[2024-01-25 18:28:35,792] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:35,799] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:35,799] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c54fca1-1125-439c-9ab9-c37d1183d6ad/dqc_reference
[2024-01-25 18:28:36,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:36,951] [INFO] Task started: Prodigal
[2024-01-25 18:28:36,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg64af79ea-1956-4534-88c9-a2047b1a67bf/GCF_014062345.1_ASM1406234v1_genomic.fna.gz | prodigal -d GCF_014062345.1_ASM1406234v1_genomic.fna/cds.fna -a GCF_014062345.1_ASM1406234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:28:42,937] [INFO] Task succeeded: Prodigal
[2024-01-25 18:28:42,937] [INFO] Task started: HMMsearch
[2024-01-25 18:28:42,937] [INFO] Running command: hmmsearch --tblout GCF_014062345.1_ASM1406234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c54fca1-1125-439c-9ab9-c37d1183d6ad/dqc_reference/reference_markers.hmm GCF_014062345.1_ASM1406234v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:28:43,124] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:28:43,125] [INFO] Found 6/6 markers.
[2024-01-25 18:28:43,149] [INFO] Query marker FASTA was written to GCF_014062345.1_ASM1406234v1_genomic.fna/markers.fasta
[2024-01-25 18:28:43,149] [INFO] Task started: Blastn
[2024-01-25 18:28:43,149] [INFO] Running command: blastn -query GCF_014062345.1_ASM1406234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c54fca1-1125-439c-9ab9-c37d1183d6ad/dqc_reference/reference_markers.fasta -out GCF_014062345.1_ASM1406234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:28:43,774] [INFO] Task succeeded: Blastn
[2024-01-25 18:28:43,777] [INFO] Selected 15 target genomes.
[2024-01-25 18:28:43,777] [INFO] Target genome list was writen to GCF_014062345.1_ASM1406234v1_genomic.fna/target_genomes.txt
[2024-01-25 18:28:43,787] [INFO] Task started: fastANI
[2024-01-25 18:28:43,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg64af79ea-1956-4534-88c9-a2047b1a67bf/GCF_014062345.1_ASM1406234v1_genomic.fna.gz --refList GCF_014062345.1_ASM1406234v1_genomic.fna/target_genomes.txt --output GCF_014062345.1_ASM1406234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:28:53,403] [INFO] Task succeeded: fastANI
[2024-01-25 18:28:53,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c54fca1-1125-439c-9ab9-c37d1183d6ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:28:53,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c54fca1-1125-439c-9ab9-c37d1183d6ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:28:53,413] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:28:53,413] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:28:53,413] [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 pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	100.0	864	866	95	conclusive
Tenacibaculum aiptasiae	strain=a4	GCA_008806755.1	426481	426481	type	True	81.7027	614	866	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	81.3647	585	866	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	80.9587	585	866	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	80.722	536	866	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	80.7211	534	866	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	80.6655	562	866	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	80.6654	575	866	95	below_threshold
Tenacibaculum holothuriorum	strain=S2-2	GCA_002120225.1	1635173	1635173	type	True	80.3666	550	866	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	80.3012	551	866	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO010	GCA_900239495.1	2781243	2781243	type	True	80.0327	457	866	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	79.1406	438	866	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	79.1228	436	866	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.3818	324	866	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.3497	315	866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:28:53,414] [INFO] DFAST Taxonomy check result was written to GCF_014062345.1_ASM1406234v1_genomic.fna/tc_result.tsv
[2024-01-25 18:28:53,415] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:28:53,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:28:53,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c54fca1-1125-439c-9ab9-c37d1183d6ad/dqc_reference/checkm_data
[2024-01-25 18:28:53,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:28:53,444] [INFO] Task started: CheckM
[2024-01-25 18:28:53,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014062345.1_ASM1406234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014062345.1_ASM1406234v1_genomic.fna/checkm_input GCF_014062345.1_ASM1406234v1_genomic.fna/checkm_result
[2024-01-25 18:29:15,419] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:15,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:15,434] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:15,434] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:15,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014062345.1_ASM1406234v1_genomic.fna/markers.fasta)
[2024-01-25 18:29:15,435] [INFO] Task started: Blastn
[2024-01-25 18:29:15,435] [INFO] Running command: blastn -query GCF_014062345.1_ASM1406234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c54fca1-1125-439c-9ab9-c37d1183d6ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_014062345.1_ASM1406234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:16,360] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:16,363] [INFO] Selected 10 target genomes.
[2024-01-25 18:29:16,363] [INFO] Target genome list was writen to GCF_014062345.1_ASM1406234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:16,395] [INFO] Task started: fastANI
[2024-01-25 18:29:16,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg64af79ea-1956-4534-88c9-a2047b1a67bf/GCF_014062345.1_ASM1406234v1_genomic.fna.gz --refList GCF_014062345.1_ASM1406234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014062345.1_ASM1406234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:29:23,899] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:23,906] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:29:23,907] [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_014062345.1	s__Tenacibaculum pelagium	100.0	864	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008806755.1	s__Tenacibaculum aiptasiae	81.7225	612	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693415.1	s__Tenacibaculum soleae	81.2452	564	866	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	80.9669	603	866	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	80.9667	585	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.63	97.63	0.88	0.88	2	-
GCF_003387615.1	s__Tenacibaculum gallaicum	80.7285	533	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664185.1	s__Tenacibaculum discolor	80.6875	560	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_002120225.1	s__Tenacibaculum holothuriorum	80.3675	551	866	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	79.9158	408	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.64	99.33	0.97	0.95	5	-
GCF_900105985.1	s__Tenacibaculum sp900105985	79.4999	521	866	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 18:29:23,909] [INFO] GTDB search result was written to GCF_014062345.1_ASM1406234v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:29:23,910] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:29:23,913] [INFO] DFAST_QC result json was written to GCF_014062345.1_ASM1406234v1_genomic.fna/dqc_result.json
[2024-01-25 18:29:23,913] [INFO] DFAST_QC completed!
[2024-01-25 18:29:23,913] [INFO] Total running time: 0h0m48s