[2024-01-24 13:18:27,881] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,882] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,883] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3a393f5-4cc9-4878-8644-e388994dc742/dqc_reference
[2024-01-24 13:18:29,141] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:29,142] [INFO] Task started: Prodigal
[2024-01-24 13:18:29,142] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d25bb8c-b637-4b94-91d5-02df0ce53b87/GCF_000384415.1_ASM38441v1_genomic.fna.gz | prodigal -d GCF_000384415.1_ASM38441v1_genomic.fna/cds.fna -a GCF_000384415.1_ASM38441v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:34,709] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:34,709] [INFO] Task started: HMMsearch
[2024-01-24 13:18:34,709] [INFO] Running command: hmmsearch --tblout GCF_000384415.1_ASM38441v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3a393f5-4cc9-4878-8644-e388994dc742/dqc_reference/reference_markers.hmm GCF_000384415.1_ASM38441v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:34,947] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:34,948] [INFO] Found 6/6 markers.
[2024-01-24 13:18:34,977] [INFO] Query marker FASTA was written to GCF_000384415.1_ASM38441v1_genomic.fna/markers.fasta
[2024-01-24 13:18:34,978] [INFO] Task started: Blastn
[2024-01-24 13:18:34,978] [INFO] Running command: blastn -query GCF_000384415.1_ASM38441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3a393f5-4cc9-4878-8644-e388994dc742/dqc_reference/reference_markers.fasta -out GCF_000384415.1_ASM38441v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:35,626] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:35,629] [INFO] Selected 24 target genomes.
[2024-01-24 13:18:35,630] [INFO] Target genome list was writen to GCF_000384415.1_ASM38441v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:35,663] [INFO] Task started: fastANI
[2024-01-24 13:18:35,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d25bb8c-b637-4b94-91d5-02df0ce53b87/GCF_000384415.1_ASM38441v1_genomic.fna.gz --refList GCF_000384415.1_ASM38441v1_genomic.fna/target_genomes.txt --output GCF_000384415.1_ASM38441v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:48,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:48,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3a393f5-4cc9-4878-8644-e388994dc742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:48,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3a393f5-4cc9-4878-8644-e388994dc742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:48,714] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:48,714] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:48,714] [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
Cycloclasticus pugetii	strain=PS-1	GCA_000384415.1	34068	34068	type	True	100.0	794	794	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:18:48,716] [INFO] DFAST Taxonomy check result was written to GCF_000384415.1_ASM38441v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:48,716] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:48,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:48,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3a393f5-4cc9-4878-8644-e388994dc742/dqc_reference/checkm_data
[2024-01-24 13:18:48,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:48,744] [INFO] Task started: CheckM
[2024-01-24 13:18:48,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000384415.1_ASM38441v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000384415.1_ASM38441v1_genomic.fna/checkm_input GCF_000384415.1_ASM38441v1_genomic.fna/checkm_result
[2024-01-24 13:19:12,214] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:12,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:12,234] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:12,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:12,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000384415.1_ASM38441v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:12,235] [INFO] Task started: Blastn
[2024-01-24 13:19:12,235] [INFO] Running command: blastn -query GCF_000384415.1_ASM38441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3a393f5-4cc9-4878-8644-e388994dc742/dqc_reference/reference_markers_gtdb.fasta -out GCF_000384415.1_ASM38441v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:13,323] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:13,327] [INFO] Selected 23 target genomes.
[2024-01-24 13:19:13,327] [INFO] Target genome list was writen to GCF_000384415.1_ASM38441v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:13,395] [INFO] Task started: fastANI
[2024-01-24 13:19:13,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d25bb8c-b637-4b94-91d5-02df0ce53b87/GCF_000384415.1_ASM38441v1_genomic.fna.gz --refList GCF_000384415.1_ASM38441v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000384415.1_ASM38441v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:25,358] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:25,375] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:25,375] [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_000384415.1	s__Cycloclasticus pugetii	100.0	794	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	98.68	98.33	0.92	0.87	8	conclusive
GCA_002700385.1	s__Cycloclasticus sp002700385	79.6428	293	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	99.97	99.95	0.99	0.97	4	-
GCA_002162705.1	s__Cycloclasticus sp002162705	78.3038	201	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002101235.1	s__Cycloclasticus sp002101235	78.2424	186	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002101225.1	s__Cycloclasticus sp002101225	77.9532	77	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959695.1	s__Cycloclasticus sp012959695	77.8468	153	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	99.70	99.70	0.87	0.87	2	-
GCA_002733135.1	s__Cycloclasticus sp002733135	77.6269	121	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960055.1	s__Cycloclasticus sp012960055	77.5302	120	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401365.1	s__Cycloclasticus sp002401365	77.4996	81	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162695.1	s__Cycloclasticus sp002162695	77.3043	136	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	97.08	97.08	0.97	0.97	2	-
GCA_019090295.1	s__Cycloclasticus sp019090295	77.259	108	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Cycloclasticaceae;g__Cycloclasticus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,379] [INFO] GTDB search result was written to GCF_000384415.1_ASM38441v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:25,380] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:25,383] [INFO] DFAST_QC result json was written to GCF_000384415.1_ASM38441v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:25,383] [INFO] DFAST_QC completed!
[2024-01-24 13:19:25,383] [INFO] Total running time: 0h0m58s