[2024-01-24 13:22:01,524] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:01,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:01,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d553369-0b85-41ed-bf16-c3a98ae75638/dqc_reference
[2024-01-24 13:22:03,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,007] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e1d5b8e-0549-4438-a257-703f5610091e/GCF_027111355.2_ASM2711135v2_genomic.fna.gz | prodigal -d GCF_027111355.2_ASM2711135v2_genomic.fna/cds.fna -a GCF_027111355.2_ASM2711135v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:19,645] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:19,646] [INFO] Task started: HMMsearch
[2024-01-24 13:22:19,646] [INFO] Running command: hmmsearch --tblout GCF_027111355.2_ASM2711135v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d553369-0b85-41ed-bf16-c3a98ae75638/dqc_reference/reference_markers.hmm GCF_027111355.2_ASM2711135v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:19,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:19,982] [INFO] Found 6/6 markers.
[2024-01-24 13:22:20,027] [INFO] Query marker FASTA was written to GCF_027111355.2_ASM2711135v2_genomic.fna/markers.fasta
[2024-01-24 13:22:20,028] [INFO] Task started: Blastn
[2024-01-24 13:22:20,028] [INFO] Running command: blastn -query GCF_027111355.2_ASM2711135v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d553369-0b85-41ed-bf16-c3a98ae75638/dqc_reference/reference_markers.fasta -out GCF_027111355.2_ASM2711135v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:20,819] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:20,822] [INFO] Selected 23 target genomes.
[2024-01-24 13:22:20,823] [INFO] Target genome list was writen to GCF_027111355.2_ASM2711135v2_genomic.fna/target_genomes.txt
[2024-01-24 13:22:20,853] [INFO] Task started: fastANI
[2024-01-24 13:22:20,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1d5b8e-0549-4438-a257-703f5610091e/GCF_027111355.2_ASM2711135v2_genomic.fna.gz --refList GCF_027111355.2_ASM2711135v2_genomic.fna/target_genomes.txt --output GCF_027111355.2_ASM2711135v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:41,692] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:41,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d553369-0b85-41ed-bf16-c3a98ae75638/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:41,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d553369-0b85-41ed-bf16-c3a98ae75638/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:41,715] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:41,715] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:41,715] [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 fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	82.4698	727	1281	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	81.766	720	1281	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	81.4501	617	1281	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	80.6378	565	1281	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	80.1159	513	1281	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	79.8619	590	1281	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	79.619	519	1281	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	79.2321	466	1281	95	below_threshold
Flavobacterium aquicola	strain=DSM 100880	GCA_003385115.1	1682742	1682742	type	True	79.2055	433	1281	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	79.185	478	1281	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	79.1127	450	1281	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	78.8134	353	1281	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	78.7014	426	1281	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	78.6695	408	1281	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	78.6407	422	1281	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	78.6004	421	1281	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.5919	401	1281	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	78.4757	424	1281	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	78.4545	441	1281	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.3497	411	1281	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.2962	452	1281	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.6503	211	1281	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.6136	117	1281	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:41,717] [INFO] DFAST Taxonomy check result was written to GCF_027111355.2_ASM2711135v2_genomic.fna/tc_result.tsv
[2024-01-24 13:22:41,718] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:41,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:41,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d553369-0b85-41ed-bf16-c3a98ae75638/dqc_reference/checkm_data
[2024-01-24 13:22:41,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:41,761] [INFO] Task started: CheckM
[2024-01-24 13:22:41,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027111355.2_ASM2711135v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027111355.2_ASM2711135v2_genomic.fna/checkm_input GCF_027111355.2_ASM2711135v2_genomic.fna/checkm_result
[2024-01-24 13:23:29,578] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:29,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:29,598] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:29,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:29,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027111355.2_ASM2711135v2_genomic.fna/markers.fasta)
[2024-01-24 13:23:29,599] [INFO] Task started: Blastn
[2024-01-24 13:23:29,599] [INFO] Running command: blastn -query GCF_027111355.2_ASM2711135v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d553369-0b85-41ed-bf16-c3a98ae75638/dqc_reference/reference_markers_gtdb.fasta -out GCF_027111355.2_ASM2711135v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:30,594] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:30,597] [INFO] Selected 20 target genomes.
[2024-01-24 13:23:30,598] [INFO] Target genome list was writen to GCF_027111355.2_ASM2711135v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:30,659] [INFO] Task started: fastANI
[2024-01-24 13:23:30,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1d5b8e-0549-4438-a257-703f5610091e/GCF_027111355.2_ASM2711135v2_genomic.fna.gz --refList GCF_027111355.2_ASM2711135v2_genomic.fna/target_genomes_gtdb.txt --output GCF_027111355.2_ASM2711135v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:46,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:46,483] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:23:46,483] [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_014379405.1	s__Flavobacterium sp014379405	82.6176	644	1281	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	82.4958	725	1281	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	81.7946	717	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097365.1	s__Flavobacterium franklandianum	81.4345	619	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCA_013823965.1	s__Flavobacterium sp013823965	81.0536	538	1281	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	80.6488	564	1281	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	80.3641	489	1281	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	80.27	522	1281	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	80.2173	385	1281	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	79.9726	514	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280815.1	s__Flavobacterium sp002280815	79.9174	450	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349355.1	s__Flavobacterium cellulosilyticum	79.8853	587	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861155.1	s__Flavobacterium sp903861155	79.8662	418	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.81	99.81	0.91	0.91	2	-
GCF_002813295.1	s__Flavobacterium sp002813295	79.8304	464	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	79.6217	518	1281	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	79.4747	337	1281	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	79.3469	480	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCA_001507425.1	s__Flavobacterium sp001507425	78.9716	449	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217285.1	s__Flavobacterium hercynium	78.8219	354	1281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422725.1	s__Flavobacterium sp001422725	78.7782	440	1281	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 13:23:46,484] [INFO] GTDB search result was written to GCF_027111355.2_ASM2711135v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:46,485] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:46,489] [INFO] DFAST_QC result json was written to GCF_027111355.2_ASM2711135v2_genomic.fna/dqc_result.json
[2024-01-24 13:23:46,489] [INFO] DFAST_QC completed!
[2024-01-24 13:23:46,489] [INFO] Total running time: 0h1m45s