[2024-01-24 12:43:54,221] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:43:54,223] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:43:54,223] [INFO] DQC Reference Directory: /var/lib/cwl/stgea786222-1926-44ee-be58-3c573038f49f/dqc_reference
[2024-01-24 12:43:59,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:43:59,336] [INFO] Task started: Prodigal
[2024-01-24 12:43:59,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg930466c6-1614-4df4-a72c-165cf871721b/GCF_027941775.1_ASM2794177v1_genomic.fna.gz | prodigal -d GCF_027941775.1_ASM2794177v1_genomic.fna/cds.fna -a GCF_027941775.1_ASM2794177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:06,240] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:06,241] [INFO] Task started: HMMsearch
[2024-01-24 12:44:06,241] [INFO] Running command: hmmsearch --tblout GCF_027941775.1_ASM2794177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea786222-1926-44ee-be58-3c573038f49f/dqc_reference/reference_markers.hmm GCF_027941775.1_ASM2794177v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:06,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:06,612] [INFO] Found 6/6 markers.
[2024-01-24 12:44:06,638] [INFO] Query marker FASTA was written to GCF_027941775.1_ASM2794177v1_genomic.fna/markers.fasta
[2024-01-24 12:44:06,639] [INFO] Task started: Blastn
[2024-01-24 12:44:06,639] [INFO] Running command: blastn -query GCF_027941775.1_ASM2794177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea786222-1926-44ee-be58-3c573038f49f/dqc_reference/reference_markers.fasta -out GCF_027941775.1_ASM2794177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:09,030] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:09,035] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:09,036] [INFO] Target genome list was writen to GCF_027941775.1_ASM2794177v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:09,042] [INFO] Task started: fastANI
[2024-01-24 12:44:09,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg930466c6-1614-4df4-a72c-165cf871721b/GCF_027941775.1_ASM2794177v1_genomic.fna.gz --refList GCF_027941775.1_ASM2794177v1_genomic.fna/target_genomes.txt --output GCF_027941775.1_ASM2794177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:17,577] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:17,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea786222-1926-44ee-be58-3c573038f49f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:17,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea786222-1926-44ee-be58-3c573038f49f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:17,600] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:44:17,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:44:17,600] [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 finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	87.334	688	930	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	87.0638	706	930	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	82.9485	605	930	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	82.2364	664	930	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	80.9571	526	930	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	79.9757	534	930	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	79.4985	470	930	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	79.2856	462	930	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	79.0623	420	930	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.908	430	930	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.2789	309	930	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.2451	330	930	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:17,603] [INFO] DFAST Taxonomy check result was written to GCF_027941775.1_ASM2794177v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:17,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:17,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:17,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea786222-1926-44ee-be58-3c573038f49f/dqc_reference/checkm_data
[2024-01-24 12:44:17,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:17,638] [INFO] Task started: CheckM
[2024-01-24 12:44:17,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027941775.1_ASM2794177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027941775.1_ASM2794177v1_genomic.fna/checkm_input GCF_027941775.1_ASM2794177v1_genomic.fna/checkm_result
[2024-01-24 12:44:45,434] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:45,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:45,459] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:45,459] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:45,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027941775.1_ASM2794177v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:45,460] [INFO] Task started: Blastn
[2024-01-24 12:44:45,460] [INFO] Running command: blastn -query GCF_027941775.1_ASM2794177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea786222-1926-44ee-be58-3c573038f49f/dqc_reference/reference_markers_gtdb.fasta -out GCF_027941775.1_ASM2794177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:46,401] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:46,404] [INFO] Selected 6 target genomes.
[2024-01-24 12:44:46,404] [INFO] Target genome list was writen to GCF_027941775.1_ASM2794177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:46,415] [INFO] Task started: fastANI
[2024-01-24 12:44:46,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg930466c6-1614-4df4-a72c-165cf871721b/GCF_027941775.1_ASM2794177v1_genomic.fna.gz --refList GCF_027941775.1_ASM2794177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027941775.1_ASM2794177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:44:51,408] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:51,415] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:44:51,415] [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_900239345.1	s__Tenacibaculum dicentrarchi	87.8543	694	930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_900239495.1	s__Tenacibaculum finnmarkense	87.3491	687	930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	96.8963	98.86	98.40	0.93	0.91	7	-
GCF_900239185.1	s__Tenacibaculum finnmarkense_A	87.1135	703	930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	96.8963	99.00	98.36	0.95	0.91	6	-
GCF_900239505.1	s__Tenacibaculum piscium	85.7219	623	930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.64	99.33	0.97	0.95	5	-
GCF_002836595.1	s__Tenacibaculum sp002836595	82.5032	669	930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430545.1	s__Tenacibaculum ovolyticum	82.2217	665	930	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:44:51,418] [INFO] GTDB search result was written to GCF_027941775.1_ASM2794177v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:44:51,418] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:44:51,422] [INFO] DFAST_QC result json was written to GCF_027941775.1_ASM2794177v1_genomic.fna/dqc_result.json
[2024-01-24 12:44:51,423] [INFO] DFAST_QC completed!
[2024-01-24 12:44:51,423] [INFO] Total running time: 0h0m57s