[2024-01-24 10:58:06,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,469] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8bf575b-3260-4c4b-9250-dc82506de3cb/dqc_reference
[2024-01-24 10:58:09,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,637] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e5e060b-698e-4cf5-9f83-eb70012cdb05/GCF_007970805.1_ASM797080v1_genomic.fna.gz | prodigal -d GCF_007970805.1_ASM797080v1_genomic.fna/cds.fna -a GCF_007970805.1_ASM797080v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:39,616] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:39,617] [INFO] Task started: HMMsearch
[2024-01-24 10:58:39,617] [INFO] Running command: hmmsearch --tblout GCF_007970805.1_ASM797080v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8bf575b-3260-4c4b-9250-dc82506de3cb/dqc_reference/reference_markers.hmm GCF_007970805.1_ASM797080v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:40,009] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:40,011] [INFO] Found 6/6 markers.
[2024-01-24 10:58:40,059] [INFO] Query marker FASTA was written to GCF_007970805.1_ASM797080v1_genomic.fna/markers.fasta
[2024-01-24 10:58:40,060] [INFO] Task started: Blastn
[2024-01-24 10:58:40,060] [INFO] Running command: blastn -query GCF_007970805.1_ASM797080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8bf575b-3260-4c4b-9250-dc82506de3cb/dqc_reference/reference_markers.fasta -out GCF_007970805.1_ASM797080v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:40,654] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:40,670] [INFO] Selected 24 target genomes.
[2024-01-24 10:58:40,670] [INFO] Target genome list was writen to GCF_007970805.1_ASM797080v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:40,696] [INFO] Task started: fastANI
[2024-01-24 10:58:40,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e5e060b-698e-4cf5-9f83-eb70012cdb05/GCF_007970805.1_ASM797080v1_genomic.fna.gz --refList GCF_007970805.1_ASM797080v1_genomic.fna/target_genomes.txt --output GCF_007970805.1_ASM797080v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:59:01,782] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:01,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8bf575b-3260-4c4b-9250-dc82506de3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:59:01,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8bf575b-3260-4c4b-9250-dc82506de3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:59:01,797] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:59:01,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:59:01,797] [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 ginsenosidimutans	strain=Gsoil 636	GCA_007970805.1	661481	661481	type	True	100.0	1691	1693	95	conclusive
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	77.2761	394	1693	95	below_threshold
Flavisolibacter ginsengisoli	strain=DSM 18119	GCA_900129295.1	462367	462367	type	True	76.8605	87	1693	95	below_threshold
Cnuella takakiae	strain=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	76.4801	135	1693	95	below_threshold
Cnuella takakiae	strain=RG1-1	GCA_001953305.1	1302690	1302690	type	True	76.4699	138	1693	95	below_threshold
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	76.3642	52	1693	95	below_threshold
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	76.242	109	1693	95	below_threshold
Flaviaesturariibacter aridisoli	strain=17J68-15	GCA_004343705.1	2545761	2545761	type	True	76.236	99	1693	95	below_threshold
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	76.1855	58	1693	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.04	66	1693	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	75.9062	67	1693	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	75.5845	69	1693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:59:01,799] [INFO] DFAST Taxonomy check result was written to GCF_007970805.1_ASM797080v1_genomic.fna/tc_result.tsv
[2024-01-24 10:59:01,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:59:01,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:59:01,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8bf575b-3260-4c4b-9250-dc82506de3cb/dqc_reference/checkm_data
[2024-01-24 10:59:01,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:59:01,854] [INFO] Task started: CheckM
[2024-01-24 10:59:01,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007970805.1_ASM797080v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007970805.1_ASM797080v1_genomic.fna/checkm_input GCF_007970805.1_ASM797080v1_genomic.fna/checkm_result
[2024-01-24 11:00:23,666] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:23,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:23,690] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:23,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:23,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007970805.1_ASM797080v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:23,691] [INFO] Task started: Blastn
[2024-01-24 11:00:23,692] [INFO] Running command: blastn -query GCF_007970805.1_ASM797080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8bf575b-3260-4c4b-9250-dc82506de3cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007970805.1_ASM797080v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:24,482] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:24,486] [INFO] Selected 12 target genomes.
[2024-01-24 11:00:24,486] [INFO] Target genome list was writen to GCF_007970805.1_ASM797080v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:24,523] [INFO] Task started: fastANI
[2024-01-24 11:00:24,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e5e060b-698e-4cf5-9f83-eb70012cdb05/GCF_007970805.1_ASM797080v1_genomic.fna.gz --refList GCF_007970805.1_ASM797080v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007970805.1_ASM797080v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:33,450] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:33,459] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:33,459] [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_007970805.1	s__Flavisolibacter ginsenosidimutans	100.0	1690	1693	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	77.4396	344	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628535.1	s__Flavisolibacter nicotianae	77.2687	395	1693	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	77.2098	318	1693	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	76.4417	203	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paracnuella	95.0	95.63	95.63	0.92	0.92	2	-
GCF_004337505.1	s__Flaviaesturariibacter flavus	76.242	109	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173235.1	s__Flaviaesturariibacter sp004173235	75.8326	90	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720775.1	s__Ferruginibacter sp016720775	75.6781	56	1693	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:33,461] [INFO] GTDB search result was written to GCF_007970805.1_ASM797080v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:33,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:33,468] [INFO] DFAST_QC result json was written to GCF_007970805.1_ASM797080v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:33,468] [INFO] DFAST_QC completed!
[2024-01-24 11:00:33,468] [INFO] Total running time: 0h2m27s