[2023-06-27 05:39:26,639] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:39:26,647] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:39:26,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg87264d70-047f-438c-8dfc-f1ab9ddad2fb/dqc_reference
[2023-06-27 05:39:28,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:39:28,011] [INFO] Task started: Prodigal
[2023-06-27 05:39:28,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg659555c7-c084-44fe-964f-dda67684eb44/GCA_027010265.1_ASM2701026v1_genomic.fna.gz | prodigal -d GCA_027010265.1_ASM2701026v1_genomic.fna/cds.fna -a GCA_027010265.1_ASM2701026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:39:38,370] [INFO] Task succeeded: Prodigal
[2023-06-27 05:39:38,371] [INFO] Task started: HMMsearch
[2023-06-27 05:39:38,371] [INFO] Running command: hmmsearch --tblout GCA_027010265.1_ASM2701026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87264d70-047f-438c-8dfc-f1ab9ddad2fb/dqc_reference/reference_markers.hmm GCA_027010265.1_ASM2701026v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:39:38,697] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:39:38,698] [INFO] Found 6/6 markers.
[2023-06-27 05:39:38,739] [INFO] Query marker FASTA was written to GCA_027010265.1_ASM2701026v1_genomic.fna/markers.fasta
[2023-06-27 05:39:38,739] [INFO] Task started: Blastn
[2023-06-27 05:39:38,739] [INFO] Running command: blastn -query GCA_027010265.1_ASM2701026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87264d70-047f-438c-8dfc-f1ab9ddad2fb/dqc_reference/reference_markers.fasta -out GCA_027010265.1_ASM2701026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:39:39,760] [INFO] Task succeeded: Blastn
[2023-06-27 05:39:39,764] [INFO] Selected 34 target genomes.
[2023-06-27 05:39:39,765] [INFO] Target genome list was writen to GCA_027010265.1_ASM2701026v1_genomic.fna/target_genomes.txt
[2023-06-27 05:39:39,768] [INFO] Task started: fastANI
[2023-06-27 05:39:39,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg659555c7-c084-44fe-964f-dda67684eb44/GCA_027010265.1_ASM2701026v1_genomic.fna.gz --refList GCA_027010265.1_ASM2701026v1_genomic.fna/target_genomes.txt --output GCA_027010265.1_ASM2701026v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:40:00,803] [INFO] Task succeeded: fastANI
[2023-06-27 05:40:00,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87264d70-047f-438c-8dfc-f1ab9ddad2fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:40:00,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87264d70-047f-438c-8dfc-f1ab9ddad2fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:40:00,831] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:40:00,831] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:40:00,832] [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
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	77.9529	198	1007	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.8728	199	1007	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.6499	193	1007	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.5095	180	1007	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	77.435	137	1007	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	77.2825	148	1007	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.2336	137	1007	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	77.0385	123	1007	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	77.0304	85	1007	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.9651	128	1007	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	76.7822	123	1007	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.7733	104	1007	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_012985915.1	237610	237610	suspected-type	True	76.751	124	1007	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.748	101	1007	95	below_threshold
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	76.7337	121	1007	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	76.7322	116	1007	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.72	99	1007	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.6764	123	1007	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.5662	79	1007	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.5326	107	1007	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	76.493	117	1007	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.4675	96	1007	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.3618	91	1007	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.1261	86	1007	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.1148	87	1007	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	76.0804	89	1007	95	below_threshold
Halomonas korlensis	strain=CGMCC 1.6981	GCA_900116705.1	463301	463301	type	True	76.0681	56	1007	95	below_threshold
Pseudomonas cedrina subsp. cedrina		GCA_900625035.1	76762	651740	type	True	75.7151	73	1007	95	below_threshold
Saccharospirillum salsuginis	strain=KCTC 22169	GCA_014651855.1	418750	418750	type	True	75.6997	52	1007	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	75.6198	61	1007	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	75.4707	50	1007	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:40:00,834] [INFO] DFAST Taxonomy check result was written to GCA_027010265.1_ASM2701026v1_genomic.fna/tc_result.tsv
[2023-06-27 05:40:00,835] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:40:00,835] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:40:00,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87264d70-047f-438c-8dfc-f1ab9ddad2fb/dqc_reference/checkm_data
[2023-06-27 05:40:00,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:40:00,870] [INFO] Task started: CheckM
[2023-06-27 05:40:00,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027010265.1_ASM2701026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027010265.1_ASM2701026v1_genomic.fna/checkm_input GCA_027010265.1_ASM2701026v1_genomic.fna/checkm_result
[2023-06-27 05:40:35,341] [INFO] Task succeeded: CheckM
[2023-06-27 05:40:35,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:40:35,371] [INFO] ===== Completeness check finished =====
[2023-06-27 05:40:35,371] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:40:35,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027010265.1_ASM2701026v1_genomic.fna/markers.fasta)
[2023-06-27 05:40:35,372] [INFO] Task started: Blastn
[2023-06-27 05:40:35,372] [INFO] Running command: blastn -query GCA_027010265.1_ASM2701026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87264d70-047f-438c-8dfc-f1ab9ddad2fb/dqc_reference/reference_markers_gtdb.fasta -out GCA_027010265.1_ASM2701026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:40:36,944] [INFO] Task succeeded: Blastn
[2023-06-27 05:40:36,949] [INFO] Selected 17 target genomes.
[2023-06-27 05:40:36,950] [INFO] Target genome list was writen to GCA_027010265.1_ASM2701026v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:40:36,957] [INFO] Task started: fastANI
[2023-06-27 05:40:36,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg659555c7-c084-44fe-964f-dda67684eb44/GCA_027010265.1_ASM2701026v1_genomic.fna.gz --refList GCA_027010265.1_ASM2701026v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027010265.1_ASM2701026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:40:47,029] [INFO] Task succeeded: fastANI
[2023-06-27 05:40:47,044] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:40:47,045] [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
GCA_011051685.1	s__SZUA-152 sp011051685	99.6713	790	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011371455.1	s__DRQN01 sp011371455	79.6735	267	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCA_011051755.1	s__DRQN01 sp011051755	78.1971	258	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051615.1	s__HyVt-448 sp011051615	78.1199	136	1007	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_013151575.1	s__JAADHZ01 sp013151575	77.7104	242	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__JAADHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	77.6696	191	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000801295.1	s__MONJU sp000801295	77.6644	154	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321815.1	s__SZUA-152 sp011321815	77.6354	283	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	97.33	97.33	0.90	0.90	2	-
GCA_013151355.1	s__SZUA-152 sp013151355	77.5877	221	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.5718	196	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_015487095.1	s__SZUA-152 sp015487095	77.2946	220	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	98.98	98.98	0.85	0.85	2	-
GCA_019136395.1	s__M0108 sp019136395	76.7899	119	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009928645.1	s__M0108 sp009928645	76.6498	101	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115905.1	s__Pseudomonas_D formosensis	76.3096	87	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCF_014651855.1	s__Saccharospirillum salsuginis	75.6798	53	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651805.1	s__Marinobacterium_A aestuarii	75.6198	61	1007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:40:47,047] [INFO] GTDB search result was written to GCA_027010265.1_ASM2701026v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:40:47,047] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:40:47,053] [INFO] DFAST_QC result json was written to GCA_027010265.1_ASM2701026v1_genomic.fna/dqc_result.json
[2023-06-27 05:40:47,053] [INFO] DFAST_QC completed!
[2023-06-27 05:40:47,053] [INFO] Total running time: 0h1m20s