[2024-01-25 20:01:50,790] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:50,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:50,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg791005c0-d0ac-4564-95c7-f1a54212e8cf/dqc_reference
[2024-01-25 20:01:51,945] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:51,946] [INFO] Task started: Prodigal
[2024-01-25 20:01:51,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg029f9cb6-11de-489c-9b75-0658f6f3dc73/GCF_014652715.1_ASM1465271v1_genomic.fna.gz | prodigal -d GCF_014652715.1_ASM1465271v1_genomic.fna/cds.fna -a GCF_014652715.1_ASM1465271v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:02,497] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:02,497] [INFO] Task started: HMMsearch
[2024-01-25 20:02:02,497] [INFO] Running command: hmmsearch --tblout GCF_014652715.1_ASM1465271v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg791005c0-d0ac-4564-95c7-f1a54212e8cf/dqc_reference/reference_markers.hmm GCF_014652715.1_ASM1465271v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:02,722] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:02,723] [INFO] Found 6/6 markers.
[2024-01-25 20:02:02,756] [INFO] Query marker FASTA was written to GCF_014652715.1_ASM1465271v1_genomic.fna/markers.fasta
[2024-01-25 20:02:02,757] [INFO] Task started: Blastn
[2024-01-25 20:02:02,757] [INFO] Running command: blastn -query GCF_014652715.1_ASM1465271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg791005c0-d0ac-4564-95c7-f1a54212e8cf/dqc_reference/reference_markers.fasta -out GCF_014652715.1_ASM1465271v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:03,555] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:03,559] [INFO] Selected 21 target genomes.
[2024-01-25 20:02:03,560] [INFO] Target genome list was writen to GCF_014652715.1_ASM1465271v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:03,567] [INFO] Task started: fastANI
[2024-01-25 20:02:03,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg029f9cb6-11de-489c-9b75-0658f6f3dc73/GCF_014652715.1_ASM1465271v1_genomic.fna.gz --refList GCF_014652715.1_ASM1465271v1_genomic.fna/target_genomes.txt --output GCF_014652715.1_ASM1465271v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:21,217] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:21,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg791005c0-d0ac-4564-95c7-f1a54212e8cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:21,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg791005c0-d0ac-4564-95c7-f1a54212e8cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:21,232] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:21,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:21,232] [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
Salinicola rhizosphaerae	strain=KCTC 32998	GCA_014652715.1	1443141	1443141	type	True	100.0	1394	1394	95	conclusive
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	81.5654	815	1394	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	81.2435	823	1394	95	below_threshold
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	81.2302	885	1394	95	below_threshold
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	81.1836	801	1394	95	below_threshold
Salinicola tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	81.1702	814	1394	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	81.1604	878	1394	95	below_threshold
Salinicola halophilus	strain=CECT 5903	GCA_003206155.1	184065	184065	type	True	80.5552	720	1394	95	below_threshold
Salinicola halimionae	strain=CPA60	GCA_003206065.1	1949081	1949081	type	True	80.2902	759	1394	95	below_threshold
Salinicola aestuarinus	strain=CPA62	GCA_003206645.1	1949082	1949082	type	True	80.1374	703	1394	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	79.143	409	1394	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.7534	368	1394	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	78.7528	352	1394	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	78.7457	414	1394	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	78.6747	407	1394	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.619	397	1394	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	78.4895	369	1394	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	78.4384	379	1394	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_002879635.1	1684789	1684789	type	True	78.3168	294	1394	95	below_threshold
Chromohalobacter nigrandesensis	strain=DSM 14323	GCA_023061285.1	119863	119863	type	True	78.23	369	1394	95	below_threshold
Kushneria avicenniae	strain=DSM 23439	GCA_900112585.1	402385	402385	type	True	77.7659	290	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:21,233] [INFO] DFAST Taxonomy check result was written to GCF_014652715.1_ASM1465271v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:21,234] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:21,234] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:21,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg791005c0-d0ac-4564-95c7-f1a54212e8cf/dqc_reference/checkm_data
[2024-01-25 20:02:21,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:21,278] [INFO] Task started: CheckM
[2024-01-25 20:02:21,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652715.1_ASM1465271v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652715.1_ASM1465271v1_genomic.fna/checkm_input GCF_014652715.1_ASM1465271v1_genomic.fna/checkm_result
[2024-01-25 20:02:55,413] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:55,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:55,429] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:55,430] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:55,430] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652715.1_ASM1465271v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:55,430] [INFO] Task started: Blastn
[2024-01-25 20:02:55,430] [INFO] Running command: blastn -query GCF_014652715.1_ASM1465271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg791005c0-d0ac-4564-95c7-f1a54212e8cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652715.1_ASM1465271v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:56,860] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:56,862] [INFO] Selected 18 target genomes.
[2024-01-25 20:02:56,862] [INFO] Target genome list was writen to GCF_014652715.1_ASM1465271v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:56,867] [INFO] Task started: fastANI
[2024-01-25 20:02:56,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg029f9cb6-11de-489c-9b75-0658f6f3dc73/GCF_014652715.1_ASM1465271v1_genomic.fna.gz --refList GCF_014652715.1_ASM1465271v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652715.1_ASM1465271v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:13,359] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:13,370] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:13,370] [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_014652715.1	s__Salinicola rhizosphaerae	100.0	1394	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003206135.1	s__Salinicola salarius	81.5826	813	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.80	97.80	0.89	0.89	2	-
GCA_000737985.1	s__Salinicola sp000737985	81.4909	852	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.18	96.18	0.88	0.88	2	-
GCA_002695065.1	s__Salinicola sp002695065	81.2674	844	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	-
GCF_003206045.1	s__Salinicola lusitanus	81.2332	885	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCF_003206575.1	s__Salinicola endophyticus	81.2125	826	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
GCF_003206715.1	s__Salinicola peritrichatus	81.2003	799	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003006155.1	s__Salinicola tamaricis	81.1585	817	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.82	99.82	0.99	0.99	2	-
GCF_003206615.1	s__Salinicola acroporae	81.1424	881	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002179555.1	s__Salinicola salarius_A	81.13	805	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298015.1	s__Salinicola sp008298015	80.9722	848	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206695.1	s__Salinicola halophyticus	80.8049	834	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.72	97.72	0.93	0.93	2	-
GCF_001937195.1	s__Salinicola socius	80.757	859	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_003206155.1	s__Salinicola halophilus	80.5467	721	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206065.1	s__Salinicola halimionae	80.2998	759	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206645.1	s__Salinicola aestuarinus	80.1163	706	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286975.1	s__Halomonas_B sp002286975	78.7356	415	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003560175.1	s__Halomonas sp003560175	77.9353	189	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:13,371] [INFO] GTDB search result was written to GCF_014652715.1_ASM1465271v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:13,372] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:13,375] [INFO] DFAST_QC result json was written to GCF_014652715.1_ASM1465271v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:13,375] [INFO] DFAST_QC completed!
[2024-01-25 20:03:13,376] [INFO] Total running time: 0h1m23s