[2024-01-25 20:15:35,638] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:35,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:35,644] [INFO] DQC Reference Directory: /var/lib/cwl/stg31422514-f6ed-462f-be2e-da13ad6b2339/dqc_reference
[2024-01-25 20:15:36,854] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:36,855] [INFO] Task started: Prodigal
[2024-01-25 20:15:36,855] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbd2b923-cb1f-46c2-b032-17729642374d/GCF_002286975.1_ASM228697v1_genomic.fna.gz | prodigal -d GCF_002286975.1_ASM228697v1_genomic.fna/cds.fna -a GCF_002286975.1_ASM228697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:51,546] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:51,547] [INFO] Task started: HMMsearch
[2024-01-25 20:15:51,547] [INFO] Running command: hmmsearch --tblout GCF_002286975.1_ASM228697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31422514-f6ed-462f-be2e-da13ad6b2339/dqc_reference/reference_markers.hmm GCF_002286975.1_ASM228697v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:51,821] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:51,822] [INFO] Found 6/6 markers.
[2024-01-25 20:15:51,870] [INFO] Query marker FASTA was written to GCF_002286975.1_ASM228697v1_genomic.fna/markers.fasta
[2024-01-25 20:15:51,871] [INFO] Task started: Blastn
[2024-01-25 20:15:51,871] [INFO] Running command: blastn -query GCF_002286975.1_ASM228697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31422514-f6ed-462f-be2e-da13ad6b2339/dqc_reference/reference_markers.fasta -out GCF_002286975.1_ASM228697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:52,722] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:52,725] [INFO] Selected 25 target genomes.
[2024-01-25 20:15:52,725] [INFO] Target genome list was writen to GCF_002286975.1_ASM228697v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:52,733] [INFO] Task started: fastANI
[2024-01-25 20:15:52,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbd2b923-cb1f-46c2-b032-17729642374d/GCF_002286975.1_ASM228697v1_genomic.fna.gz --refList GCF_002286975.1_ASM228697v1_genomic.fna/target_genomes.txt --output GCF_002286975.1_ASM228697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:17,032] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:17,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31422514-f6ed-462f-be2e-da13ad6b2339/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:17,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31422514-f6ed-462f-be2e-da13ad6b2339/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:17,047] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:16:17,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:17,048] [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 salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	100.0	1808	1810	95	conclusive
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	88.8866	1208	1810	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	83.0752	828	1810	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	82.8258	771	1810	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	82.7822	886	1810	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	82.7157	868	1810	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	82.7088	799	1810	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	82.7076	754	1810	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	82.4811	758	1810	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	82.4055	866	1810	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	82.2679	856	1810	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	82.2355	781	1810	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	82.2342	720	1810	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	82.1725	676	1810	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	82.0392	859	1810	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.9998	899	1810	95	below_threshold
Halomonas montanilacus	strain=PYC7W	GCA_003336675.1	2282305	2282305	type	True	81.7472	831	1810	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	81.6265	811	1810	95	below_threshold
Halomonas cerina	strain=CECT 7282	GCA_014192215.1	447424	447424	type	True	81.2284	677	1810	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	81.2144	708	1810	95	below_threshold
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	80.8829	601	1810	95	below_threshold
Halomonas xinjiangensis	strain=TRM 0175	GCA_000759345.1	1166948	1166948	type	True	79.6244	543	1810	95	below_threshold
Tepidimonas charontis	strain=SPSP-6	GCA_007556685.1	2267262	2267262	type	True	76.2859	96	1810	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	75.8385	214	1810	95	below_threshold
Tepidimonas thermarum	strain=AA-1	GCA_007556705.1	335431	335431	type	True	75.7787	125	1810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:17,049] [INFO] DFAST Taxonomy check result was written to GCF_002286975.1_ASM228697v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:17,049] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:17,050] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:17,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31422514-f6ed-462f-be2e-da13ad6b2339/dqc_reference/checkm_data
[2024-01-25 20:16:17,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:17,100] [INFO] Task started: CheckM
[2024-01-25 20:16:17,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002286975.1_ASM228697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002286975.1_ASM228697v1_genomic.fna/checkm_input GCF_002286975.1_ASM228697v1_genomic.fna/checkm_result
[2024-01-25 20:16:59,199] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:59,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:59,217] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:59,217] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:59,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002286975.1_ASM228697v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:59,218] [INFO] Task started: Blastn
[2024-01-25 20:16:59,218] [INFO] Running command: blastn -query GCF_002286975.1_ASM228697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31422514-f6ed-462f-be2e-da13ad6b2339/dqc_reference/reference_markers_gtdb.fasta -out GCF_002286975.1_ASM228697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:00,745] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:00,749] [INFO] Selected 11 target genomes.
[2024-01-25 20:17:00,749] [INFO] Target genome list was writen to GCF_002286975.1_ASM228697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:00,757] [INFO] Task started: fastANI
[2024-01-25 20:17:00,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbd2b923-cb1f-46c2-b032-17729642374d/GCF_002286975.1_ASM228697v1_genomic.fna.gz --refList GCF_002286975.1_ASM228697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002286975.1_ASM228697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:13,603] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:13,611] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:13,611] [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_002286975.1	s__Halomonas_B sp002286975	100.0	1808	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010977575.1	s__Halomonas_B socia	93.1875	1285	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	91.2031	1119	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102875.1	s__Halomonas_B pantelleriensis	88.8721	1209	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779595.1	s__Halomonas_B sp014779595	87.5045	1278	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	83.0874	825	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	82.7925	736	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCF_010994375.1	s__Halomonas sp010994375	82.2205	797	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017868935.1	s__Halomonas sp017868935	82.0571	855	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100195.1	s__Halomonas gudaonensis	81.6504	790	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192215.1	s__Halomonas cerina	81.254	673	1810	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 20:17:13,613] [INFO] GTDB search result was written to GCF_002286975.1_ASM228697v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:13,614] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:13,617] [INFO] DFAST_QC result json was written to GCF_002286975.1_ASM228697v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:13,618] [INFO] DFAST_QC completed!
[2024-01-25 20:17:13,618] [INFO] Total running time: 0h1m38s