[2024-01-24 13:19:00,077] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:00,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:00,079] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7e7fc15-1e53-4995-b06f-8f246af6bced/dqc_reference
[2024-01-24 13:19:01,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:01,440] [INFO] Task started: Prodigal
[2024-01-24 13:19:01,440] [INFO] Running command: gunzip -c /var/lib/cwl/stg3365b4b1-1078-4436-8df2-ff2acebc9651/GCF_008298015.1_ASM829801v1_genomic.fna.gz | prodigal -d GCF_008298015.1_ASM829801v1_genomic.fna/cds.fna -a GCF_008298015.1_ASM829801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:15,819] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:15,819] [INFO] Task started: HMMsearch
[2024-01-24 13:19:15,819] [INFO] Running command: hmmsearch --tblout GCF_008298015.1_ASM829801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7e7fc15-1e53-4995-b06f-8f246af6bced/dqc_reference/reference_markers.hmm GCF_008298015.1_ASM829801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:16,170] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:16,172] [INFO] Found 6/6 markers.
[2024-01-24 13:19:16,214] [INFO] Query marker FASTA was written to GCF_008298015.1_ASM829801v1_genomic.fna/markers.fasta
[2024-01-24 13:19:16,215] [INFO] Task started: Blastn
[2024-01-24 13:19:16,215] [INFO] Running command: blastn -query GCF_008298015.1_ASM829801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7e7fc15-1e53-4995-b06f-8f246af6bced/dqc_reference/reference_markers.fasta -out GCF_008298015.1_ASM829801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:17,086] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:17,090] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:17,091] [INFO] Target genome list was writen to GCF_008298015.1_ASM829801v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:17,101] [INFO] Task started: fastANI
[2024-01-24 13:19:17,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg3365b4b1-1078-4436-8df2-ff2acebc9651/GCF_008298015.1_ASM829801v1_genomic.fna.gz --refList GCF_008298015.1_ASM829801v1_genomic.fna/target_genomes.txt --output GCF_008298015.1_ASM829801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:31,791] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:31,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7e7fc15-1e53-4995-b06f-8f246af6bced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:31,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7e7fc15-1e53-4995-b06f-8f246af6bced/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:31,805] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:31,805] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:31,806] [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
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	89.6896	1191	1537	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	89.5632	1190	1537	95	below_threshold
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	85.2551	1014	1537	95	below_threshold
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	85.1626	1082	1537	95	below_threshold
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	85.1551	1080	1537	95	below_threshold
Salinicola halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	84.4618	1024	1537	95	below_threshold
Salinicola halimionae	strain=CPA60	GCA_003206065.1	1949081	1949081	type	True	83.3781	1008	1537	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	82.4197	895	1537	95	below_threshold
Salinicola tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	82.2516	907	1537	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.9405	418	1537	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	78.8427	453	1537	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.8223	424	1537	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.8031	449	1537	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	78.7807	397	1537	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.6236	349	1537	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.5781	433	1537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:31,807] [INFO] DFAST Taxonomy check result was written to GCF_008298015.1_ASM829801v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:31,808] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:31,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:31,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7e7fc15-1e53-4995-b06f-8f246af6bced/dqc_reference/checkm_data
[2024-01-24 13:19:31,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:31,855] [INFO] Task started: CheckM
[2024-01-24 13:19:31,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008298015.1_ASM829801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008298015.1_ASM829801v1_genomic.fna/checkm_input GCF_008298015.1_ASM829801v1_genomic.fna/checkm_result
[2024-01-24 13:20:13,672] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:13,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:13,691] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:13,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:13,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008298015.1_ASM829801v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:13,693] [INFO] Task started: Blastn
[2024-01-24 13:20:13,693] [INFO] Running command: blastn -query GCF_008298015.1_ASM829801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7e7fc15-1e53-4995-b06f-8f246af6bced/dqc_reference/reference_markers_gtdb.fasta -out GCF_008298015.1_ASM829801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:15,031] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:15,034] [INFO] Selected 8 target genomes.
[2024-01-24 13:20:15,034] [INFO] Target genome list was writen to GCF_008298015.1_ASM829801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:15,040] [INFO] Task started: fastANI
[2024-01-24 13:20:15,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg3365b4b1-1078-4436-8df2-ff2acebc9651/GCF_008298015.1_ASM829801v1_genomic.fna.gz --refList GCF_008298015.1_ASM829801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008298015.1_ASM829801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:23,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:23,323] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:23,323] [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_008298015.1	s__Salinicola sp008298015	100.0	1537	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002695065.1	s__Salinicola sp002695065	94.0278	1179	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	-
GCF_003206045.1	s__Salinicola lusitanus	89.6769	1192	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCF_003206615.1	s__Salinicola acroporae	89.5632	1190	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206135.1	s__Salinicola salarius	85.2488	1015	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.80	97.80	0.89	0.89	2	-
GCF_001937195.1	s__Salinicola socius	85.1451	1081	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_002179555.1	s__Salinicola salarius_A	85.0252	975	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652715.1	s__Salinicola rhizosphaerae	80.9705	844	1537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:23,325] [INFO] GTDB search result was written to GCF_008298015.1_ASM829801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:23,326] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:23,329] [INFO] DFAST_QC result json was written to GCF_008298015.1_ASM829801v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:23,329] [INFO] DFAST_QC completed!
[2024-01-24 13:20:23,330] [INFO] Total running time: 0h1m23s