[2024-01-24 12:39:41,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg3786cd53-ff6e-4168-9f29-8da67caed901/dqc_reference
[2024-01-24 12:39:43,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:43,044] [INFO] Task started: Prodigal
[2024-01-24 12:39:43,044] [INFO] Running command: gunzip -c /var/lib/cwl/stg90da1087-0db6-4f02-bbfe-a4312c441574/GCF_900445115.1_52121_E02_genomic.fna.gz | prodigal -d GCF_900445115.1_52121_E02_genomic.fna/cds.fna -a GCF_900445115.1_52121_E02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:59,124] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:59,125] [INFO] Task started: HMMsearch
[2024-01-24 12:39:59,125] [INFO] Running command: hmmsearch --tblout GCF_900445115.1_52121_E02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3786cd53-ff6e-4168-9f29-8da67caed901/dqc_reference/reference_markers.hmm GCF_900445115.1_52121_E02_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:59,442] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:59,443] [INFO] Found 6/6 markers.
[2024-01-24 12:39:59,492] [INFO] Query marker FASTA was written to GCF_900445115.1_52121_E02_genomic.fna/markers.fasta
[2024-01-24 12:39:59,493] [INFO] Task started: Blastn
[2024-01-24 12:39:59,493] [INFO] Running command: blastn -query GCF_900445115.1_52121_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stg3786cd53-ff6e-4168-9f29-8da67caed901/dqc_reference/reference_markers.fasta -out GCF_900445115.1_52121_E02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:00,441] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:00,450] [INFO] Selected 10 target genomes.
[2024-01-24 12:40:00,451] [INFO] Target genome list was writen to GCF_900445115.1_52121_E02_genomic.fna/target_genomes.txt
[2024-01-24 12:40:00,454] [INFO] Task started: fastANI
[2024-01-24 12:40:00,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg90da1087-0db6-4f02-bbfe-a4312c441574/GCF_900445115.1_52121_E02_genomic.fna.gz --refList GCF_900445115.1_52121_E02_genomic.fna/target_genomes.txt --output GCF_900445115.1_52121_E02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:10,882] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:10,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3786cd53-ff6e-4168-9f29-8da67caed901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:10,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3786cd53-ff6e-4168-9f29-8da67caed901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:10,892] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:40:10,892] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:10,892] [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
Aeromonas salmonicida	strain=NCTC12959	GCA_900445115.1	645	645	type	True	100.0	1634	1639	95	conclusive
Aeromonas salmonicida subsp. salmonicida	strain=CIP 103209	GCA_000820065.1	29491	645	type	True	99.9318	1506	1639	95	conclusive
Aeromonas salmonicida subsp. salmonicida	strain=ATCC 33658	GCA_001643305.1	29491	645	type	True	99.9119	1514	1639	95	conclusive
Aeromonas salmonicida subsp. masoucida	strain=NBRC 13784	GCA_000647955.1	197700	645	type	True	99.6761	1337	1639	95	conclusive
Aeromonas salmonicida subsp. pectinolytica	strain=34mel	GCA_000447435.2	96473	645	type	True	96.9815	1306	1639	95	conclusive
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.9869	130	1639	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.6723	121	1639	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.1857	124	1639	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.0777	144	1639	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.0357	136	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:10,894] [INFO] DFAST Taxonomy check result was written to GCF_900445115.1_52121_E02_genomic.fna/tc_result.tsv
[2024-01-24 12:40:10,895] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:10,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:10,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3786cd53-ff6e-4168-9f29-8da67caed901/dqc_reference/checkm_data
[2024-01-24 12:40:10,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:10,943] [INFO] Task started: CheckM
[2024-01-24 12:40:10,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445115.1_52121_E02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445115.1_52121_E02_genomic.fna/checkm_input GCF_900445115.1_52121_E02_genomic.fna/checkm_result
[2024-01-24 12:40:57,939] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:57,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:57,966] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:57,967] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:57,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445115.1_52121_E02_genomic.fna/markers.fasta)
[2024-01-24 12:40:57,968] [INFO] Task started: Blastn
[2024-01-24 12:40:57,968] [INFO] Running command: blastn -query GCF_900445115.1_52121_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stg3786cd53-ff6e-4168-9f29-8da67caed901/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445115.1_52121_E02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:59,515] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:59,519] [INFO] Selected 8 target genomes.
[2024-01-24 12:40:59,519] [INFO] Target genome list was writen to GCF_900445115.1_52121_E02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:59,526] [INFO] Task started: fastANI
[2024-01-24 12:40:59,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg90da1087-0db6-4f02-bbfe-a4312c441574/GCF_900445115.1_52121_E02_genomic.fna.gz --refList GCF_900445115.1_52121_E02_genomic.fna/target_genomes_gtdb.txt --output GCF_900445115.1_52121_E02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:08,922] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:08,933] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:08,933] [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_001643305.1	s__Aeromonas salmonicida	99.9119	1514	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.08	96.89	0.95	0.86	74	conclusive
GCF_000820005.1	s__Aeromonas piscicola	92.022	1324	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.81	97.81	0.93	0.93	2	-
GCF_000819745.1	s__Aeromonas bestiarum	91.261	1296	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_000820025.1	s__Aeromonas popoffii	89.9463	1201	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.17	98.00	0.92	0.89	4	-
GCF_900637545.1	s__Aeromonas encheleia	87.1934	1204	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.38	97.80	0.95	0.91	5	-
GCF_000764655.1	s__Aeromonas aquatica	86.4453	1147	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764645.1	s__Aeromonas finlandensis	86.233	1055	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000388115.1	s__Aeromonas molluscorum	83.9152	935	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:08,934] [INFO] GTDB search result was written to GCF_900445115.1_52121_E02_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:08,935] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:08,938] [INFO] DFAST_QC result json was written to GCF_900445115.1_52121_E02_genomic.fna/dqc_result.json
[2024-01-24 12:41:08,938] [INFO] DFAST_QC completed!
[2024-01-24 12:41:08,938] [INFO] Total running time: 0h1m27s