[2024-01-24 12:54:21,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:21,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:21,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8c1e95a-fcf9-4823-83c4-1bbf053efd09/dqc_reference
[2024-01-24 12:54:23,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:23,879] [INFO] Task started: Prodigal
[2024-01-24 12:54:23,879] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdc70690-4ff4-4732-9273-ceee65224385/GCF_024808875.1_ASM2480887v1_genomic.fna.gz | prodigal -d GCF_024808875.1_ASM2480887v1_genomic.fna/cds.fna -a GCF_024808875.1_ASM2480887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:31,681] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:31,681] [INFO] Task started: HMMsearch
[2024-01-24 12:54:31,681] [INFO] Running command: hmmsearch --tblout GCF_024808875.1_ASM2480887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8c1e95a-fcf9-4823-83c4-1bbf053efd09/dqc_reference/reference_markers.hmm GCF_024808875.1_ASM2480887v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:31,991] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:31,993] [INFO] Found 6/6 markers.
[2024-01-24 12:54:32,019] [INFO] Query marker FASTA was written to GCF_024808875.1_ASM2480887v1_genomic.fna/markers.fasta
[2024-01-24 12:54:32,020] [INFO] Task started: Blastn
[2024-01-24 12:54:32,020] [INFO] Running command: blastn -query GCF_024808875.1_ASM2480887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8c1e95a-fcf9-4823-83c4-1bbf053efd09/dqc_reference/reference_markers.fasta -out GCF_024808875.1_ASM2480887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:32,772] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:32,776] [INFO] Selected 28 target genomes.
[2024-01-24 12:54:32,777] [INFO] Target genome list was writen to GCF_024808875.1_ASM2480887v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:32,812] [INFO] Task started: fastANI
[2024-01-24 12:54:32,813] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdc70690-4ff4-4732-9273-ceee65224385/GCF_024808875.1_ASM2480887v1_genomic.fna.gz --refList GCF_024808875.1_ASM2480887v1_genomic.fna/target_genomes.txt --output GCF_024808875.1_ASM2480887v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:49,776] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:49,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8c1e95a-fcf9-4823-83c4-1bbf053efd09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:49,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8c1e95a-fcf9-4823-83c4-1bbf053efd09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:49,795] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:49,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:49,795] [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
Methylohalomonas lacus	strain=HMT 1	GCA_024808875.1	398773	398773	type	True	100.0	902	903	95	conclusive
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	77.248	87	903	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.9192	78	903	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	76.8267	60	903	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.7462	84	903	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.7328	122	903	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.6945	104	903	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.6152	106	903	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.5806	77	903	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	76.5779	86	903	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.5772	114	903	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	76.5117	91	903	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	76.5087	89	903	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	76.5018	79	903	95	below_threshold
Halofilum ochraceum	strain=XJ16	GCA_001614315.2	1611323	1611323	type	True	76.4542	97	903	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.4212	82	903	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	76.3436	93	903	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.3102	80	903	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	76.2871	70	903	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.2432	80	903	95	below_threshold
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	76.0542	77	903	95	below_threshold
Halomonas halmophila	strain=NBRC 15537	GCA_006540005.1	252	252	type	True	75.9932	56	903	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	75.9902	108	903	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	75.9442	81	903	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:49,798] [INFO] DFAST Taxonomy check result was written to GCF_024808875.1_ASM2480887v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:49,799] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:49,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:49,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8c1e95a-fcf9-4823-83c4-1bbf053efd09/dqc_reference/checkm_data
[2024-01-24 12:54:49,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:49,834] [INFO] Task started: CheckM
[2024-01-24 12:54:49,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024808875.1_ASM2480887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024808875.1_ASM2480887v1_genomic.fna/checkm_input GCF_024808875.1_ASM2480887v1_genomic.fna/checkm_result
[2024-01-24 12:55:17,601] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:17,602] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:17,625] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:17,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:17,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024808875.1_ASM2480887v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:17,626] [INFO] Task started: Blastn
[2024-01-24 12:55:17,626] [INFO] Running command: blastn -query GCF_024808875.1_ASM2480887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8c1e95a-fcf9-4823-83c4-1bbf053efd09/dqc_reference/reference_markers_gtdb.fasta -out GCF_024808875.1_ASM2480887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:18,792] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:18,798] [INFO] Selected 35 target genomes.
[2024-01-24 12:55:18,799] [INFO] Target genome list was writen to GCF_024808875.1_ASM2480887v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:18,845] [INFO] Task started: fastANI
[2024-01-24 12:55:18,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdc70690-4ff4-4732-9273-ceee65224385/GCF_024808875.1_ASM2480887v1_genomic.fna.gz --refList GCF_024808875.1_ASM2480887v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024808875.1_ASM2480887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:37,946] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:37,976] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:55:37,977] [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_000385215.1	s__Thioalkalivibrio thiocyanoxidans	77.248	87	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	99.32	98.64	0.97	0.95	3	-
GCF_000377785.1	s__Thioalkalivibrio sp000377785	77.1061	90	903	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	77.0739	105	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.90	97.79	0.93	0.92	11	-
GCA_014359565.1	s__Immundisolibacter sp014359565	77.0049	103	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376845.1	s__Thioalkalivibrio sp000376845	76.9708	91	903	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	76.938	96	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381825.1	s__Thioalkalivibrio sp000381825	76.8972	82	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012044895.1	s__Aquisalimonas sp012044895	76.834	73	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.8271	128	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013519935.1	s__WFHF3C12 sp013519935	76.7575	91	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__WFHF3C12	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420165.1	s__Thioalkalivibrio sp000420165	76.6448	98	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584105.1	s__Ectothiorhodospira shaposhnikovii	76.6285	60	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	76.6152	106	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_000225005.1	s__Ectothiorhodospira sp000225005	76.6122	59	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.5396	90	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.4746	123	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017589465.1	s__Pseudomonas sp017589465	76.4714	108	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001614315.2	s__Halofilum ochraceum	76.4542	97	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XJ16;f__Halofilaceae;g__Halofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	76.3934	122	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_900103845.1	s__Pseudomonas jinjuensis	76.381	117	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_011051615.1	s__HyVt-448 sp011051615	76.369	62	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6429;f__UBA6429;g__HyVt-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	76.3379	76	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	76.2868	90	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCA_001830245.1	s__Lysobacter sp001830245	76.2517	81	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCA_019136105.1	s__RPQJ01 sp019136105	76.1645	52	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242685.1	s__ZC4RG24 sp003242685	76.1348	59	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420645.1	s__Nevskia ramosa	76.0984	75	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012523465.1	s__JAAYIK01 sp012523465	76.0965	82	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__JAAYIK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559025.1	s__Luteimonas huabeiensis	75.976	109	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050835.1	s__Pseudomonas_E sp003050835	75.9073	71	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_009846755.1	s__Alcanivorax_A sp009846755	75.8794	74	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006218035.1	s__VBWC01 sp006218035	75.8363	54	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__VBWC01;f__VBWC01;g__VBWC01	95.0	99.95	99.95	0.98	0.98	2	-
GCF_003131185.1	s__Pseudomonas_E ovata	75.6209	73	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.40	98.37	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:37,979] [INFO] GTDB search result was written to GCF_024808875.1_ASM2480887v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:37,981] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:37,986] [INFO] DFAST_QC result json was written to GCF_024808875.1_ASM2480887v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:37,987] [INFO] DFAST_QC completed!
[2024-01-24 12:55:37,987] [INFO] Total running time: 0h1m16s