[2024-01-24 13:19:12,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:12,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:12,670] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1773c12-2ada-4b39-8c20-456341b9960d/dqc_reference
[2024-01-24 13:19:13,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:13,886] [INFO] Task started: Prodigal
[2024-01-24 13:19:13,886] [INFO] Running command: gunzip -c /var/lib/cwl/stgf223311b-c3ad-490c-82db-c0cf06beef19/GCF_000153565.1_ASM15356v1_genomic.fna.gz | prodigal -d GCF_000153565.1_ASM15356v1_genomic.fna/cds.fna -a GCF_000153565.1_ASM15356v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:22,348] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:22,349] [INFO] Task started: HMMsearch
[2024-01-24 13:19:22,349] [INFO] Running command: hmmsearch --tblout GCF_000153565.1_ASM15356v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1773c12-2ada-4b39-8c20-456341b9960d/dqc_reference/reference_markers.hmm GCF_000153565.1_ASM15356v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:22,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:22,623] [INFO] Found 6/6 markers.
[2024-01-24 13:19:22,658] [INFO] Query marker FASTA was written to GCF_000153565.1_ASM15356v1_genomic.fna/markers.fasta
[2024-01-24 13:19:22,659] [INFO] Task started: Blastn
[2024-01-24 13:19:22,659] [INFO] Running command: blastn -query GCF_000153565.1_ASM15356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1773c12-2ada-4b39-8c20-456341b9960d/dqc_reference/reference_markers.fasta -out GCF_000153565.1_ASM15356v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:23,393] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:23,397] [INFO] Selected 25 target genomes.
[2024-01-24 13:19:23,397] [INFO] Target genome list was writen to GCF_000153565.1_ASM15356v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:23,409] [INFO] Task started: fastANI
[2024-01-24 13:19:23,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgf223311b-c3ad-490c-82db-c0cf06beef19/GCF_000153565.1_ASM15356v1_genomic.fna.gz --refList GCF_000153565.1_ASM15356v1_genomic.fna/target_genomes.txt --output GCF_000153565.1_ASM15356v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:39,363] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:39,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1773c12-2ada-4b39-8c20-456341b9960d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:39,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1773c12-2ada-4b39-8c20-456341b9960d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:39,368] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:39,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:39,369] [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
Bermanella marisrubri	strain=RED65	GCA_000153565.1	207949	207949	type	True	99.9981	1162	1171	95	conclusive
Bermanella marisrubri	strain=RED65	GCA_012295615.1	207949	207949	type	True	99.9845	1162	1171	95	conclusive
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	77.4948	66	1171	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	77.248	57	1171	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:39,370] [INFO] DFAST Taxonomy check result was written to GCF_000153565.1_ASM15356v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:39,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:39,370] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:39,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1773c12-2ada-4b39-8c20-456341b9960d/dqc_reference/checkm_data
[2024-01-24 13:19:39,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:39,406] [INFO] Task started: CheckM
[2024-01-24 13:19:39,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000153565.1_ASM15356v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000153565.1_ASM15356v1_genomic.fna/checkm_input GCF_000153565.1_ASM15356v1_genomic.fna/checkm_result
[2024-01-24 13:20:10,407] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:10,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:10,433] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:10,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:10,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000153565.1_ASM15356v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:10,435] [INFO] Task started: Blastn
[2024-01-24 13:20:10,435] [INFO] Running command: blastn -query GCF_000153565.1_ASM15356v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1773c12-2ada-4b39-8c20-456341b9960d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000153565.1_ASM15356v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:11,554] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:11,557] [INFO] Selected 26 target genomes.
[2024-01-24 13:20:11,557] [INFO] Target genome list was writen to GCF_000153565.1_ASM15356v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:11,657] [INFO] Task started: fastANI
[2024-01-24 13:20:11,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgf223311b-c3ad-490c-82db-c0cf06beef19/GCF_000153565.1_ASM15356v1_genomic.fna.gz --refList GCF_000153565.1_ASM15356v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000153565.1_ASM15356v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:27,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:27,723] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:27,723] [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_012295615.1	s__Bermanella marisrubri	99.9845	1162	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCA_013373125.1	s__Bermanella sp013373125	78.603	166	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683575.1	s__Bermanella sp002683575	77.6012	161	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	99.58	99.58	0.89	0.89	2	-
GCA_000967895.1	s__Oleispira antarctica	77.5456	56	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	99.07	99.06	0.98	0.98	3	-
GCF_000355675.1	s__Thalassolituus oleivorans	77.4498	67	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Thalassolituus	95.0	98.27	98.03	0.89	0.78	10	-
GCF_900156675.1	s__Oleibacter marinus	77.3345	55	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCA_002162985.1	s__Bermanella sp002162985	77.2431	66	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724925.1	s__Oleibacter sp002724925	76.9202	51	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.64	97.85	0.94	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:27,725] [INFO] GTDB search result was written to GCF_000153565.1_ASM15356v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:27,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:27,729] [INFO] DFAST_QC result json was written to GCF_000153565.1_ASM15356v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:27,730] [INFO] DFAST_QC completed!
[2024-01-24 13:20:27,730] [INFO] Total running time: 0h1m15s