[2024-01-24 14:22:33,211] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,213] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,213] [INFO] DQC Reference Directory: /var/lib/cwl/stg8258ba23-2526-4118-87ff-b4b87dff1e81/dqc_reference
[2024-01-24 14:22:34,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,563] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg8de6a161-8b3b-40c1-ad75-ecb6f4707bc4/GCF_014651775.1_ASM1465177v1_genomic.fna.gz | prodigal -d GCF_014651775.1_ASM1465177v1_genomic.fna/cds.fna -a GCF_014651775.1_ASM1465177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:46,660] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:46,660] [INFO] Task started: HMMsearch
[2024-01-24 14:22:46,660] [INFO] Running command: hmmsearch --tblout GCF_014651775.1_ASM1465177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8258ba23-2526-4118-87ff-b4b87dff1e81/dqc_reference/reference_markers.hmm GCF_014651775.1_ASM1465177v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:47,166] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:47,167] [INFO] Found 6/6 markers.
[2024-01-24 14:22:47,250] [INFO] Query marker FASTA was written to GCF_014651775.1_ASM1465177v1_genomic.fna/markers.fasta
[2024-01-24 14:22:47,250] [INFO] Task started: Blastn
[2024-01-24 14:22:47,250] [INFO] Running command: blastn -query GCF_014651775.1_ASM1465177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8258ba23-2526-4118-87ff-b4b87dff1e81/dqc_reference/reference_markers.fasta -out GCF_014651775.1_ASM1465177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:48,648] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:48,651] [INFO] Selected 17 target genomes.
[2024-01-24 14:22:48,651] [INFO] Target genome list was writen to GCF_014651775.1_ASM1465177v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:48,661] [INFO] Task started: fastANI
[2024-01-24 14:22:48,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg8de6a161-8b3b-40c1-ad75-ecb6f4707bc4/GCF_014651775.1_ASM1465177v1_genomic.fna.gz --refList GCF_014651775.1_ASM1465177v1_genomic.fna/target_genomes.txt --output GCF_014651775.1_ASM1465177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:03,263] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:03,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8258ba23-2526-4118-87ff-b4b87dff1e81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:03,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8258ba23-2526-4118-87ff-b4b87dff1e81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:03,283] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:23:03,283] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:23:03,284] [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
Halomonas hamiltonii	strain=KCTC 22154	GCA_014651775.1	502829	502829	type	True	100.0	1276	1277	95	inconclusive
Halomonas johnsoniae	strain=KCTC 22157	GCA_014651795.1	502832	502832	type	True	97.5135	1103	1277	95	inconclusive
Halomonas stevensii	strain=S18214	GCA_000275725.1	502821	502821	type	True	95.6707	1062	1277	95	inconclusive
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	84.05	696	1277	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	83.989	735	1277	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	83.8037	706	1277	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	82.9721	834	1277	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	82.94	825	1277	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	82.139	793	1277	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	80.6292	655	1277	95	below_threshold
Halomonas humidisoli	strain=WN018	GCA_002286955.1	2032624	2032624	type	True	79.6232	521	1277	95	below_threshold
Halomonas alkaliphila	strain=DSM 16354	GCA_016107625.1	272774	272774	type	True	79.3568	496	1277	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.965	476	1277	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.9099	466	1277	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.7114	435	1277	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.5084	487	1277	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.4179	392	1277	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:03,286] [INFO] DFAST Taxonomy check result was written to GCF_014651775.1_ASM1465177v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:03,287] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:03,287] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:03,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8258ba23-2526-4118-87ff-b4b87dff1e81/dqc_reference/checkm_data
[2024-01-24 14:23:03,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:03,331] [INFO] Task started: CheckM
[2024-01-24 14:23:03,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651775.1_ASM1465177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651775.1_ASM1465177v1_genomic.fna/checkm_input GCF_014651775.1_ASM1465177v1_genomic.fna/checkm_result
[2024-01-24 14:23:41,713] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:41,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:41,738] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:41,739] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:41,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651775.1_ASM1465177v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:41,740] [INFO] Task started: Blastn
[2024-01-24 14:23:41,740] [INFO] Running command: blastn -query GCF_014651775.1_ASM1465177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8258ba23-2526-4118-87ff-b4b87dff1e81/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651775.1_ASM1465177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:43,333] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:43,337] [INFO] Selected 11 target genomes.
[2024-01-24 14:23:43,338] [INFO] Target genome list was writen to GCF_014651775.1_ASM1465177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:43,348] [INFO] Task started: fastANI
[2024-01-24 14:23:43,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg8de6a161-8b3b-40c1-ad75-ecb6f4707bc4/GCF_014651775.1_ASM1465177v1_genomic.fna.gz --refList GCF_014651775.1_ASM1465177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651775.1_ASM1465177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:52,760] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:52,771] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:52,772] [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_014651775.1	s__Halomonas hamiltonii	100.0	1276	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	conclusive
GCF_000275725.1	s__Halomonas stevensii	95.6707	1062	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_900110265.1	s__Halomonas aquamarina	83.8024	707	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_012427705.1	s__Halomonas piezotolerans	82.9672	835	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_009846525.1	s__Halomonas sp002696125	82.6861	795	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_002087295.1	s__Halomonas lionensis	82.3639	663	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640815.1	s__Halomonas lutescens	82.1382	793	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002925.1	s__Halomonas songnenensis	80.6292	655	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107625.1	s__Halomonas alkaliphila	79.3568	496	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	96.32	95.46	0.84	0.80	12	-
GCF_007989465.1	s__Halomonas halophila	78.9681	404	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_003202205.1	s__Halomonas sp003202205	78.829	475	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:52,774] [INFO] GTDB search result was written to GCF_014651775.1_ASM1465177v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:52,775] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:52,782] [INFO] DFAST_QC result json was written to GCF_014651775.1_ASM1465177v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:52,782] [INFO] DFAST_QC completed!
[2024-01-24 14:23:52,782] [INFO] Total running time: 0h1m20s