[2024-01-24 10:47:08,410] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:08,411] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:08,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg3256a1df-ccaf-4f28-82fe-40833d0bf60b/dqc_reference
[2024-01-24 10:47:11,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,915] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg1aa98eeb-d69e-4151-8f85-e3013bb29a23/GCF_002217475.1_ASM221747v1_genomic.fna.gz | prodigal -d GCF_002217475.1_ASM221747v1_genomic.fna/cds.fna -a GCF_002217475.1_ASM221747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:28,849] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:28,849] [INFO] Task started: HMMsearch
[2024-01-24 10:47:28,849] [INFO] Running command: hmmsearch --tblout GCF_002217475.1_ASM221747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3256a1df-ccaf-4f28-82fe-40833d0bf60b/dqc_reference/reference_markers.hmm GCF_002217475.1_ASM221747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:29,138] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:29,141] [INFO] Found 6/6 markers.
[2024-01-24 10:47:29,186] [INFO] Query marker FASTA was written to GCF_002217475.1_ASM221747v1_genomic.fna/markers.fasta
[2024-01-24 10:47:29,186] [INFO] Task started: Blastn
[2024-01-24 10:47:29,186] [INFO] Running command: blastn -query GCF_002217475.1_ASM221747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3256a1df-ccaf-4f28-82fe-40833d0bf60b/dqc_reference/reference_markers.fasta -out GCF_002217475.1_ASM221747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:29,905] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:29,909] [INFO] Selected 22 target genomes.
[2024-01-24 10:47:29,910] [INFO] Target genome list was writen to GCF_002217475.1_ASM221747v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:30,134] [INFO] Task started: fastANI
[2024-01-24 10:47:30,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg1aa98eeb-d69e-4151-8f85-e3013bb29a23/GCF_002217475.1_ASM221747v1_genomic.fna.gz --refList GCF_002217475.1_ASM221747v1_genomic.fna/target_genomes.txt --output GCF_002217475.1_ASM221747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:54,747] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:54,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3256a1df-ccaf-4f28-82fe-40833d0bf60b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:54,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3256a1df-ccaf-4f28-82fe-40833d0bf60b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:54,764] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:54,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:54,764] [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 tructae	strain=CCUG 60100	GCA_002217475.1	1114873	1114873	type	True	100.0	1603	1607	95	conclusive
Flavobacterium collinsii		GCA_902804485.1	1114861	1114861	type	True	88.1541	1315	1607	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	83.0435	1004	1607	95	below_threshold
Flavobacterium chilense	strain=DSM 24724	GCA_900142685.1	946677	946677	type	True	83.0115	1075	1607	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	82.9882	1070	1607	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	82.9751	982	1607	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	82.8905	973	1607	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_001686925.1	1114874	1114874	type	True	82.8887	980	1607	95	below_threshold
Flavobacterium piscis	strain=CCUG 60099	GCA_002222045.1	1114874	1114874	type	True	82.7928	975	1607	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	82.7778	1004	1607	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_003148525.1	946678	946678	type	True	82.7364	1022	1607	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	82.4184	924	1607	95	below_threshold
Flavobacterium panici		GCA_903819335.1	2654843	2654843	type	True	82.181	910	1607	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	82.0334	888	1607	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	81.8721	890	1607	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	81.7435	874	1607	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.3046	848	1607	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.2762	829	1607	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.2171	835	1607	95	below_threshold
Flavobacterium hydatis	strain=DSM 2063	GCA_000737695.1	991	991	type	True	79.7515	711	1607	95	below_threshold
Flavobacterium hydatis	strain=ATCC 29551	GCA_002217335.1	991	991	type	True	79.7011	716	1607	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.5239	200	1607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:54,766] [INFO] DFAST Taxonomy check result was written to GCF_002217475.1_ASM221747v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:54,767] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:54,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:54,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3256a1df-ccaf-4f28-82fe-40833d0bf60b/dqc_reference/checkm_data
[2024-01-24 10:47:54,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:54,820] [INFO] Task started: CheckM
[2024-01-24 10:47:54,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217475.1_ASM221747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217475.1_ASM221747v1_genomic.fna/checkm_input GCF_002217475.1_ASM221747v1_genomic.fna/checkm_result
[2024-01-24 10:48:45,576] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:45,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:45,599] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:45,599] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:45,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217475.1_ASM221747v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:45,600] [INFO] Task started: Blastn
[2024-01-24 10:48:45,600] [INFO] Running command: blastn -query GCF_002217475.1_ASM221747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3256a1df-ccaf-4f28-82fe-40833d0bf60b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217475.1_ASM221747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:46,586] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:46,591] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:46,591] [INFO] Target genome list was writen to GCF_002217475.1_ASM221747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:46,643] [INFO] Task started: fastANI
[2024-01-24 10:48:46,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg1aa98eeb-d69e-4151-8f85-e3013bb29a23/GCF_002217475.1_ASM221747v1_genomic.fna.gz --refList GCF_002217475.1_ASM221747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217475.1_ASM221747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:08,390] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:08,410] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:08,410] [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_002217475.1	s__Flavobacterium tructae	100.0	1603	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.59	96.94	0.94	0.93	4	conclusive
GCF_903469665.1	s__Flavobacterium sp903469665	94.5324	1384	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804485.1	s__Flavobacterium collinsii	88.1578	1315	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975985.1	s__Flavobacterium sp001975985	83.0501	993	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001602525.1	s__Flavobacterium chilense	82.9644	1074	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.61	0.93	0.86	3	-
GCF_003217415.1	s__Flavobacterium sp003217415	82.9077	1050	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.56	98.67	0.98	0.94	4	-
GCF_001686925.1	s__Flavobacterium piscis	82.8784	982	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.33	97.30	0.93	0.88	4	-
GCF_001422725.1	s__Flavobacterium sp001422725	82.8689	1011	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009664855.1	s__Flavobacterium sp009664855	82.7879	1018	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.90	98.90	0.89	0.89	2	-
GCF_004339525.1	s__Flavobacterium sp004339525	82.7699	1047	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006438875.1	s__Flavobacterium pectinovorum_A	82.5724	1049	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129795.1	s__Flavobacterium sp900129795	82.2541	915	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_009711135.1	s__Flavobacterium sp009711135	82.062	881	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482975.1	s__Flavobacterium sp002482975	81.9656	894	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833855.1	s__Flavobacterium sp017833855	81.9299	847	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217355.1	s__Flavobacterium oncorhynchi	81.8805	889	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.71	96.71	0.90	0.90	2	-
GCF_011751075.1	s__Flavobacterium sp011751075	81.7166	884	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737695.1	s__Flavobacterium hydatis	79.7354	714	1607	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:08,412] [INFO] GTDB search result was written to GCF_002217475.1_ASM221747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:08,413] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:08,418] [INFO] DFAST_QC result json was written to GCF_002217475.1_ASM221747v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:08,419] [INFO] DFAST_QC completed!
[2024-01-24 10:49:08,419] [INFO] Total running time: 0h2m0s