904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:10,712] [INFO] Task started: fastANI
[2024-01-25 20:14:10,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg50a70008-401b-4db5-9fa8-b8a0a487328b/GCF_001889045.1_ASM188904v1_genomic.fna.gz --refList GCF_001889045.1_ASM188904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001889045.1_ASM188904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:27,114] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:27,127] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:27,127] [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	100.0	1000	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000766795.1	s__Polaribacter sp000766795	80.5451	550	1006	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	80.4332	556	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	80.142	550	1006	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	80.102	523	1006	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	80.0495	531	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	80.0459	513	1006	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	79.9978	525	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_001761365.1	s__Polaribacter vadi	79.9665	504	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002814075.1	s__Polaribacter sejongensis	79.798	532	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCA_905480405.1	s__Polaribacter sp905480405	79.7686	486	1006	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	79.6485	516	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_007827455.1	s__VISM01 sp007827455	79.5703	475	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693415.1	s__Tenacibaculum soleae	79.5103	439	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954665.1	s__Polaribacter glomeratus	79.2381	476	1006	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	79.1711	435	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836595.1	s__Tenacibaculum sp002836595	79.1117	468	1006	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	78.9706	376	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	78.7861	455	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCA_004762155.1	s__Tenacibaculum sp004762155	78.7014	469	1006	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	78.2594	378	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCF_003387615.1	s__Tenacibaculum gallaicum	78.0398	363	1006	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:27,128] [INFO] GTDB search result was written to GCF_001889045.1_ASM188904v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:27,130] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:27,134] [INFO] DFAST_QC result json was written to GCF_001889045.1_ASM188904v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:27,134] [INFO] DFAST_QC completed!
[2024-01-25 20:14:27,134] [INFO] Total running time: 0h1m6s