[2023-06-30 14:48:24,799] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:48:24,801] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:48:24,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c144556-bc71-42a4-b270-2939aa009775/dqc_reference
[2023-06-30 14:48:26,001] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:48:26,002] [INFO] Task started: Prodigal
[2023-06-30 14:48:26,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg19316a09-63a4-42a8-adcf-a33033ad72ef/GCA_016708845.1_ASM1670884v1_genomic.fna.gz | prodigal -d GCA_016708845.1_ASM1670884v1_genomic.fna/cds.fna -a GCA_016708845.1_ASM1670884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:48:38,129] [INFO] Task succeeded: Prodigal
[2023-06-30 14:48:38,129] [INFO] Task started: HMMsearch
[2023-06-30 14:48:38,129] [INFO] Running command: hmmsearch --tblout GCA_016708845.1_ASM1670884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c144556-bc71-42a4-b270-2939aa009775/dqc_reference/reference_markers.hmm GCA_016708845.1_ASM1670884v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:48:38,397] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:48:38,398] [INFO] Found 6/6 markers.
[2023-06-30 14:48:38,438] [INFO] Query marker FASTA was written to GCA_016708845.1_ASM1670884v1_genomic.fna/markers.fasta
[2023-06-30 14:48:38,439] [INFO] Task started: Blastn
[2023-06-30 14:48:38,439] [INFO] Running command: blastn -query GCA_016708845.1_ASM1670884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c144556-bc71-42a4-b270-2939aa009775/dqc_reference/reference_markers.fasta -out GCA_016708845.1_ASM1670884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:48:39,058] [INFO] Task succeeded: Blastn
[2023-06-30 14:48:39,063] [INFO] Selected 40 target genomes.
[2023-06-30 14:48:39,063] [INFO] Target genome list was writen to GCA_016708845.1_ASM1670884v1_genomic.fna/target_genomes.txt
[2023-06-30 14:48:39,066] [INFO] Task started: fastANI
[2023-06-30 14:48:39,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg19316a09-63a4-42a8-adcf-a33033ad72ef/GCA_016708845.1_ASM1670884v1_genomic.fna.gz --refList GCA_016708845.1_ASM1670884v1_genomic.fna/target_genomes.txt --output GCA_016708845.1_ASM1670884v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:49:01,867] [INFO] Task succeeded: fastANI
[2023-06-30 14:49:01,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c144556-bc71-42a4-b270-2939aa009775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:49:01,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c144556-bc71-42a4-b270-2939aa009775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:49:01,895] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:49:01,895] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:49:01,895] [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
Flavobacterium urocaniciphilum	strain=DSM 27078	GCA_900110615.1	1299341	1299341	type	True	76.4252	51	1271	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	76.1539	50	1271	95	below_threshold
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	75.9423	53	1271	95	below_threshold
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	75.8857	54	1271	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.8838	53	1271	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	75.8769	53	1271	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	75.7988	55	1271	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	75.68	54	1271	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	75.6778	54	1271	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	75.6179	55	1271	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	75.6099	50	1271	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	75.5538	57	1271	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	75.5436	53	1271	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	75.5131	52	1271	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	75.4911	52	1271	95	below_threshold
Tenacibaculum finnmarkense	strain=TNO006	GCA_900239185.1	2781243	2781243	type	True	75.4306	51	1271	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:49:01,898] [INFO] DFAST Taxonomy check result was written to GCA_016708845.1_ASM1670884v1_genomic.fna/tc_result.tsv
[2023-06-30 14:49:01,898] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:49:01,898] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:49:01,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c144556-bc71-42a4-b270-2939aa009775/dqc_reference/checkm_data
[2023-06-30 14:49:01,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:49:01,945] [INFO] Task started: CheckM
[2023-06-30 14:49:01,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708845.1_ASM1670884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708845.1_ASM1670884v1_genomic.fna/checkm_input GCA_016708845.1_ASM1670884v1_genomic.fna/checkm_result
[2023-06-30 14:49:40,606] [INFO] Task succeeded: CheckM
[2023-06-30 14:49:40,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 14:49:40,632] [INFO] ===== Completeness check finished =====
[2023-06-30 14:49:40,632] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:49:40,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708845.1_ASM1670884v1_genomic.fna/markers.fasta)
[2023-06-30 14:49:40,633] [INFO] Task started: Blastn
[2023-06-30 14:49:40,634] [INFO] Running command: blastn -query GCA_016708845.1_ASM1670884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c144556-bc71-42a4-b270-2939aa009775/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708845.1_ASM1670884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:49:41,426] [INFO] Task succeeded: Blastn
[2023-06-30 14:49:41,431] [INFO] Selected 9 target genomes.
[2023-06-30 14:49:41,432] [INFO] Target genome list was writen to GCA_016708845.1_ASM1670884v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:49:41,434] [INFO] Task started: fastANI
[2023-06-30 14:49:41,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg19316a09-63a4-42a8-adcf-a33033ad72ef/GCA_016708845.1_ASM1670884v1_genomic.fna.gz --refList GCA_016708845.1_ASM1670884v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708845.1_ASM1670884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:49:48,658] [INFO] Task succeeded: fastANI
[2023-06-30 14:49:48,669] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:49:48,669] [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
GCA_016708845.1	s__UBA4416 sp016708845	100.0	1266	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016711805.1	s__UBA4416 sp016711805	94.2898	1066	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005800865.1	s__UBA4416 sp005800865	93.9029	558	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893815.1	s__UBA4416 sp903893815	92.0387	875	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	97.38	96.70	0.85	0.80	6	-
GCA_002420145.1	s__UBA4416 sp002420145	82.5381	740	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823565.1	s__UBA4416 sp013823565	82.2459	778	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787365.1	s__UBA4416 sp016787365	82.022	484	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928655.1	s__UBA4416 sp903928655	78.5437	336	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:49:48,672] [INFO] GTDB search result was written to GCA_016708845.1_ASM1670884v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:49:48,672] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:49:48,676] [INFO] DFAST_QC result json was written to GCA_016708845.1_ASM1670884v1_genomic.fna/dqc_result.json
[2023-06-30 14:49:48,676] [INFO] DFAST_QC completed!
[2023-06-30 14:49:48,676] [INFO] Total running time: 0h1m24s