[2024-01-24 14:19:19,347] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:19,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:19,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfe0c7fa-7e75-4411-b677-44c588aa4abb/dqc_reference
[2024-01-24 14:19:20,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,709] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,710] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa1bf8cf-c565-4534-a5d2-edf543f59142/GCF_004151275.2_ASM415127v2_genomic.fna.gz | prodigal -d GCF_004151275.2_ASM415127v2_genomic.fna/cds.fna -a GCF_004151275.2_ASM415127v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:31,916] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:31,916] [INFO] Task started: HMMsearch
[2024-01-24 14:19:31,916] [INFO] Running command: hmmsearch --tblout GCF_004151275.2_ASM415127v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfe0c7fa-7e75-4411-b677-44c588aa4abb/dqc_reference/reference_markers.hmm GCF_004151275.2_ASM415127v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:32,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:32,168] [INFO] Found 6/6 markers.
[2024-01-24 14:19:32,197] [INFO] Query marker FASTA was written to GCF_004151275.2_ASM415127v2_genomic.fna/markers.fasta
[2024-01-24 14:19:32,197] [INFO] Task started: Blastn
[2024-01-24 14:19:32,197] [INFO] Running command: blastn -query GCF_004151275.2_ASM415127v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfe0c7fa-7e75-4411-b677-44c588aa4abb/dqc_reference/reference_markers.fasta -out GCF_004151275.2_ASM415127v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:32,913] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:32,917] [INFO] Selected 15 target genomes.
[2024-01-24 14:19:32,917] [INFO] Target genome list was writen to GCF_004151275.2_ASM415127v2_genomic.fna/target_genomes.txt
[2024-01-24 14:19:32,925] [INFO] Task started: fastANI
[2024-01-24 14:19:32,925] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa1bf8cf-c565-4534-a5d2-edf543f59142/GCF_004151275.2_ASM415127v2_genomic.fna.gz --refList GCF_004151275.2_ASM415127v2_genomic.fna/target_genomes.txt --output GCF_004151275.2_ASM415127v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:44,324] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:44,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfe0c7fa-7e75-4411-b677-44c588aa4abb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:44,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfe0c7fa-7e75-4411-b677-44c588aa4abb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:44,337] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:19:44,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:19:44,337] [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 ummariense	strain=DS-12	GCA_900115115.1	913024	913024	type	True	85.8205	653	981	95	below_threshold
Flavobacterium baculatum	strain=SNL9	GCA_008629655.1	2608000	2608000	type	True	85.5553	627	981	95	below_threshold
Flavobacterium viscosum	strain=YIM 102796	GCA_003858535.1	2488729	2488729	type	True	84.1322	618	981	95	below_threshold
Flavobacterium tangerinum	strain=YIM 102701-2	GCA_003865405.1	2488728	2488728	type	True	78.402	293	981	95	below_threshold
Myroides marinus	strain=DSM 23048	GCA_900109075.1	703342	703342	type	True	78.3304	86	981	95	below_threshold
Flavobacterium inviolabile	strain=P2-65	GCA_013389455.1	2748320	2748320	type	True	78.2988	121	981	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.7299	116	981	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.3774	107	981	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	77.3524	139	981	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	77.1512	152	981	95	below_threshold
Flavobacterium terrigena	strain=DSM 17934	GCA_900108955.1	402734	402734	type	True	77.0046	136	981	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.6181	89	981	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	76.4135	105	981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:44,339] [INFO] DFAST Taxonomy check result was written to GCF_004151275.2_ASM415127v2_genomic.fna/tc_result.tsv
[2024-01-24 14:19:44,340] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:44,340] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:44,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfe0c7fa-7e75-4411-b677-44c588aa4abb/dqc_reference/checkm_data
[2024-01-24 14:19:44,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:44,373] [INFO] Task started: CheckM
[2024-01-24 14:19:44,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004151275.2_ASM415127v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004151275.2_ASM415127v2_genomic.fna/checkm_input GCF_004151275.2_ASM415127v2_genomic.fna/checkm_result
[2024-01-24 14:20:20,487] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:20,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:20,509] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:20,510] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:20,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004151275.2_ASM415127v2_genomic.fna/markers.fasta)
[2024-01-24 14:20:20,511] [INFO] Task started: Blastn
[2024-01-24 14:20:20,511] [INFO] Running command: blastn -query GCF_004151275.2_ASM415127v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfe0c7fa-7e75-4411-b677-44c588aa4abb/dqc_reference/reference_markers_gtdb.fasta -out GCF_004151275.2_ASM415127v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:21,545] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:21,549] [INFO] Selected 8 target genomes.
[2024-01-24 14:20:21,550] [INFO] Target genome list was writen to GCF_004151275.2_ASM415127v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:21,556] [INFO] Task started: fastANI
[2024-01-24 14:20:21,557] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa1bf8cf-c565-4534-a5d2-edf543f59142/GCF_004151275.2_ASM415127v2_genomic.fna.gz --refList GCF_004151275.2_ASM415127v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004151275.2_ASM415127v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:27,148] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:27,157] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:27,157] [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_004151275.1	s__Flavobacterium sp004151275	99.972	925	981	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_900108395.1	s__Flavobacterium marinum	87.3334	713	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115115.1	s__Flavobacterium ummariense	85.806	654	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629655.1	s__Flavobacterium baculatum	85.5513	627	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858535.1	s__Flavobacterium viscosum	84.0747	621	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018384465.1	s__Flavobacterium sp018384465	80.6634	313	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013874595.1	s__Flavobacterium sp013874595	80.5632	482	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	0.97	0.97	3	-
GCA_002360925.1	s__Flavobacterium sp002360925	80.0433	457	981	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 14:20:27,163] [INFO] GTDB search result was written to GCF_004151275.2_ASM415127v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:27,167] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:27,175] [INFO] DFAST_QC result json was written to GCF_004151275.2_ASM415127v2_genomic.fna/dqc_result.json
[2024-01-24 14:20:27,176] [INFO] DFAST_QC completed!
[2024-01-24 14:20:27,176] [INFO] Total running time: 0h1m8s