[2024-01-24 13:37:04,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:04,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:04,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2ce05f6-2415-4029-8bfe-de1130309773/dqc_reference
[2024-01-24 13:37:06,286] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,287] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,287] [INFO] Running command: gunzip -c /var/lib/cwl/stg7995e989-f6e3-489e-84db-11c6896c3a3c/GCF_007097365.1_ASM709736v1_genomic.fna.gz | prodigal -d GCF_007097365.1_ASM709736v1_genomic.fna/cds.fna -a GCF_007097365.1_ASM709736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:22,802] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:22,802] [INFO] Task started: HMMsearch
[2024-01-24 13:37:22,802] [INFO] Running command: hmmsearch --tblout GCF_007097365.1_ASM709736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2ce05f6-2415-4029-8bfe-de1130309773/dqc_reference/reference_markers.hmm GCF_007097365.1_ASM709736v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:23,146] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:23,147] [INFO] Found 6/6 markers.
[2024-01-24 13:37:23,189] [INFO] Query marker FASTA was written to GCF_007097365.1_ASM709736v1_genomic.fna/markers.fasta
[2024-01-24 13:37:23,190] [INFO] Task started: Blastn
[2024-01-24 13:37:23,190] [INFO] Running command: blastn -query GCF_007097365.1_ASM709736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ce05f6-2415-4029-8bfe-de1130309773/dqc_reference/reference_markers.fasta -out GCF_007097365.1_ASM709736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:23,976] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:23,979] [INFO] Selected 15 target genomes.
[2024-01-24 13:37:23,979] [INFO] Target genome list was writen to GCF_007097365.1_ASM709736v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:23,985] [INFO] Task started: fastANI
[2024-01-24 13:37:23,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg7995e989-f6e3-489e-84db-11c6896c3a3c/GCF_007097365.1_ASM709736v1_genomic.fna.gz --refList GCF_007097365.1_ASM709736v1_genomic.fna/target_genomes.txt --output GCF_007097365.1_ASM709736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:38,565] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:38,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2ce05f6-2415-4029-8bfe-de1130309773/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:38,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2ce05f6-2415-4029-8bfe-de1130309773/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:38,580] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:38,581] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:38,581] [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 franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	100.0	1255	1257	95	conclusive
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	83.1016	782	1257	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	82.6683	778	1257	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	82.1344	694	1257	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	80.3981	643	1257	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.418	506	1257	95	below_threshold
Flavobacterium restrictum	strain=LB1R34	GCA_007097245.1	2594428	2594428	type	True	79.3392	474	1257	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	79.0042	423	1257	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.9282	469	1257	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	78.1133	320	1257	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.9729	343	1257	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.8671	335	1257	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.8596	311	1257	95	below_threshold
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	77.7996	336	1257	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.4055	62	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:38,583] [INFO] DFAST Taxonomy check result was written to GCF_007097365.1_ASM709736v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:38,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:38,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:38,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2ce05f6-2415-4029-8bfe-de1130309773/dqc_reference/checkm_data
[2024-01-24 13:37:38,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:38,628] [INFO] Task started: CheckM
[2024-01-24 13:37:38,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007097365.1_ASM709736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007097365.1_ASM709736v1_genomic.fna/checkm_input GCF_007097365.1_ASM709736v1_genomic.fna/checkm_result
[2024-01-24 13:38:29,185] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:29,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:29,207] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:29,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:29,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007097365.1_ASM709736v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:29,209] [INFO] Task started: Blastn
[2024-01-24 13:38:29,209] [INFO] Running command: blastn -query GCF_007097365.1_ASM709736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ce05f6-2415-4029-8bfe-de1130309773/dqc_reference/reference_markers_gtdb.fasta -out GCF_007097365.1_ASM709736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:30,150] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:30,154] [INFO] Selected 15 target genomes.
[2024-01-24 13:38:30,154] [INFO] Target genome list was writen to GCF_007097365.1_ASM709736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:30,465] [INFO] Task started: fastANI
[2024-01-24 13:38:30,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg7995e989-f6e3-489e-84db-11c6896c3a3c/GCF_007097365.1_ASM709736v1_genomic.fna.gz --refList GCF_007097365.1_ASM709736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007097365.1_ASM709736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:41,637] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:41,662] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:41,663] [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_007097365.1	s__Flavobacterium franklandianum	100.0	1255	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	conclusive
GCA_003449615.1	s__Flavobacterium sp003449615	83.2952	504	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920895.1	s__Flavobacterium alvei	83.1285	779	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365135.1	s__Flavobacterium sp010365135	82.8778	646	1257	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	82.7982	625	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355225.1	s__Flavobacterium nackdongense	82.7103	774	1257	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	82.1428	675	1257	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	81.8478	622	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413745.1	s__Flavobacterium sp002413745	80.9182	633	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
GCA_903861155.1	s__Flavobacterium sp903861155	80.5858	506	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.81	99.81	0.91	0.91	2	-
GCF_004349355.1	s__Flavobacterium cellulosilyticum	80.3718	646	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	79.8957	402	1257	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	79.0529	419	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668995.1	s__Flavobacterium sp003668995	78.4178	327	1257	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842575.1	s__Flavobacterium sp903842575	77.8325	253	1257	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 13:38:41,664] [INFO] GTDB search result was written to GCF_007097365.1_ASM709736v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:41,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:41,670] [INFO] DFAST_QC result json was written to GCF_007097365.1_ASM709736v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:41,670] [INFO] DFAST_QC completed!
[2024-01-24 13:38:41,670] [INFO] Total running time: 0h1m37s