[2024-01-25 18:14:20,826] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:20,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:20,827] [INFO] DQC Reference Directory: /var/lib/cwl/stgaca5d023-4976-4964-a3f5-5c5b6a66e59b/dqc_reference
[2024-01-25 18:14:21,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:21,978] [INFO] Task started: Prodigal
[2024-01-25 18:14:21,978] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4a26375-45ce-4820-9bf6-a5d44509a7f4/GCF_012295615.1_ASM1229561v1_genomic.fna.gz | prodigal -d GCF_012295615.1_ASM1229561v1_genomic.fna/cds.fna -a GCF_012295615.1_ASM1229561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:29,659] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:29,659] [INFO] Task started: HMMsearch
[2024-01-25 18:14:29,660] [INFO] Running command: hmmsearch --tblout GCF_012295615.1_ASM1229561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaca5d023-4976-4964-a3f5-5c5b6a66e59b/dqc_reference/reference_markers.hmm GCF_012295615.1_ASM1229561v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:29,895] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:29,896] [INFO] Found 6/6 markers.
[2024-01-25 18:14:29,932] [INFO] Query marker FASTA was written to GCF_012295615.1_ASM1229561v1_genomic.fna/markers.fasta
[2024-01-25 18:14:29,932] [INFO] Task started: Blastn
[2024-01-25 18:14:29,932] [INFO] Running command: blastn -query GCF_012295615.1_ASM1229561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaca5d023-4976-4964-a3f5-5c5b6a66e59b/dqc_reference/reference_markers.fasta -out GCF_012295615.1_ASM1229561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:30,638] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:30,641] [INFO] Selected 25 target genomes.
[2024-01-25 18:14:30,642] [INFO] Target genome list was writen to GCF_012295615.1_ASM1229561v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:30,662] [INFO] Task started: fastANI
[2024-01-25 18:14:30,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a26375-45ce-4820-9bf6-a5d44509a7f4/GCF_012295615.1_ASM1229561v1_genomic.fna.gz --refList GCF_012295615.1_ASM1229561v1_genomic.fna/target_genomes.txt --output GCF_012295615.1_ASM1229561v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:49,742] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:49,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaca5d023-4976-4964-a3f5-5c5b6a66e59b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:49,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaca5d023-4976-4964-a3f5-5c5b6a66e59b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:49,748] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:14:49,748] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:49,748] [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_012295615.1	207949	207949	type	True	100.0	1181	1182	95	conclusive
Bermanella marisrubri	strain=RED65	GCA_000153565.1	207949	207949	type	True	99.9692	1156	1182	95	conclusive
Thalassolituus oleivorans	strain=MIL-1	GCA_000355675.1	187493	187493	type	True	77.4284	72	1182	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	77.4076	55	1182	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:49,750] [INFO] DFAST Taxonomy check result was written to GCF_012295615.1_ASM1229561v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:49,750] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:49,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:49,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaca5d023-4976-4964-a3f5-5c5b6a66e59b/dqc_reference/checkm_data
[2024-01-25 18:14:49,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:49,790] [INFO] Task started: CheckM
[2024-01-25 18:14:49,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012295615.1_ASM1229561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012295615.1_ASM1229561v1_genomic.fna/checkm_input GCF_012295615.1_ASM1229561v1_genomic.fna/checkm_result
[2024-01-25 18:15:16,618] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:16,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:16,634] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:16,634] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:16,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012295615.1_ASM1229561v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:16,634] [INFO] Task started: Blastn
[2024-01-25 18:15:16,634] [INFO] Running command: blastn -query GCF_012295615.1_ASM1229561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaca5d023-4976-4964-a3f5-5c5b6a66e59b/dqc_reference/reference_markers_gtdb.fasta -out GCF_012295615.1_ASM1229561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:17,714] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:17,717] [INFO] Selected 26 target genomes.
[2024-01-25 18:15:17,717] [INFO] Target genome list was writen to GCF_012295615.1_ASM1229561v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:17,736] [INFO] Task started: fastANI
[2024-01-25 18:15:17,736] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4a26375-45ce-4820-9bf6-a5d44509a7f4/GCF_012295615.1_ASM1229561v1_genomic.fna.gz --refList GCF_012295615.1_ASM1229561v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012295615.1_ASM1229561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:34,883] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:34,889] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:34,889] [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	100.0	1181	1182	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	78.5248	181	1182	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_000967895.1	s__Oleispira antarctica	77.8613	58	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	99.07	99.06	0.98	0.98	3	-
GCA_002683575.1	s__Bermanella sp002683575	77.588	162	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	99.58	99.58	0.89	0.89	2	-
GCF_900156675.1	s__Oleibacter marinus	77.4592	54	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCF_000355675.1	s__Thalassolituus oleivorans	77.4079	72	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Thalassolituus	95.0	98.27	98.03	0.89	0.78	10	-
GCA_002162985.1	s__Bermanella sp002162985	77.2285	67	1182	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	76.8719	53	1182	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.64	97.85	0.94	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:34,890] [INFO] GTDB search result was written to GCF_012295615.1_ASM1229561v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:34,891] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:34,895] [INFO] DFAST_QC result json was written to GCF_012295615.1_ASM1229561v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:34,895] [INFO] DFAST_QC completed!
[2024-01-25 18:15:34,895] [INFO] Total running time: 0h1m14s