[2024-01-24 14:47:18,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:18,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:18,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cf7effc-f86b-4f7c-b79a-7441c7ceee39/dqc_reference
[2024-01-24 14:47:20,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:20,224] [INFO] Task started: Prodigal
[2024-01-24 14:47:20,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a11944b-5e0e-4cea-89ac-2ca238b7a345/GCF_001995255.1_Tv_HL17_v1_genomic.fna.gz | prodigal -d GCF_001995255.1_Tv_HL17_v1_genomic.fna/cds.fna -a GCF_001995255.1_Tv_HL17_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:28,814] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:28,814] [INFO] Task started: HMMsearch
[2024-01-24 14:47:28,814] [INFO] Running command: hmmsearch --tblout GCF_001995255.1_Tv_HL17_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cf7effc-f86b-4f7c-b79a-7441c7ceee39/dqc_reference/reference_markers.hmm GCF_001995255.1_Tv_HL17_v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:29,078] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:29,079] [INFO] Found 6/6 markers.
[2024-01-24 14:47:29,107] [INFO] Query marker FASTA was written to GCF_001995255.1_Tv_HL17_v1_genomic.fna/markers.fasta
[2024-01-24 14:47:29,108] [INFO] Task started: Blastn
[2024-01-24 14:47:29,108] [INFO] Running command: blastn -query GCF_001995255.1_Tv_HL17_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cf7effc-f86b-4f7c-b79a-7441c7ceee39/dqc_reference/reference_markers.fasta -out GCF_001995255.1_Tv_HL17_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:30,169] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:30,173] [INFO] Selected 16 target genomes.
[2024-01-24 14:47:30,173] [INFO] Target genome list was writen to GCF_001995255.1_Tv_HL17_v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:30,180] [INFO] Task started: fastANI
[2024-01-24 14:47:30,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a11944b-5e0e-4cea-89ac-2ca238b7a345/GCF_001995255.1_Tv_HL17_v1_genomic.fna.gz --refList GCF_001995255.1_Tv_HL17_v1_genomic.fna/target_genomes.txt --output GCF_001995255.1_Tv_HL17_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:41,315] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:41,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cf7effc-f86b-4f7c-b79a-7441c7ceee39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:41,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cf7effc-f86b-4f7c-b79a-7441c7ceee39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:41,328] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:41,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:41,328] [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
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	100.0	907	909	95	conclusive
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	81.7035	483	909	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	81.5165	524	909	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	78.8654	297	909	95	below_threshold
Thioalkalivibrio nitratireducens	strain=DSM 14787	GCA_000321415.2	186931	186931	type	True	78.4658	299	909	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	78.411	281	909	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.0167	155	909	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.975	161	909	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.889	129	909	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	76.8062	104	909	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.7819	145	909	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	76.7665	104	909	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.6777	142	909	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.449	163	909	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.4435	164	909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:41,330] [INFO] DFAST Taxonomy check result was written to GCF_001995255.1_Tv_HL17_v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:41,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:41,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:41,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cf7effc-f86b-4f7c-b79a-7441c7ceee39/dqc_reference/checkm_data
[2024-01-24 14:47:41,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:41,371] [INFO] Task started: CheckM
[2024-01-24 14:47:41,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001995255.1_Tv_HL17_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001995255.1_Tv_HL17_v1_genomic.fna/checkm_input GCF_001995255.1_Tv_HL17_v1_genomic.fna/checkm_result
[2024-01-24 14:48:13,450] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:13,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:13,477] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:13,478] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:13,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001995255.1_Tv_HL17_v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:13,478] [INFO] Task started: Blastn
[2024-01-24 14:48:13,478] [INFO] Running command: blastn -query GCF_001995255.1_Tv_HL17_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cf7effc-f86b-4f7c-b79a-7441c7ceee39/dqc_reference/reference_markers_gtdb.fasta -out GCF_001995255.1_Tv_HL17_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:15,508] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:15,513] [INFO] Selected 11 target genomes.
[2024-01-24 14:48:15,513] [INFO] Target genome list was writen to GCF_001995255.1_Tv_HL17_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:15,535] [INFO] Task started: fastANI
[2024-01-24 14:48:15,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a11944b-5e0e-4cea-89ac-2ca238b7a345/GCF_001995255.1_Tv_HL17_v1_genomic.fna.gz --refList GCF_001995255.1_Tv_HL17_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001995255.1_Tv_HL17_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:22,928] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:22,938] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:22,938] [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_001995255.1	s__Thioalkalivibrio halophilus	100.0	907	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	96.06	95.07	0.84	0.81	11	conclusive
GCF_000381945.1	s__Thioalkalivibrio sp000381945	89.5733	733	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377785.1	s__Thioalkalivibrio sp000377785	89.1754	696	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376845.1	s__Thioalkalivibrio sp000376845	82.3538	552	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	99.89	99.89	0.97	0.97	2	-
GCF_000377345.1	s__Thioalkalivibrio sp000377345	81.9143	539	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420165.1	s__Thioalkalivibrio sp000420165	81.8917	529	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377905.1	s__Thioalkalivibrio sp000377905	81.8913	560	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377405.1	s__Thioalkalivibrio sp000377405	81.7798	540	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.90	97.79	0.93	0.92	11	-
GCF_000385215.1	s__Thioalkalivibrio thiocyanoxidans	81.717	481	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	99.32	98.64	0.97	0.95	3	-
GCF_000381825.1	s__Thioalkalivibrio sp000381825	81.3654	480	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377205.1	s__Thioalkalivibrio sp000377205	81.3137	468	909	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	99.40	99.38	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:22,940] [INFO] GTDB search result was written to GCF_001995255.1_Tv_HL17_v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:22,941] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:22,947] [INFO] DFAST_QC result json was written to GCF_001995255.1_Tv_HL17_v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:22,947] [INFO] DFAST_QC completed!
[2024-01-24 14:48:22,948] [INFO] Total running time: 0h1m4s