[2024-01-24 14:15:34,244] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,247] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg06d611ed-ac18-47e6-bea2-e719928bde90/dqc_reference
[2024-01-24 14:15:35,699] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,716] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,716] [INFO] Running command: gunzip -c /var/lib/cwl/stgc51e666b-fbf0-4563-809e-4765235ac940/GCF_000820145.1_PRJEB7040_genomic.fna.gz | prodigal -d GCF_000820145.1_PRJEB7040_genomic.fna/cds.fna -a GCF_000820145.1_PRJEB7040_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:50,033] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:50,034] [INFO] Task started: HMMsearch
[2024-01-24 14:15:50,034] [INFO] Running command: hmmsearch --tblout GCF_000820145.1_PRJEB7040_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06d611ed-ac18-47e6-bea2-e719928bde90/dqc_reference/reference_markers.hmm GCF_000820145.1_PRJEB7040_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:50,419] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:50,420] [INFO] Found 6/6 markers.
[2024-01-24 14:15:50,471] [INFO] Query marker FASTA was written to GCF_000820145.1_PRJEB7040_genomic.fna/markers.fasta
[2024-01-24 14:15:50,478] [INFO] Task started: Blastn
[2024-01-24 14:15:50,478] [INFO] Running command: blastn -query GCF_000820145.1_PRJEB7040_genomic.fna/markers.fasta -db /var/lib/cwl/stg06d611ed-ac18-47e6-bea2-e719928bde90/dqc_reference/reference_markers.fasta -out GCF_000820145.1_PRJEB7040_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:51,433] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:51,436] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:51,437] [INFO] Target genome list was writen to GCF_000820145.1_PRJEB7040_genomic.fna/target_genomes.txt
[2024-01-24 14:15:51,446] [INFO] Task started: fastANI
[2024-01-24 14:15:51,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgc51e666b-fbf0-4563-809e-4765235ac940/GCF_000820145.1_PRJEB7040_genomic.fna.gz --refList GCF_000820145.1_PRJEB7040_genomic.fna/target_genomes.txt --output GCF_000820145.1_PRJEB7040_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:09,664] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:09,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06d611ed-ac18-47e6-bea2-e719928bde90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:09,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06d611ed-ac18-47e6-bea2-e719928bde90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:09,681] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:16:09,681] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:09,682] [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 sobria	strain=CECT 4245	GCA_000820145.1	646	646	suspected-type	True	100.0	1538	1541	95	conclusive
Aeromonas sobria	strain=CIP 74.33	GCA_018359945.1	646	646	suspected-type	True	99.996	1520	1541	95	conclusive
Aeromonas finlandensis	strain=4287D	GCA_000764645.1	1543375	1543375	type	True	92.066	1146	1541	95	below_threshold
Aeromonas allosaccharophila	strain=CECT 4199	GCA_000819685.1	656	656	type	True	91.9892	1238	1541	95	below_threshold
Aeromonas veronii	strain=CECT 4257	GCA_000820225.1	654	654	type	True	91.7401	1269	1541	95	below_threshold
Aeromonas veronii	strain=ATCC 35624	GCA_018359905.1	654	654	type	True	91.675	1279	1541	95	below_threshold
Aeromonas fluvialis	strain=LMG 24681	GCA_000819885.1	591962	591962	type	True	90.3257	1086	1541	95	below_threshold
Aeromonas popoffii	strain=CIP 105493	GCA_000820025.1	70856	70856	type	True	87.0304	1126	1541	95	below_threshold
Aeromonas piscicola	strain=LMG 24783	GCA_000820005.1	600645	600645	type	True	86.811	1192	1541	95	below_threshold
Aeromonas salmonicida subsp. masoucida	strain=NBRC 13784	GCA_000647955.1	197700	645	type	True	86.0731	1042	1541	95	below_threshold
Aeromonas salmonicida	strain=NCTC12959	GCA_900445115.1	645	645	type	True	85.9487	1114	1541	95	below_threshold
Aeromonas aquatica	strain=AE235	GCA_000764655.1	558964	558964	type	True	84.8876	1054	1541	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	76.7992	128	1541	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.2545	114	1541	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.2464	123	1541	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.2374	116	1541	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.1124	119	1541	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:09,683] [INFO] DFAST Taxonomy check result was written to GCF_000820145.1_PRJEB7040_genomic.fna/tc_result.tsv
