[2024-01-25 18:46:35,532] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:35,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:35,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ffcfda5-7432-4822-9514-800dea957825/dqc_reference
[2024-01-25 18:46:36,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:36,650] [INFO] Task started: Prodigal
[2024-01-25 18:46:36,650] [INFO] Running command: gunzip -c /var/lib/cwl/stgd690fdcf-955b-49c3-92c9-5426f3b3e7e0/GCF_002863865.1_ASM286386v1_genomic.fna.gz | prodigal -d GCF_002863865.1_ASM286386v1_genomic.fna/cds.fna -a GCF_002863865.1_ASM286386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:52,379] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:52,379] [INFO] Task started: HMMsearch
[2024-01-25 18:46:52,379] [INFO] Running command: hmmsearch --tblout GCF_002863865.1_ASM286386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ffcfda5-7432-4822-9514-800dea957825/dqc_reference/reference_markers.hmm GCF_002863865.1_ASM286386v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:52,726] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:52,727] [INFO] Found 6/6 markers.
[2024-01-25 18:46:52,773] [INFO] Query marker FASTA was written to GCF_002863865.1_ASM286386v1_genomic.fna/markers.fasta
[2024-01-25 18:46:52,774] [INFO] Task started: Blastn
[2024-01-25 18:46:52,774] [INFO] Running command: blastn -query GCF_002863865.1_ASM286386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ffcfda5-7432-4822-9514-800dea957825/dqc_reference/reference_markers.fasta -out GCF_002863865.1_ASM286386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:53,490] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:53,494] [INFO] Selected 30 target genomes.
[2024-01-25 18:46:53,494] [INFO] Target genome list was writen to GCF_002863865.1_ASM286386v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:53,514] [INFO] Task started: fastANI
[2024-01-25 18:46:53,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgd690fdcf-955b-49c3-92c9-5426f3b3e7e0/GCF_002863865.1_ASM286386v1_genomic.fna.gz --refList GCF_002863865.1_ASM286386v1_genomic.fna/target_genomes.txt --output GCF_002863865.1_ASM286386v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:15,342] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:15,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ffcfda5-7432-4822-9514-800dea957825/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:15,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ffcfda5-7432-4822-9514-800dea957825/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:15,347] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:47:15,347] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:15,347] [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
Ketobacter alkanivorans	strain=GI5	GCA_002863865.1	1917421	1917421	type	True	100.0	1635	1638	95	conclusive
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	77.1043	54	1638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:15,349] [INFO] DFAST Taxonomy check result was written to GCF_002863865.1_ASM286386v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:15,349] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:15,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:15,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ffcfda5-7432-4822-9514-800dea957825/dqc_reference/checkm_data
[2024-01-25 18:47:15,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:15,399] [INFO] Task started: CheckM
[2024-01-25 18:47:15,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002863865.1_ASM286386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002863865.1_ASM286386v1_genomic.fna/checkm_input GCF_002863865.1_ASM286386v1_genomic.fna/checkm_result
[2024-01-25 18:48:03,415] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:03,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:03,442] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:03,443] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:03,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002863865.1_ASM286386v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:03,444] [INFO] Task started: Blastn
[2024-01-25 18:48:03,444] [INFO] Running command: blastn -query GCF_002863865.1_ASM286386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ffcfda5-7432-4822-9514-800dea957825/dqc_reference/reference_markers_gtdb.fasta -out GCF_002863865.1_ASM286386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:04,623] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:04,626] [INFO] Selected 17 target genomes.
[2024-01-25 18:48:04,626] [INFO] Target genome list was writen to GCF_002863865.1_ASM286386v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:04,645] [INFO] Task started: fastANI
[2024-01-25 18:48:04,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgd690fdcf-955b-49c3-92c9-5426f3b3e7e0/GCF_002863865.1_ASM286386v1_genomic.fna.gz --refList GCF_002863865.1_ASM286386v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002863865.1_ASM286386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:19,056] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:19,063] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:19,063] [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_002863865.1	s__Ketobacter alkanivorans	100.0	1635	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002701845.1	s__Ketobacter sp002701845	79.7022	385	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471665.1	s__Ketobacter sp002471665	79.3117	603	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.82	99.43	0.96	0.93	14	-
GCF_009746715.1	s__Ketobacter sp003667185	78.7419	223	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	99.27	99.27	0.91	0.91	2	-
GCA_003671495.1	s__Ketobacter sp003671495	78.6926	582	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708905.1	s__Ketobacter sp002708905	78.6383	544	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ketobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000198515.1	s__HdN1 sp000198515	78.2997	59	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__HdN1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	76.8491	50	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003596405.1	s__Pseudomonas_E sp003596405	76.8301	53	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013367775.1	s__Microbulbifer sp013367775	76.5173	52	1638	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:19,064] [INFO] GTDB search result was written to GCF_002863865.1_ASM286386v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:19,065] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:19,067] [INFO] DFAST_QC result json was written to GCF_002863865.1_ASM286386v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:19,067] [INFO] DFAST_QC completed!
[2024-01-25 18:48:19,067] [INFO] Total running time: 0h1m44s