[2024-01-25 19:49:20,643] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:20,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:20,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgf50efb70-4ef9-4f7a-b915-f481d69eee7f/dqc_reference
[2024-01-25 19:49:21,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:21,819] [INFO] Task started: Prodigal
[2024-01-25 19:49:21,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg4012fa8d-dddc-4b87-adab-f589120aeb3f/GCF_018069925.1_ASM1806992v1_genomic.fna.gz | prodigal -d GCF_018069925.1_ASM1806992v1_genomic.fna/cds.fna -a GCF_018069925.1_ASM1806992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:33,036] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:33,036] [INFO] Task started: HMMsearch
[2024-01-25 19:49:33,036] [INFO] Running command: hmmsearch --tblout GCF_018069925.1_ASM1806992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf50efb70-4ef9-4f7a-b915-f481d69eee7f/dqc_reference/reference_markers.hmm GCF_018069925.1_ASM1806992v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:33,285] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:33,286] [INFO] Found 6/6 markers.
[2024-01-25 19:49:33,314] [INFO] Query marker FASTA was written to GCF_018069925.1_ASM1806992v1_genomic.fna/markers.fasta
[2024-01-25 19:49:33,314] [INFO] Task started: Blastn
[2024-01-25 19:49:33,314] [INFO] Running command: blastn -query GCF_018069925.1_ASM1806992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf50efb70-4ef9-4f7a-b915-f481d69eee7f/dqc_reference/reference_markers.fasta -out GCF_018069925.1_ASM1806992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:33,976] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:33,979] [INFO] Selected 22 target genomes.
[2024-01-25 19:49:33,980] [INFO] Target genome list was writen to GCF_018069925.1_ASM1806992v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:33,987] [INFO] Task started: fastANI
[2024-01-25 19:49:33,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg4012fa8d-dddc-4b87-adab-f589120aeb3f/GCF_018069925.1_ASM1806992v1_genomic.fna.gz --refList GCF_018069925.1_ASM1806992v1_genomic.fna/target_genomes.txt --output GCF_018069925.1_ASM1806992v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:50,954] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:50,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf50efb70-4ef9-4f7a-b915-f481d69eee7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:50,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf50efb70-4ef9-4f7a-b915-f481d69eee7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:50,967] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:49:50,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:50,967] [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 erciyesense	strain=F-328	GCA_018069925.1	2825842	2825842	type	True	100.0	1123	1124	95	conclusive
Flavobacterium turcicum	strain=F-339	GCA_011365745.1	2764718	2764718	type	True	93.8292	946	1124	95	below_threshold
Flavobacterium tiangeerense	strain=CGMCC 1.6847	GCA_007830355.1	459471	459471	type	True	83.109	582	1124	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	81.0032	561	1124	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	80.9308	560	1124	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	80.354	540	1124	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	80.3036	541	1124	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	80.0852	497	1124	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	79.9738	504	1124	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	79.7429	489	1124	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	79.1777	433	1124	95	below_threshold
Flavobacterium kayseriense	strain=F-47	GCA_014305095.1	2764714	2764714	type	True	78.9193	351	1124	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	78.7508	358	1124	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	78.6589	329	1124	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	78.6055	338	1124	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	78.5681	313	1124	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.4482	333	1124	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	78.4469	330	1124	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.3937	324	1124	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.3395	293	1124	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.1657	326	1124	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.0101	130	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:50,969] [INFO] DFAST Taxonomy check result was written to GCF_018069925.1_ASM1806992v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:50,969] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:50,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:50,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf50efb70-4ef9-4f7a-b915-f481d69eee7f/dqc_reference/checkm_data
[2024-01-25 19:49:50,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:51,012] [INFO] Task started: CheckM
[2024-01-25 19:49:51,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018069925.1_ASM1806992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018069925.1_ASM1806992v1_genomic.fna/checkm_input GCF_018069925.1_ASM1806992v1_genomic.fna/checkm_result
[2024-01-25 19:50:26,190] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:26,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:26,208] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:26,208] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:26,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018069925.1_ASM1806992v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:26,209] [INFO] Task started: Blastn
[2024-01-25 19:50:26,209] [INFO] Running command: blastn -query GCF_018069925.1_ASM1806992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf50efb70-4ef9-4f7a-b915-f481d69eee7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_018069925.1_ASM1806992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:27,133] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:27,136] [INFO] Selected 14 target genomes.
[2024-01-25 19:50:27,137] [INFO] Target genome list was writen to GCF_018069925.1_ASM1806992v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:27,150] [INFO] Task started: fastANI
[2024-01-25 19:50:27,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg4012fa8d-dddc-4b87-adab-f589120aeb3f/GCF_018069925.1_ASM1806992v1_genomic.fna.gz --refList GCF_018069925.1_ASM1806992v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018069925.1_ASM1806992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:37,744] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:37,755] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:37,755] [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_018069925.1	s__Flavobacterium sp018069925	100.0	1123	1124	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_011365745.1	s__Flavobacterium turcicum	93.8472	945	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002150205.1	s__Flavobacterium sp002150205	83.6565	543	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830355.1	s__Flavobacterium tiangeerense	83.1236	581	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.91	95.91	0.85	0.85	2	-
GCF_009764685.1	s__Flavobacterium sp009764685	82.9761	580	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.83	99.83	0.96	0.96	2	-
GCF_003312425.1	s__Flavobacterium psychrolimnae	80.3651	539	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003314435.2	s__Flavobacterium petrolei	80.314	540	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_003634755.1	s__Flavobacterium limicola	80.0852	497	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112975.1	s__Flavobacterium xueshanense	79.7537	488	1124	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	79.1642	440	1124	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	79.0551	370	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014305095.1	s__Flavobacterium kayseriense	78.9059	351	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.16	98.32	0.96	0.92	3	-
GCF_003668995.1	s__Flavobacterium sp003668995	78.7847	334	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804475.1	s__Flavobacterium bizetiae	78.6586	328	1124	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:37,756] [INFO] GTDB search result was written to GCF_018069925.1_ASM1806992v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:37,757] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:37,760] [INFO] DFAST_QC result json was written to GCF_018069925.1_ASM1806992v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:37,760] [INFO] DFAST_QC completed!
[2024-01-25 19:50:37,760] [INFO] Total running time: 0h1m17s