[2024-01-25 19:06:20,665] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:20,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:20,666] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6b3fa68-ee29-4925-bd51-fc0a298996a9/dqc_reference
[2024-01-25 19:06:21,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:21,791] [INFO] Task started: Prodigal
[2024-01-25 19:06:21,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg9dffc619-a7c5-4220-a581-1efe59db5402/GCF_000520015.2_ASM52001v2_genomic.fna.gz | prodigal -d GCF_000520015.2_ASM52001v2_genomic.fna/cds.fna -a GCF_000520015.2_ASM52001v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:35,602] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:35,602] [INFO] Task started: HMMsearch
[2024-01-25 19:06:35,602] [INFO] Running command: hmmsearch --tblout GCF_000520015.2_ASM52001v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6b3fa68-ee29-4925-bd51-fc0a298996a9/dqc_reference/reference_markers.hmm GCF_000520015.2_ASM52001v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:35,906] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:35,907] [INFO] Found 6/6 markers.
[2024-01-25 19:06:35,954] [INFO] Query marker FASTA was written to GCF_000520015.2_ASM52001v2_genomic.fna/markers.fasta
[2024-01-25 19:06:35,955] [INFO] Task started: Blastn
[2024-01-25 19:06:35,955] [INFO] Running command: blastn -query GCF_000520015.2_ASM52001v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6b3fa68-ee29-4925-bd51-fc0a298996a9/dqc_reference/reference_markers.fasta -out GCF_000520015.2_ASM52001v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:36,737] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:36,740] [INFO] Selected 25 target genomes.
[2024-01-25 19:06:36,740] [INFO] Target genome list was writen to GCF_000520015.2_ASM52001v2_genomic.fna/target_genomes.txt
[2024-01-25 19:06:36,757] [INFO] Task started: fastANI
[2024-01-25 19:06:36,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dffc619-a7c5-4220-a581-1efe59db5402/GCF_000520015.2_ASM52001v2_genomic.fna.gz --refList GCF_000520015.2_ASM52001v2_genomic.fna/target_genomes.txt --output GCF_000520015.2_ASM52001v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:58,693] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:58,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6b3fa68-ee29-4925-bd51-fc0a298996a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:58,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6b3fa68-ee29-4925-bd51-fc0a298996a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:58,705] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:06:58,705] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:58,705] [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
Chania multitudinisentens	strain=RB-25	GCA_000520015.2	1639108	1639108	type	True	100.0	1828	1829	95	conclusive
Chania multitudinisentens	strain=RB-25	GCA_000568195.1	1639108	1639108	type	True	99.955	1769	1829	95	conclusive
Serratia fonticola	strain=DSM 4576	GCA_001006005.1	47917	47917	suspected-type	True	81.887	1001	1829	95	below_threshold
Serratia fonticola	strain=LMG 7882	GCA_000469035.1	47917	47917	suspected-type	True	81.7484	933	1829	95	below_threshold
Serratia plymuthica	strain=FDAARGOS_895	GCA_016027675.1	82996	82996	type	True	81.2374	806	1829	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	81.1707	781	1829	95	below_threshold
Serratia grimesii	strain=NCTC11543	GCA_900456935.1	82995	82995	type	True	81.1632	755	1829	95	below_threshold
Serratia proteamaculans	strain=CCUG 14510	GCA_008830365.1	28151	28151	type	True	81.0546	794	1829	95	below_threshold
Serratia plymuthica	strain=NBRC 102599	GCA_001590925.1	82996	82996	type	True	81.012	788	1829	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	80.8559	738	1829	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	80.7723	723	1829	95	below_threshold
Serratia rubidaea	strain=CIP 103234	GCA_001304675.1	61652	61652	type	True	80.3789	653	1829	95	below_threshold
Gibbsiella quercinecans	strain=FRB97	GCA_003666185.1	929813	929813	type	True	80.2536	655	1829	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	78.9819	416	1829	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.7166	376	1829	95	below_threshold
Edwardsiella anguillarum	strain=ET080813	GCA_000264765.2	1821960	1821960	type	True	78.4404	277	1829	95	below_threshold
Edwardsiella anguillarum	strain=CCUG 64215	GCA_008801815.1	1821960	1821960	type	True	77.883	265	1829	95	below_threshold
Photobacterium ganghwense	strain=DSM 22954	GCA_001029455.1	320778	320778	type	True	76.5665	87	1829	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	76.3628	87	1829	95	below_threshold
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	76.1013	72	1829	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:58,707] [INFO] DFAST Taxonomy check result was written to GCF_000520015.2_ASM52001v2_genomic.fna/tc_result.tsv
[2024-01-25 19:06:58,708] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:58,708] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:58,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6b3fa68-ee29-4925-bd51-fc0a298996a9/dqc_reference/checkm_data
[2024-01-25 19:06:58,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:58,762] [INFO] Task started: CheckM
[2024-01-25 19:06:58,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000520015.2_ASM52001v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000520015.2_ASM52001v2_genomic.fna/checkm_input GCF_000520015.2_ASM52001v2_genomic.fna/checkm_result
[2024-01-25 19:07:41,115] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:41,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:41,134] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:41,134] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:41,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000520015.2_ASM52001v2_genomic.fna/markers.fasta)
[2024-01-25 19:07:41,135] [INFO] Task started: Blastn
[2024-01-25 19:07:41,135] [INFO] Running command: blastn -query GCF_000520015.2_ASM52001v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6b3fa68-ee29-4925-bd51-fc0a298996a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000520015.2_ASM52001v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:42,195] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:42,198] [INFO] Selected 17 target genomes.
[2024-01-25 19:07:42,198] [INFO] Target genome list was writen to GCF_000520015.2_ASM52001v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:42,218] [INFO] Task started: fastANI
[2024-01-25 19:07:42,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dffc619-a7c5-4220-a581-1efe59db5402/GCF_000520015.2_ASM52001v2_genomic.fna.gz --refList GCF_000520015.2_ASM52001v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000520015.2_ASM52001v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:01,977] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:01,985] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:01,985] [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_000520015.2	s__Chania multitudinisentens	100.0	1828	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001976145.1	s__Chania oryzae	84.0938	1140	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	-
GCF_000743355.1	s__Chania sp000743355	83.2506	1129	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	99.97	99.97	0.98	0.98	2	-
GCF_006715025.1	s__Serratia_A fonticola_A	81.882	963	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	4	-
GCF_001006005.1	s__Serratia_A fonticola	81.88	1000	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	96.10	95.03	0.87	0.81	45	-
GCF_000633355.1	s__Serratia_A sp000633355	81.7576	964	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018336935.1	s__Serratia plymuthica_B	81.4574	815	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187015.1	s__Serratia ficaria	81.3352	771	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_002220655.1	s__Serratia marcescens_K	81.0425	765	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
GCF_000496755.2	s__Serratia_A sp000496755	79.7004	630	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095535.1	s__Pantoea cypripedii	78.2437	344	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_010131535.1	s__Acerihabitans arboris	77.8322	294	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025595.1	s__Photobacterium ganghwense	76.3953	87	1829	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:08:01,987] [INFO] GTDB search result was written to GCF_000520015.2_ASM52001v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:01,987] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:01,990] [INFO] DFAST_QC result json was written to GCF_000520015.2_ASM52001v2_genomic.fna/dqc_result.json
[2024-01-25 19:08:01,991] [INFO] DFAST_QC completed!
[2024-01-25 19:08:01,991] [INFO] Total running time: 0h1m41s