[2024-01-24 14:16:09,684] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:09,684] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:09,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06d611ed-ac18-47e6-bea2-e719928bde90/dqc_reference/checkm_data
[2024-01-24 14:16:09,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:09,736] [INFO] Task started: CheckM
[2024-01-24 14:16:09,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000820145.1_PRJEB7040_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000820145.1_PRJEB7040_genomic.fna/checkm_input GCF_000820145.1_PRJEB7040_genomic.fna/checkm_result
[2024-01-24 14:16:56,853] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:56,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:56,878] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:56,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:56,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000820145.1_PRJEB7040_genomic.fna/markers.fasta)
[2024-01-24 14:16:56,879] [INFO] Task started: Blastn
[2024-01-24 14:16:56,879] [INFO] Running command: blastn -query GCF_000820145.1_PRJEB7040_genomic.fna/markers.fasta -db /var/lib/cwl/stg06d611ed-ac18-47e6-bea2-e719928bde90/dqc_reference/reference_markers_gtdb.fasta -out GCF_000820145.1_PRJEB7040_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:58,356] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:58,360] [INFO] Selected 12 target genomes.
[2024-01-24 14:16:58,360] [INFO] Target genome list was writen to GCF_000820145.1_PRJEB7040_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:58,369] [INFO] Task started: fastANI
[2024-01-24 14:16:58,369] [INFO] Running command: fastANI --query /var/lib/cwl/stgc51e666b-fbf0-4563-809e-4765235ac940/GCF_000820145.1_PRJEB7040_genomic.fna.gz --refList GCF_000820145.1_PRJEB7040_genomic.fna/target_genomes_gtdb.txt --output GCF_000820145.1_PRJEB7040_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:11,947] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:11,957] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:11,958] [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_000820145.1	s__Aeromonas sobria	100.0	1538	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.57	95.21	0.89	0.85	13	conclusive
GCF_000764645.1	s__Aeromonas finlandensis	92.0744	1146	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819685.1	s__Aeromonas allosaccharophila	91.9892	1238	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.32	95.53	0.87	0.85	15	-
GCF_000820225.1	s__Aeromonas veronii	91.7435	1268	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.54	96.01	0.90	0.86	159	-
GCF_019048265.1	s__Aeromonas veronii_A	91.1273	1244	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	96.07	95.82	0.91	0.90	4	-
GCF_000819885.1	s__Aeromonas fluvialis	90.3257	1086	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204135.1	s__Aeromonas fluvialis_A	89.3617	1115	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820025.1	s__Aeromonas popoffii	87.008	1128	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	98.17	98.00	0.92	0.89	4	-
GCF_000820005.1	s__Aeromonas piscicola	86.8062	1192	1541	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	86.6501	1144	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.5033	97.44	97.31	0.93	0.91	4	-
GCF_001643305.1	s__Aeromonas salmonicida	85.908	1101	1541	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Aeromonas	95.0	99.08	96.89	0.95	0.86	74	-
GCF_000764655.1	s__Aeromonas aquatica	84.88	1056	1541	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 14:17:11,960] [INFO] GTDB search result was written to GCF_000820145.1_PRJEB7040_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:11,960] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:11,965] [INFO] DFAST_QC result json was written to GCF_000820145.1_PRJEB7040_genomic.fna/dqc_result.json
[2024-01-24 14:17:11,966] [INFO] DFAST_QC completed!
[2024-01-24 14:17:11,966] [INFO] Total running time: 0h1m38s