[2024-01-24 11:51:37,089] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,091] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg63041bef-36cf-48b6-a924-583b71a3db08/dqc_reference
[2024-01-24 11:51:38,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,383] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,383] [INFO] Running command: gunzip -c /var/lib/cwl/stgf40c6230-2c00-4a2c-9624-954c7d64124a/GCF_019351435.1_ASM1935143v1_genomic.fna.gz | prodigal -d GCF_019351435.1_ASM1935143v1_genomic.fna/cds.fna -a GCF_019351435.1_ASM1935143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:56,713] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:56,713] [INFO] Task started: HMMsearch
[2024-01-24 11:51:56,713] [INFO] Running command: hmmsearch --tblout GCF_019351435.1_ASM1935143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63041bef-36cf-48b6-a924-583b71a3db08/dqc_reference/reference_markers.hmm GCF_019351435.1_ASM1935143v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:56,984] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:56,986] [INFO] Found 6/6 markers.
[2024-01-24 11:51:57,045] [INFO] Query marker FASTA was written to GCF_019351435.1_ASM1935143v1_genomic.fna/markers.fasta
[2024-01-24 11:51:57,046] [INFO] Task started: Blastn
[2024-01-24 11:51:57,046] [INFO] Running command: blastn -query GCF_019351435.1_ASM1935143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63041bef-36cf-48b6-a924-583b71a3db08/dqc_reference/reference_markers.fasta -out GCF_019351435.1_ASM1935143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:57,737] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:57,743] [INFO] Selected 17 target genomes.
[2024-01-24 11:51:57,744] [INFO] Target genome list was writen to GCF_019351435.1_ASM1935143v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:57,752] [INFO] Task started: fastANI
[2024-01-24 11:51:57,752] [INFO] Running command: fastANI --query /var/lib/cwl/stgf40c6230-2c00-4a2c-9624-954c7d64124a/GCF_019351435.1_ASM1935143v1_genomic.fna.gz --refList GCF_019351435.1_ASM1935143v1_genomic.fna/target_genomes.txt --output GCF_019351435.1_ASM1935143v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:13,518] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:13,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63041bef-36cf-48b6-a924-583b71a3db08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:13,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63041bef-36cf-48b6-a924-583b71a3db08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:13,534] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:13,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:13,535] [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 taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	100.0	1535	1538	95	conclusive
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	86.5198	1092	1538	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	82.9532	843	1538	95	below_threshold
Flavobacterium aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	81.4975	839	1538	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_000735535.1	1492737	1492737	type	True	81.4654	704	1538	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_001761465.1	1492737	1492737	type	True	81.4327	752	1538	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	79.3144	459	1538	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	79.2608	473	1538	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.2081	533	1538	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	79.1811	493	1538	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.05	487	1538	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.5225	360	1538	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	78.4067	454	1538	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	78.4028	457	1538	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.3615	390	1538	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.2896	424	1538	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.26	372	1538	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:13,537] [INFO] DFAST Taxonomy check result was written to GCF_019351435.1_ASM1935143v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:13,537] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:13,537] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:13,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63041bef-36cf-48b6-a924-583b71a3db08/dqc_reference/checkm_data
[2024-01-24 11:52:13,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:13,592] [INFO] Task started: CheckM
[2024-01-24 11:52:13,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019351435.1_ASM1935143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019351435.1_ASM1935143v1_genomic.fna/checkm_input GCF_019351435.1_ASM1935143v1_genomic.fna/checkm_result
[2024-01-24 11:53:07,148] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:07,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:07,170] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:07,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:07,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019351435.1_ASM1935143v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:07,171] [INFO] Task started: Blastn
[2024-01-24 11:53:07,171] [INFO] Running command: blastn -query GCF_019351435.1_ASM1935143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63041bef-36cf-48b6-a924-583b71a3db08/dqc_reference/reference_markers_gtdb.fasta -out GCF_019351435.1_ASM1935143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:08,111] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:08,115] [INFO] Selected 15 target genomes.
[2024-01-24 11:53:08,115] [INFO] Target genome list was writen to GCF_019351435.1_ASM1935143v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:08,141] [INFO] Task started: fastANI
[2024-01-24 11:53:08,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgf40c6230-2c00-4a2c-9624-954c7d64124a/GCF_019351435.1_ASM1935143v1_genomic.fna.gz --refList GCF_019351435.1_ASM1935143v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019351435.1_ASM1935143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:21,497] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:21,512] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:53:21,513] [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_003254745.1	s__Flavobacterium aquariorum	86.5084	1093	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284035.1	s__Flavobacterium sp003096795	86.3926	1055	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCF_002001005.1	s__Flavobacterium sp002001005	84.9975	944	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797935.1	s__Flavobacterium sp002797935	82.9958	894	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097655.1	s__Flavobacterium laiguense	82.9417	844	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097385.1	s__Flavobacterium sp007097385	82.7748	859	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813295.1	s__Flavobacterium sp002813295	82.0033	895	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385115.1	s__Flavobacterium aquicola	81.4918	837	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761465.1	s__Flavobacterium gilvum	81.4381	752	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015351475.1	s__Flavobacterium sp015351475	81.2446	799	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634755.1	s__Flavobacterium limicola	79.3006	460	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110375.1	s__Flavobacterium sinopsychrotolerans	79.2402	476	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995345.1	s__Flavobacterium sp017995345	79.2119	368	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.61	99.55	0.85	0.83	4	-
GCF_900108015.1	s__Flavobacterium urumqiense	79.0468	485	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097245.1	s__Flavobacterium sp007097245	79.0223	484	1538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:21,514] [INFO] GTDB search result was written to GCF_019351435.1_ASM1935143v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:21,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:21,519] [INFO] DFAST_QC result json was written to GCF_019351435.1_ASM1935143v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:21,519] [INFO] DFAST_QC completed!
[2024-01-24 11:53:21,520] [INFO] Total running time: 0h1m44s