[2024-01-24 12:53:37,277] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:37,279] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:37,279] [INFO] DQC Reference Directory: /var/lib/cwl/stgb689b73b-c69d-4195-a03d-0e8712c2caa3/dqc_reference
[2024-01-24 12:53:38,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:38,483] [INFO] Task started: Prodigal
[2024-01-24 12:53:38,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg609cce98-6090-466a-b57e-606cfc0cce3a/GCF_004355225.1_ASM435522v1_genomic.fna.gz | prodigal -d GCF_004355225.1_ASM435522v1_genomic.fna/cds.fna -a GCF_004355225.1_ASM435522v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:56,782] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:56,783] [INFO] Task started: HMMsearch
[2024-01-24 12:53:56,783] [INFO] Running command: hmmsearch --tblout GCF_004355225.1_ASM435522v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb689b73b-c69d-4195-a03d-0e8712c2caa3/dqc_reference/reference_markers.hmm GCF_004355225.1_ASM435522v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:57,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:57,033] [INFO] Found 6/6 markers.
[2024-01-24 12:53:57,070] [INFO] Query marker FASTA was written to GCF_004355225.1_ASM435522v1_genomic.fna/markers.fasta
[2024-01-24 12:53:57,071] [INFO] Task started: Blastn
[2024-01-24 12:53:57,071] [INFO] Running command: blastn -query GCF_004355225.1_ASM435522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb689b73b-c69d-4195-a03d-0e8712c2caa3/dqc_reference/reference_markers.fasta -out GCF_004355225.1_ASM435522v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:57,746] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:57,749] [INFO] Selected 15 target genomes.
[2024-01-24 12:53:57,749] [INFO] Target genome list was writen to GCF_004355225.1_ASM435522v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:57,759] [INFO] Task started: fastANI
[2024-01-24 12:53:57,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg609cce98-6090-466a-b57e-606cfc0cce3a/GCF_004355225.1_ASM435522v1_genomic.fna.gz --refList GCF_004355225.1_ASM435522v1_genomic.fna/target_genomes.txt --output GCF_004355225.1_ASM435522v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:09,858] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:09,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb689b73b-c69d-4195-a03d-0e8712c2caa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:09,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb689b73b-c69d-4195-a03d-0e8712c2caa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:09,876] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:09,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:09,876] [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 nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	100.0	1405	1405	95	conclusive
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	82.5568	783	1405	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	81.7719	707	1405	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	80.6402	621	1405	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	79.3362	515	1405	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	78.6545	418	1405	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	78.5484	383	1405	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	78.4128	361	1405	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	78.2831	404	1405	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.9688	272	1405	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	77.8127	293	1405	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.8125	289	1405	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.5721	284	1405	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.3165	162	1405	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.1289	201	1405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:09,878] [INFO] DFAST Taxonomy check result was written to GCF_004355225.1_ASM435522v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:09,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:09,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:09,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb689b73b-c69d-4195-a03d-0e8712c2caa3/dqc_reference/checkm_data
[2024-01-24 12:54:09,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:09,921] [INFO] Task started: CheckM
[2024-01-24 12:54:09,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004355225.1_ASM435522v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004355225.1_ASM435522v1_genomic.fna/checkm_input GCF_004355225.1_ASM435522v1_genomic.fna/checkm_result
[2024-01-24 12:55:03,262] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:03,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:03,282] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:03,282] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:03,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004355225.1_ASM435522v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:03,283] [INFO] Task started: Blastn
[2024-01-24 12:55:03,283] [INFO] Running command: blastn -query GCF_004355225.1_ASM435522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb689b73b-c69d-4195-a03d-0e8712c2caa3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004355225.1_ASM435522v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:04,207] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:04,210] [INFO] Selected 10 target genomes.
[2024-01-24 12:55:04,210] [INFO] Target genome list was writen to GCF_004355225.1_ASM435522v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:04,218] [INFO] Task started: fastANI
[2024-01-24 12:55:04,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg609cce98-6090-466a-b57e-606cfc0cce3a/GCF_004355225.1_ASM435522v1_genomic.fna.gz --refList GCF_004355225.1_ASM435522v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004355225.1_ASM435522v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:12,649] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:12,663] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:12,663] [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_004355225.1	s__Flavobacterium nackdongense	100.0	1405	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007097365.1	s__Flavobacterium franklandianum	82.597	778	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCF_002920895.1	s__Flavobacterium alvei	81.7909	704	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003449615.1	s__Flavobacterium sp003449615	81.4221	468	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379405.1	s__Flavobacterium sp014379405	80.9143	558	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129545.1	s__Flavobacterium fluvii	80.6496	621	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823965.1	s__Flavobacterium sp013823965	80.6275	570	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277675.1	s__Flavobacterium soyangense	80.5956	605	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017989775.1	s__Flavobacterium sp017989775	80.1351	306	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.62	98.46	0.76	0.72	3	-
GCA_002413745.1	s__Flavobacterium sp002413745	79.7861	538	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:12,665] [INFO] GTDB search result was written to GCF_004355225.1_ASM435522v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:12,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:12,668] [INFO] DFAST_QC result json was written to GCF_004355225.1_ASM435522v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:12,669] [INFO] DFAST_QC completed!
[2024-01-24 12:55:12,669] [INFO] Total running time: 0h1m35s