[2024-01-25 20:12:20,480] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:20,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:20,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f6701b7-323a-4ada-bb13-bd4007877ba0/dqc_reference
[2024-01-25 20:12:21,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:21,575] [INFO] Task started: Prodigal
[2024-01-25 20:12:21,576] [INFO] Running command: gunzip -c /var/lib/cwl/stg728f060f-36f8-473a-8c9d-9b495715b357/GCF_028829235.1_ASM2882923v1_genomic.fna.gz | prodigal -d GCF_028829235.1_ASM2882923v1_genomic.fna/cds.fna -a GCF_028829235.1_ASM2882923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:30,377] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:30,377] [INFO] Task started: HMMsearch
[2024-01-25 20:12:30,377] [INFO] Running command: hmmsearch --tblout GCF_028829235.1_ASM2882923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f6701b7-323a-4ada-bb13-bd4007877ba0/dqc_reference/reference_markers.hmm GCF_028829235.1_ASM2882923v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:30,601] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:30,602] [INFO] Found 6/6 markers.
[2024-01-25 20:12:30,632] [INFO] Query marker FASTA was written to GCF_028829235.1_ASM2882923v1_genomic.fna/markers.fasta
[2024-01-25 20:12:30,632] [INFO] Task started: Blastn
[2024-01-25 20:12:30,632] [INFO] Running command: blastn -query GCF_028829235.1_ASM2882923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f6701b7-323a-4ada-bb13-bd4007877ba0/dqc_reference/reference_markers.fasta -out GCF_028829235.1_ASM2882923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:31,246] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:31,249] [INFO] Selected 12 target genomes.
[2024-01-25 20:12:31,250] [INFO] Target genome list was writen to GCF_028829235.1_ASM2882923v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:31,272] [INFO] Task started: fastANI
[2024-01-25 20:12:31,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg728f060f-36f8-473a-8c9d-9b495715b357/GCF_028829235.1_ASM2882923v1_genomic.fna.gz --refList GCF_028829235.1_ASM2882923v1_genomic.fna/target_genomes.txt --output GCF_028829235.1_ASM2882923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:40,272] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:40,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f6701b7-323a-4ada-bb13-bd4007877ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:40,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f6701b7-323a-4ada-bb13-bd4007877ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:40,281] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:12:40,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:12:40,282] [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 discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	94.7732	975	1199	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	90.2976	961	1199	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	89.1385	880	1199	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	89.0716	889	1199	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	89.0441	895	1199	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	88.775	947	1199	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	88.1397	791	1199	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.3298	380	1199	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.8048	258	1199	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.7626	336	1199	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.7347	281	1199	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	77.2238	273	1199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:40,287] [INFO] DFAST Taxonomy check result was written to GCF_028829235.1_ASM2882923v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:40,288] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:40,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:40,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f6701b7-323a-4ada-bb13-bd4007877ba0/dqc_reference/checkm_data
[2024-01-25 20:12:40,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:40,337] [INFO] Task started: CheckM
[2024-01-25 20:12:40,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028829235.1_ASM2882923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028829235.1_ASM2882923v1_genomic.fna/checkm_input GCF_028829235.1_ASM2882923v1_genomic.fna/checkm_result
[2024-01-25 20:13:09,305] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:09,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:09,324] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:09,324] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:09,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028829235.1_ASM2882923v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:09,325] [INFO] Task started: Blastn
[2024-01-25 20:13:09,325] [INFO] Running command: blastn -query GCF_028829235.1_ASM2882923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f6701b7-323a-4ada-bb13-bd4007877ba0/dqc_reference/reference_markers_gtdb.fasta -out GCF_028829235.1_ASM2882923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:10,230] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:10,234] [INFO] Selected 6 target genomes.
[2024-01-25 20:13:10,234] [INFO] Target genome list was writen to GCF_028829235.1_ASM2882923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:10,245] [INFO] Task started: fastANI
[2024-01-25 20:13:10,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg728f060f-36f8-473a-8c9d-9b495715b357/GCF_028829235.1_ASM2882923v1_genomic.fna.gz --refList GCF_028829235.1_ASM2882923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028829235.1_ASM2882923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:15,364] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:15,369] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:13:15,370] [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_003664185.1	s__Tenacibaculum discolor	94.7732	975	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_003867015.1	s__Tenacibaculum singaporense	90.2976	961	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_003867075.1	s__Tenacibaculum mesophilum	89.1385	880	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCF_003387615.1	s__Tenacibaculum gallaicum	88.7825	946	1199	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	88.1397	791	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	84.303	819	1199	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 20:13:15,371] [INFO] GTDB search result was written to GCF_028829235.1_ASM2882923v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:15,371] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:15,374] [INFO] DFAST_QC result json was written to GCF_028829235.1_ASM2882923v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:15,374] [INFO] DFAST_QC completed!
[2024-01-25 20:13:15,374] [INFO] Total running time: 0h0m55s