[2024-01-24 12:09:05,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg7732f414-f913-4e5d-8ae6-100606158991/dqc_reference
[2024-01-24 12:09:07,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:07,025] [INFO] Task started: Prodigal
[2024-01-24 12:09:07,026] [INFO] Running command: gunzip -c /var/lib/cwl/stgd663bb8f-e4a2-44ad-8f60-a9ff6d5810eb/GCF_003628535.1_ASM362853v1_genomic.fna.gz | prodigal -d GCF_003628535.1_ASM362853v1_genomic.fna/cds.fna -a GCF_003628535.1_ASM362853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:43,223] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:43,224] [INFO] Task started: HMMsearch
[2024-01-24 12:09:43,224] [INFO] Running command: hmmsearch --tblout GCF_003628535.1_ASM362853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7732f414-f913-4e5d-8ae6-100606158991/dqc_reference/reference_markers.hmm GCF_003628535.1_ASM362853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:43,544] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:43,546] [INFO] Found 6/6 markers.
[2024-01-24 12:09:43,607] [INFO] Query marker FASTA was written to GCF_003628535.1_ASM362853v1_genomic.fna/markers.fasta
[2024-01-24 12:09:43,607] [INFO] Task started: Blastn
[2024-01-24 12:09:43,608] [INFO] Running command: blastn -query GCF_003628535.1_ASM362853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7732f414-f913-4e5d-8ae6-100606158991/dqc_reference/reference_markers.fasta -out GCF_003628535.1_ASM362853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:44,209] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:44,216] [INFO] Selected 16 target genomes.
[2024-01-24 12:09:44,216] [INFO] Target genome list was writen to GCF_003628535.1_ASM362853v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:44,224] [INFO] Task started: fastANI
[2024-01-24 12:09:44,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgd663bb8f-e4a2-44ad-8f60-a9ff6d5810eb/GCF_003628535.1_ASM362853v1_genomic.fna.gz --refList GCF_003628535.1_ASM362853v1_genomic.fna/target_genomes.txt --output GCF_003628535.1_ASM362853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:59,831] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:59,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7732f414-f913-4e5d-8ae6-100606158991/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:59,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7732f414-f913-4e5d-8ae6-100606158991/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:59,847] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:59,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:59,847] [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
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	100.0	1994	1995	95	conclusive
Flavisolibacter ginsenosidimutans	strain=Gsoil 636	GCA_007970805.1	661481	661481	type	True	77.2858	374	1995	95	below_threshold
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	76.8988	152	1995	95	below_threshold
Flavisolibacter tropicus	strain=LCS9	GCA_001644645.1	1492898	1492898	type	True	76.7876	96	1995	95	below_threshold
Flaviaesturariibacter aridisoli	strain=17J68-15	GCA_004343705.1	2545761	2545761	type	True	76.7759	187	1995	95	below_threshold
Cnuella takakiae	strain=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	76.7674	205	1995	95	below_threshold
Cnuella takakiae	strain=RG1-1	GCA_001953305.1	1302690	1302690	type	True	76.7619	209	1995	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.4791	60	1995	95	below_threshold
Flavihumibacter fluminis	strain=IMCC34837	GCA_018595675.2	2838157	2838157	type	True	76.3462	54	1995	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	76.2273	116	1995	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	76.0464	117	1995	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	76.0321	121	1995	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	75.9786	94	1995	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	75.818	66	1995	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	75.781	76	1995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:59,849] [INFO] DFAST Taxonomy check result was written to GCF_003628535.1_ASM362853v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:59,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:59,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:59,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7732f414-f913-4e5d-8ae6-100606158991/dqc_reference/checkm_data
[2024-01-24 12:09:59,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:59,907] [INFO] Task started: CheckM
[2024-01-24 12:09:59,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003628535.1_ASM362853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003628535.1_ASM362853v1_genomic.fna/checkm_input GCF_003628535.1_ASM362853v1_genomic.fna/checkm_result
[2024-01-24 12:11:36,090] [INFO] Task succeeded: CheckM
[2024-01-24 12:11:36,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:11:36,116] [INFO] ===== Completeness check finished =====
[2024-01-24 12:11:36,116] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:11:36,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003628535.1_ASM362853v1_genomic.fna/markers.fasta)
[2024-01-24 12:11:36,117] [INFO] Task started: Blastn
[2024-01-24 12:11:36,117] [INFO] Running command: blastn -query GCF_003628535.1_ASM362853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7732f414-f913-4e5d-8ae6-100606158991/dqc_reference/reference_markers_gtdb.fasta -out GCF_003628535.1_ASM362853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:11:36,886] [INFO] Task succeeded: Blastn
[2024-01-24 12:11:36,890] [INFO] Selected 13 target genomes.
[2024-01-24 12:11:36,891] [INFO] Target genome list was writen to GCF_003628535.1_ASM362853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:11:37,036] [INFO] Task started: fastANI
[2024-01-24 12:11:37,037] [INFO] Running command: fastANI --query /var/lib/cwl/stgd663bb8f-e4a2-44ad-8f60-a9ff6d5810eb/GCF_003628535.1_ASM362853v1_genomic.fna.gz --refList GCF_003628535.1_ASM362853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003628535.1_ASM362853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:11:48,499] [INFO] Task succeeded: fastANI
[2024-01-24 12:11:48,514] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:11:48,514] [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_003628535.1	s__Flavisolibacter nicotianae	100.0	1994	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013327885.1	s__Flavisolibacter sp013327885	78.4682	613	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014163555.1	s__Flavisolibacter sp014163555	78.4199	546	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970805.1	s__Flavisolibacter ginsenosidimutans	77.2858	374	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332885.2	s__Paracnuella aquatica	76.9535	245	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paracnuella	95.0	95.63	95.63	0.92	0.92	2	-
GCF_001644645.1	s__Flavisolibacter_B tropicus	76.7876	96	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953305.1	s__Cnuella takakiae	76.7834	207	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Cnuella	95.0	99.98	99.98	1.00	1.00	2	-
GCA_004173235.1	s__Flaviaesturariibacter sp004173235	76.6353	133	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247775.1	s__Sediminibacterium sp019247775	76.3876	79	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192105.1	s__JJ008 sp016192105	76.2659	85	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018595675.1	s__Flavihumibacter sp018595675	76.2258	55	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173255.1	s__46-32 sp004173255	75.7744	65	1995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:11:48,516] [INFO] GTDB search result was written to GCF_003628535.1_ASM362853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:11:48,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:11:48,519] [INFO] DFAST_QC result json was written to GCF_003628535.1_ASM362853v1_genomic.fna/dqc_result.json
[2024-01-24 12:11:48,519] [INFO] DFAST_QC completed!
[2024-01-24 12:11:48,519] [INFO] Total running time: 0h2m43s