[2024-01-25 17:38:35,464] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:35,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:35,465] [INFO] DQC Reference Directory: /var/lib/cwl/stg45d00176-03e4-4766-961d-7bbfcc46dbdf/dqc_reference
[2024-01-25 17:38:36,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:36,584] [INFO] Task started: Prodigal
[2024-01-25 17:38:36,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg8533e646-57f6-4835-b31f-27615498e951/GCF_027111335.1_ASM2711133v2_genomic.fna.gz | prodigal -d GCF_027111335.1_ASM2711133v2_genomic.fna/cds.fna -a GCF_027111335.1_ASM2711133v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:53,953] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:53,953] [INFO] Task started: HMMsearch
[2024-01-25 17:38:53,953] [INFO] Running command: hmmsearch --tblout GCF_027111335.1_ASM2711133v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45d00176-03e4-4766-961d-7bbfcc46dbdf/dqc_reference/reference_markers.hmm GCF_027111335.1_ASM2711133v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:54,192] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:54,193] [INFO] Found 6/6 markers.
[2024-01-25 17:38:54,230] [INFO] Query marker FASTA was written to GCF_027111335.1_ASM2711133v2_genomic.fna/markers.fasta
[2024-01-25 17:38:54,230] [INFO] Task started: Blastn
[2024-01-25 17:38:54,230] [INFO] Running command: blastn -query GCF_027111335.1_ASM2711133v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d00176-03e4-4766-961d-7bbfcc46dbdf/dqc_reference/reference_markers.fasta -out GCF_027111335.1_ASM2711133v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:54,863] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:54,867] [INFO] Selected 18 target genomes.
[2024-01-25 17:38:54,867] [INFO] Target genome list was writen to GCF_027111335.1_ASM2711133v2_genomic.fna/target_genomes.txt
[2024-01-25 17:38:54,889] [INFO] Task started: fastANI
[2024-01-25 17:38:54,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg8533e646-57f6-4835-b31f-27615498e951/GCF_027111335.1_ASM2711133v2_genomic.fna.gz --refList GCF_027111335.1_ASM2711133v2_genomic.fna/target_genomes.txt --output GCF_027111335.1_ASM2711133v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:11,026] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:11,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45d00176-03e4-4766-961d-7bbfcc46dbdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:11,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45d00176-03e4-4766-961d-7bbfcc46dbdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:11,037] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:39:11,038] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:39:11,038] [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 gilvum	strain=EM1308	GCA_001761465.1	1492737	1492737	type	True	82.8817	969	1684	95	below_threshold
Flavobacterium gilvum	strain=EM1308	GCA_000735535.1	1492737	1492737	type	True	82.8488	921	1684	95	below_threshold
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	82.4592	920	1684	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	81.6648	868	1684	95	below_threshold
Flavobacterium aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	81.1136	809	1684	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	80.4798	703	1684	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	79.1208	454	1684	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	79.1067	446	1684	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	78.5578	385	1684	95	below_threshold
Flavobacterium granuli	strain=DSM 19729	GCA_900129705.1	280093	280093	type	True	78.53	390	1684	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.4956	458	1684	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.4913	483	1684	95	below_threshold
Flavobacterium hydatis	strain=DSM 2063	GCA_000737695.1	991	991	type	True	78.4493	398	1684	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	78.4298	466	1684	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.4181	469	1684	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.3892	507	1684	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.6588	157	1684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:11,039] [INFO] DFAST Taxonomy check result was written to GCF_027111335.1_ASM2711133v2_genomic.fna/tc_result.tsv
[2024-01-25 17:39:11,040] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:11,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:11,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45d00176-03e4-4766-961d-7bbfcc46dbdf/dqc_reference/checkm_data
[2024-01-25 17:39:11,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:11,093] [INFO] Task started: CheckM
[2024-01-25 17:39:11,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027111335.1_ASM2711133v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027111335.1_ASM2711133v2_genomic.fna/checkm_input GCF_027111335.1_ASM2711133v2_genomic.fna/checkm_result
[2024-01-25 17:40:01,298] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:01,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:01,318] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:01,318] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:01,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027111335.1_ASM2711133v2_genomic.fna/markers.fasta)
[2024-01-25 17:40:01,319] [INFO] Task started: Blastn
[2024-01-25 17:40:01,319] [INFO] Running command: blastn -query GCF_027111335.1_ASM2711133v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d00176-03e4-4766-961d-7bbfcc46dbdf/dqc_reference/reference_markers_gtdb.fasta -out GCF_027111335.1_ASM2711133v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:02,300] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:02,302] [INFO] Selected 17 target genomes.
[2024-01-25 17:40:02,302] [INFO] Target genome list was writen to GCF_027111335.1_ASM2711133v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:02,319] [INFO] Task started: fastANI
[2024-01-25 17:40:02,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg8533e646-57f6-4835-b31f-27615498e951/GCF_027111335.1_ASM2711133v2_genomic.fna.gz --refList GCF_027111335.1_ASM2711133v2_genomic.fna/target_genomes_gtdb.txt --output GCF_027111335.1_ASM2711133v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:19,656] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:19,674] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:40:19,674] [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_001761465.1	s__Flavobacterium gilvum	82.8475	971	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013284035.1	s__Flavobacterium sp003096795	82.6543	957	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCF_015351475.1	s__Flavobacterium sp015351475	82.5527	964	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254745.1	s__Flavobacterium aquariorum	82.4591	920	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001005.1	s__Flavobacterium sp002001005	82.2146	904	1684	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	81.1816	945	1684	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	81.1138	808	1684	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	80.5881	787	1684	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	80.4671	705	1684	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	80.2137	727	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129705.1	s__Flavobacterium granuli	78.5402	388	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000737695.1	s__Flavobacterium hydatis	78.4395	399	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_002217355.1	s__Flavobacterium oncorhynchi	78.4385	465	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.71	96.71	0.90	0.90	2	-
GCF_900129795.1	s__Flavobacterium sp900129795	78.4038	523	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_011365745.1	s__Flavobacterium turcicum	78.2219	310	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900107635.1	s__Flavobacterium gillisiae	78.107	343	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299535.1	s__Aquimarina sp900299535	75.8775	88	1684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:19,676] [INFO] GTDB search result was written to GCF_027111335.1_ASM2711133v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:19,676] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:19,680] [INFO] DFAST_QC result json was written to GCF_027111335.1_ASM2711133v2_genomic.fna/dqc_result.json
[2024-01-25 17:40:19,680] [INFO] DFAST_QC completed!
[2024-01-25 17:40:19,680] [INFO] Total running time: 0h1m44s