[2024-01-24 14:15:34,564] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg623e5c37-e4ea-47bb-a50e-5e0505708277/dqc_reference
[2024-01-24 14:15:35,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,970] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,970] [INFO] Running command: gunzip -c /var/lib/cwl/stgb939a9a4-6921-48e4-857a-a34afa24eb63/GCF_011365745.1_ASM1136574v1_genomic.fna.gz | prodigal -d GCF_011365745.1_ASM1136574v1_genomic.fna/cds.fna -a GCF_011365745.1_ASM1136574v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:49,708] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:49,709] [INFO] Task started: HMMsearch
[2024-01-24 14:15:49,709] [INFO] Running command: hmmsearch --tblout GCF_011365745.1_ASM1136574v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg623e5c37-e4ea-47bb-a50e-5e0505708277/dqc_reference/reference_markers.hmm GCF_011365745.1_ASM1136574v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:50,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:50,005] [INFO] Found 6/6 markers.
[2024-01-24 14:15:50,035] [INFO] Query marker FASTA was written to GCF_011365745.1_ASM1136574v1_genomic.fna/markers.fasta
[2024-01-24 14:15:50,035] [INFO] Task started: Blastn
[2024-01-24 14:15:50,036] [INFO] Running command: blastn -query GCF_011365745.1_ASM1136574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623e5c37-e4ea-47bb-a50e-5e0505708277/dqc_reference/reference_markers.fasta -out GCF_011365745.1_ASM1136574v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:50,747] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:50,751] [INFO] Selected 23 target genomes.
[2024-01-24 14:15:50,752] [INFO] Target genome list was writen to GCF_011365745.1_ASM1136574v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:50,763] [INFO] Task started: fastANI
[2024-01-24 14:15:50,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgb939a9a4-6921-48e4-857a-a34afa24eb63/GCF_011365745.1_ASM1136574v1_genomic.fna.gz --refList GCF_011365745.1_ASM1136574v1_genomic.fna/target_genomes.txt --output GCF_011365745.1_ASM1136574v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:09,030] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:09,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg623e5c37-e4ea-47bb-a50e-5e0505708277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:09,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg623e5c37-e4ea-47bb-a50e-5e0505708277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:09,056] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:16:09,056] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:09,056] [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 turcicum	strain=F-339	GCA_011365745.1	2764718	2764718	type	True	100.0	1119	1120	95	conclusive
Flavobacterium erciyesense	strain=F-328	GCA_018069925.1	2825842	2825842	type	True	93.9146	939	1120	95	below_threshold
Flavobacterium tiangeerense	strain=CGMCC 1.6847	GCA_007830355.1	459471	459471	type	True	83.0806	581	1120	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	81.0236	549	1120	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	80.9168	562	1120	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	80.2386	556	1120	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	80.0945	511	1120	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	79.7161	502	1120	95	below_threshold
Flavobacterium xanthum	strain=DSM 3661	GCA_900142695.1	69322	69322	type	True	79.5985	511	1120	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	79.1963	423	1120	95	below_threshold
Flavobacterium weaverense	strain=DSM 19727	GCA_003688495.1	271156	271156	type	True	79.1476	382	1120	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	78.7261	313	1120	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	78.7009	347	1120	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	78.6656	361	1120	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	78.6305	324	1120	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	78.6028	362	1120	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	78.5673	368	1120	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	78.5551	372	1120	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.4176	330	1120	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.2906	325	1120	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.2024	324	1120	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.0141	336	1120	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.911	118	1120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:09,058] [INFO] DFAST Taxonomy check result was written to GCF_011365745.1_ASM1136574v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:09,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:09,060] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:09,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg623e5c37-e4ea-47bb-a50e-5e0505708277/dqc_reference/checkm_data
[2024-01-24 14:16:09,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:09,103] [INFO] Task started: CheckM
[2024-01-24 14:16:09,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011365745.1_ASM1136574v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011365745.1_ASM1136574v1_genomic.fna/checkm_input GCF_011365745.1_ASM1136574v1_genomic.fna/checkm_result
[2024-01-24 14:16:53,442] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:53,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:53,462] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:53,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:53,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011365745.1_ASM1136574v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:53,463] [INFO] Task started: Blastn
[2024-01-24 14:16:53,463] [INFO] Running command: blastn -query GCF_011365745.1_ASM1136574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg623e5c37-e4ea-47bb-a50e-5e0505708277/dqc_reference/reference_markers_gtdb.fasta -out GCF_011365745.1_ASM1136574v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:54,557] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:54,561] [INFO] Selected 15 target genomes.
[2024-01-24 14:16:54,561] [INFO] Target genome list was writen to GCF_011365745.1_ASM1136574v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:54,573] [INFO] Task started: fastANI
[2024-01-24 14:16:54,573] [INFO] Running command: fastANI --query /var/lib/cwl/stgb939a9a4-6921-48e4-857a-a34afa24eb63/GCF_011365745.1_ASM1136574v1_genomic.fna.gz --refList GCF_011365745.1_ASM1136574v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011365745.1_ASM1136574v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:06,673] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:06,694] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:06,694] [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_011365745.1	s__Flavobacterium turcicum	100.0	1119	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_018069925.1	s__Flavobacterium sp018069925	93.9146	939	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150205.1	s__Flavobacterium sp002150205	84.4327	565	1120	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	83.1034	566	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.83	99.83	0.96	0.96	2	-
GCF_007830355.1	s__Flavobacterium tiangeerense	83.0847	581	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.91	95.91	0.85	0.85	2	-
GCF_003314435.2	s__Flavobacterium petrolei	80.2391	556	1120	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	80.1094	510	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099915.1	s__Flavobacterium omnivorum	79.6598	537	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142695.1	s__Flavobacterium xanthum	79.5985	511	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.99	97.99	0.90	0.90	2	-
GCA_017995345.1	s__Flavobacterium sp017995345	79.4289	384	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.61	99.55	0.85	0.83	4	-
GCF_902804475.1	s__Flavobacterium bizetiae	78.6773	350	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
GCF_002217285.1	s__Flavobacterium hercynium	78.6426	323	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142715.1	s__Flavobacterium pectinovorum	78.5718	370	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.60	0.94	0.89	3	-
GCA_017984035.1	s__Flavobacterium sp017984035	78.3831	164	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004119495.1	s__Flavobacterium sp004119495	78.3082	356	1120	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 14:17:06,696] [INFO] GTDB search result was written to GCF_011365745.1_ASM1136574v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:06,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:06,701] [INFO] DFAST_QC result json was written to GCF_011365745.1_ASM1136574v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:06,701] [INFO] DFAST_QC completed!
[2024-01-24 14:17:06,701] [INFO] Total running time: 0h1m32s