[2024-01-24 12:31:51,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,433] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,433] [INFO] DQC Reference Directory: /var/lib/cwl/stge2cb1055-d800-4544-8b9f-182161ff8d04/dqc_reference
[2024-01-24 12:31:52,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,682] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg3088e518-2673-49f0-9b14-a4b691d7a66f/GCF_007830355.1_ASM783035v1_genomic.fna.gz | prodigal -d GCF_007830355.1_ASM783035v1_genomic.fna/cds.fna -a GCF_007830355.1_ASM783035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:05,188] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:05,189] [INFO] Task started: HMMsearch
[2024-01-24 12:32:05,189] [INFO] Running command: hmmsearch --tblout GCF_007830355.1_ASM783035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2cb1055-d800-4544-8b9f-182161ff8d04/dqc_reference/reference_markers.hmm GCF_007830355.1_ASM783035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:05,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:05,463] [INFO] Found 6/6 markers.
[2024-01-24 12:32:05,495] [INFO] Query marker FASTA was written to GCF_007830355.1_ASM783035v1_genomic.fna/markers.fasta
[2024-01-24 12:32:05,496] [INFO] Task started: Blastn
[2024-01-24 12:32:05,496] [INFO] Running command: blastn -query GCF_007830355.1_ASM783035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2cb1055-d800-4544-8b9f-182161ff8d04/dqc_reference/reference_markers.fasta -out GCF_007830355.1_ASM783035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:06,192] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:06,196] [INFO] Selected 24 target genomes.
[2024-01-24 12:32:06,197] [INFO] Target genome list was writen to GCF_007830355.1_ASM783035v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:06,203] [INFO] Task started: fastANI
[2024-01-24 12:32:06,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg3088e518-2673-49f0-9b14-a4b691d7a66f/GCF_007830355.1_ASM783035v1_genomic.fna.gz --refList GCF_007830355.1_ASM783035v1_genomic.fna/target_genomes.txt --output GCF_007830355.1_ASM783035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:23,229] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:23,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2cb1055-d800-4544-8b9f-182161ff8d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:23,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2cb1055-d800-4544-8b9f-182161ff8d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:23,252] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:23,253] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:23,253] [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 tiangeerense	strain=CGMCC 1.6847	GCA_007830355.1	459471	459471	type	True	100.0	1156	1157	95	conclusive
Flavobacterium turcicum	strain=F-339	GCA_011365745.1	2764718	2764718	type	True	83.0778	582	1157	95	below_threshold
Flavobacterium erciyesense	strain=F-328	GCA_018069925.1	2825842	2825842	type	True	83.0485	585	1157	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	81.7584	603	1157	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	81.7184	604	1157	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	81.047	607	1157	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	80.9153	614	1157	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	80.8447	580	1157	95	below_threshold
Flavobacterium omnivorum	strain=CGMCC 1.2747	GCA_900099915.1	178355	178355	type	True	80.1471	547	1157	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	80.0828	567	1157	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	80.0661	571	1157	95	below_threshold
Flavobacterium fryxellicola	strain=DSM 16209	GCA_001637185.1	249352	249352	type	True	79.7962	516	1157	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.6055	471	1157	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	79.5384	467	1157	95	below_threshold
Flavobacterium micromati	strain=DSM 17659	GCA_900129585.1	229205	229205	type	True	79.0904	451	1157	95	below_threshold
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	78.7353	343	1157	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	78.6689	390	1157	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	78.4247	316	1157	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	78.35	295	1157	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.291	352	1157	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.2633	323	1157	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.2223	330	1157	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.516	182	1157	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.178	197	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:23,255] [INFO] DFAST Taxonomy check result was written to GCF_007830355.1_ASM783035v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:23,255] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:23,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:23,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2cb1055-d800-4544-8b9f-182161ff8d04/dqc_reference/checkm_data
[2024-01-24 12:32:23,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:23,297] [INFO] Task started: CheckM
[2024-01-24 12:32:23,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830355.1_ASM783035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830355.1_ASM783035v1_genomic.fna/checkm_input GCF_007830355.1_ASM783035v1_genomic.fna/checkm_result
[2024-01-24 12:33:03,206] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:03,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:03,229] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:03,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:03,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830355.1_ASM783035v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:03,230] [INFO] Task started: Blastn
[2024-01-24 12:33:03,230] [INFO] Running command: blastn -query GCF_007830355.1_ASM783035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2cb1055-d800-4544-8b9f-182161ff8d04/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830355.1_ASM783035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:04,195] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:04,200] [INFO] Selected 13 target genomes.
[2024-01-24 12:33:04,201] [INFO] Target genome list was writen to GCF_007830355.1_ASM783035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:04,211] [INFO] Task started: fastANI
[2024-01-24 12:33:04,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg3088e518-2673-49f0-9b14-a4b691d7a66f/GCF_007830355.1_ASM783035v1_genomic.fna.gz --refList GCF_007830355.1_ASM783035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830355.1_ASM783035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:13,405] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:13,427] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:13,428] [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_007830355.1	s__Flavobacterium tiangeerense	100.0	1156	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.91	95.91	0.85	0.85	2	conclusive
GCF_002150205.1	s__Flavobacterium sp002150205	93.4149	808	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009764685.1	s__Flavobacterium sp009764685	92.6507	929	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.83	99.83	0.96	0.96	2	-
GCF_011365745.1	s__Flavobacterium turcicum	83.1027	580	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018069925.1	s__Flavobacterium sp018069925	83.0568	584	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754315.1	s__Flavobacterium sp002754315	80.4589	584	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_004349135.1	s__Flavobacterium sandaracinum	80.0851	569	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281985.1	s__Flavobacterium sp014281985	79.4698	472	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCF_003634825.1	s__Flavobacterium sp003634825	79.1977	423	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129585.1	s__Flavobacterium micromati	79.0805	452	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425505.1	s__Flavobacterium frigidarium	78.7566	342	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106645.1	s__Flavobacterium degerlachei	78.6644	391	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838055.1	s__Flavobacterium sp903838055	77.9721	197	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.95	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:13,430] [INFO] GTDB search result was written to GCF_007830355.1_ASM783035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:13,431] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:13,435] [INFO] DFAST_QC result json was written to GCF_007830355.1_ASM783035v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:13,435] [INFO] DFAST_QC completed!
[2024-01-24 12:33:13,435] [INFO] Total running time: 0h1m22s