[2024-01-24 12:13:28,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,966] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg178278f3-f552-451f-8404-45454b5e8b65/dqc_reference
[2024-01-24 12:13:30,489] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:30,490] [INFO] Task started: Prodigal
[2024-01-24 12:13:30,491] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc7b3103-dc4a-4358-aea7-f15b02dec3ec/GCF_002245495.1_ASM224549v1_genomic.fna.gz | prodigal -d GCF_002245495.1_ASM224549v1_genomic.fna/cds.fna -a GCF_002245495.1_ASM224549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:41,665] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:41,666] [INFO] Task started: HMMsearch
[2024-01-24 12:13:41,666] [INFO] Running command: hmmsearch --tblout GCF_002245495.1_ASM224549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg178278f3-f552-451f-8404-45454b5e8b65/dqc_reference/reference_markers.hmm GCF_002245495.1_ASM224549v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:41,958] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:41,960] [INFO] Found 6/6 markers.
[2024-01-24 12:13:42,000] [INFO] Query marker FASTA was written to GCF_002245495.1_ASM224549v1_genomic.fna/markers.fasta
[2024-01-24 12:13:42,001] [INFO] Task started: Blastn
[2024-01-24 12:13:42,001] [INFO] Running command: blastn -query GCF_002245495.1_ASM224549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg178278f3-f552-451f-8404-45454b5e8b65/dqc_reference/reference_markers.fasta -out GCF_002245495.1_ASM224549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:42,889] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:42,892] [INFO] Selected 10 target genomes.
[2024-01-24 12:13:42,892] [INFO] Target genome list was writen to GCF_002245495.1_ASM224549v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:42,896] [INFO] Task started: fastANI
[2024-01-24 12:13:42,896] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7b3103-dc4a-4358-aea7-f15b02dec3ec/GCF_002245495.1_ASM224549v1_genomic.fna.gz --refList GCF_002245495.1_ASM224549v1_genomic.fna/target_genomes.txt --output GCF_002245495.1_ASM224549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:52,689] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:52,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg178278f3-f552-451f-8404-45454b5e8b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:52,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg178278f3-f552-451f-8404-45454b5e8b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:52,700] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:13:52,700] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:52,700] [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
Oceanimonas baumannii	strain=ATCC 700832	GCA_002245495.1	129578	129578	type	True	100.0	1238	1239	95	conclusive
Oceanimonas baumannii	strain=DSM 15594	GCA_004365405.1	129578	129578	type	True	99.9784	1227	1239	95	conclusive
Oceanimonas smirnovii	strain=ATCC BAA-899	GCA_000381965.1	264574	264574	type	True	83.9259	860	1239	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	83.7773	784	1239	95	below_threshold
Oceanimonas doudoroffii	strain=ATCC 27123	GCA_002242685.1	84158	84158	type	True	83.282	832	1239	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	76.3381	91	1239	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.0949	56	1239	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.8495	65	1239	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.7159	67	1239	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.7116	71	1239	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:52,711] [INFO] DFAST Taxonomy check result was written to GCF_002245495.1_ASM224549v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:52,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:52,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:52,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg178278f3-f552-451f-8404-45454b5e8b65/dqc_reference/checkm_data
[2024-01-24 12:13:52,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:52,754] [INFO] Task started: CheckM
[2024-01-24 12:13:52,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002245495.1_ASM224549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002245495.1_ASM224549v1_genomic.fna/checkm_input GCF_002245495.1_ASM224549v1_genomic.fna/checkm_result
[2024-01-24 12:14:31,562] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:31,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:31,579] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:31,580] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:31,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002245495.1_ASM224549v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:31,581] [INFO] Task started: Blastn
[2024-01-24 12:14:31,581] [INFO] Running command: blastn -query GCF_002245495.1_ASM224549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg178278f3-f552-451f-8404-45454b5e8b65/dqc_reference/reference_markers_gtdb.fasta -out GCF_002245495.1_ASM224549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:33,107] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:33,113] [INFO] Selected 6 target genomes.
[2024-01-24 12:14:33,113] [INFO] Target genome list was writen to GCF_002245495.1_ASM224549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:33,120] [INFO] Task started: fastANI
[2024-01-24 12:14:33,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7b3103-dc4a-4358-aea7-f15b02dec3ec/GCF_002245495.1_ASM224549v1_genomic.fna.gz --refList GCF_002245495.1_ASM224549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002245495.1_ASM224549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:38,815] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:38,826] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:38,827] [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_002245495.1	s__Oceanimonas baumannii	100.0	1238	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000381965.1	s__Oceanimonas smirnovii	83.9309	860	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003049725.1	s__Oceanimonas marisflavi	83.8005	782	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243075.1	s__Oceanimonas sp000243075	83.639	849	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002242685.1	s__Oceanimonas doudoroffii	83.2794	832	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	98.80	98.80	0.94	0.94	2	-
GCF_003075035.1	s__Zobellella_A maritima	79.475	497	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:38,830] [INFO] GTDB search result was written to GCF_002245495.1_ASM224549v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:38,831] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:38,834] [INFO] DFAST_QC result json was written to GCF_002245495.1_ASM224549v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:38,834] [INFO] DFAST_QC completed!
[2024-01-24 12:14:38,834] [INFO] Total running time: 0h1m10s