[2024-01-25 19:43:20,473] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:20,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:20,475] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1b65bf3-c69c-4d09-8713-c4bb4be45e0a/dqc_reference
[2024-01-25 19:43:21,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:21,685] [INFO] Task started: Prodigal
[2024-01-25 19:43:21,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg81f441ea-596d-4b8c-bb65-2d1b0b196f24/GCF_025215075.1_ASM2521507v1_genomic.fna.gz | prodigal -d GCF_025215075.1_ASM2521507v1_genomic.fna/cds.fna -a GCF_025215075.1_ASM2521507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:28,576] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:28,576] [INFO] Task started: HMMsearch
[2024-01-25 19:43:28,576] [INFO] Running command: hmmsearch --tblout GCF_025215075.1_ASM2521507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1b65bf3-c69c-4d09-8713-c4bb4be45e0a/dqc_reference/reference_markers.hmm GCF_025215075.1_ASM2521507v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:28,784] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:28,785] [INFO] Found 6/6 markers.
[2024-01-25 19:43:28,810] [INFO] Query marker FASTA was written to GCF_025215075.1_ASM2521507v1_genomic.fna/markers.fasta
[2024-01-25 19:43:28,810] [INFO] Task started: Blastn
[2024-01-25 19:43:28,810] [INFO] Running command: blastn -query GCF_025215075.1_ASM2521507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b65bf3-c69c-4d09-8713-c4bb4be45e0a/dqc_reference/reference_markers.fasta -out GCF_025215075.1_ASM2521507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:29,445] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:29,448] [INFO] Selected 14 target genomes.
[2024-01-25 19:43:29,448] [INFO] Target genome list was writen to GCF_025215075.1_ASM2521507v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:29,458] [INFO] Task started: fastANI
[2024-01-25 19:43:29,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg81f441ea-596d-4b8c-bb65-2d1b0b196f24/GCF_025215075.1_ASM2521507v1_genomic.fna.gz --refList GCF_025215075.1_ASM2521507v1_genomic.fna/target_genomes.txt --output GCF_025215075.1_ASM2521507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:39,158] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:39,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1b65bf3-c69c-4d09-8713-c4bb4be45e0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:39,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1b65bf3-c69c-4d09-8713-c4bb4be45e0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:39,172] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:43:39,172] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:39,173] [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 haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	100.0	977	977	95	conclusive
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	83.508	701	977	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	81.639	567	977	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	81.3958	580	977	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	81.297	584	977	95	below_threshold
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	80.2795	584	977	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	79.8303	454	977	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	79.7591	530	977	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	79.654	529	977	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	79.6431	545	977	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	79.5347	472	977	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.8624	417	977	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	78.7014	403	977	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.1703	368	977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:39,176] [INFO] DFAST Taxonomy check result was written to GCF_025215075.1_ASM2521507v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:39,177] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:39,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:39,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1b65bf3-c69c-4d09-8713-c4bb4be45e0a/dqc_reference/checkm_data
[2024-01-25 19:43:39,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:39,208] [INFO] Task started: CheckM
[2024-01-25 19:43:39,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025215075.1_ASM2521507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025215075.1_ASM2521507v1_genomic.fna/checkm_input GCF_025215075.1_ASM2521507v1_genomic.fna/checkm_result
[2024-01-25 19:44:03,056] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:03,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:03,079] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:03,079] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:03,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025215075.1_ASM2521507v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:03,080] [INFO] Task started: Blastn
[2024-01-25 19:44:03,080] [INFO] Running command: blastn -query GCF_025215075.1_ASM2521507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b65bf3-c69c-4d09-8713-c4bb4be45e0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_025215075.1_ASM2521507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:04,051] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:04,054] [INFO] Selected 11 target genomes.
[2024-01-25 19:44:04,054] [INFO] Target genome list was writen to GCF_025215075.1_ASM2521507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:04,065] [INFO] Task started: fastANI
[2024-01-25 19:44:04,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg81f441ea-596d-4b8c-bb65-2d1b0b196f24/GCF_025215075.1_ASM2521507v1_genomic.fna.gz --refList GCF_025215075.1_ASM2521507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025215075.1_ASM2521507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:12,045] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:12,053] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:44:12,053] [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_001693415.1	s__Tenacibaculum soleae	86.421	768	977	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	83.5176	699	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_002836595.1	s__Tenacibaculum sp002836595	83.1872	710	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239345.1	s__Tenacibaculum dicentrarchi	81.8391	574	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.61	97.94	0.93	0.91	10	-
GCF_900239185.1	s__Tenacibaculum finnmarkense_A	81.6488	566	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	96.8963	99.00	98.36	0.95	0.91	6	-
GCF_900239495.1	s__Tenacibaculum finnmarkense	81.3769	581	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	96.8963	98.86	98.40	0.93	0.91	7	-
GCF_014062345.1	s__Tenacibaculum pelagium	81.3177	583	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900239505.1	s__Tenacibaculum piscium	81.2964	525	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.64	99.33	0.97	0.95	5	-
GCF_008806755.1	s__Tenacibaculum aiptasiae	80.2893	583	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003867015.1	s__Tenacibaculum singaporense	79.6417	544	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_900105985.1	s__Tenacibaculum sp900105985	79.1573	502	977	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:12,054] [INFO] GTDB search result was written to GCF_025215075.1_ASM2521507v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:12,055] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:12,058] [INFO] DFAST_QC result json was written to GCF_025215075.1_ASM2521507v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:12,058] [INFO] DFAST_QC completed!
[2024-01-25 19:44:12,058] [INFO] Total running time: 0h0m52s