[2023-06-27 18:25:50,545] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:25:50,548] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:25:50,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg019b9f90-ce3e-4861-9a79-fb9fc45fcee7/dqc_reference
[2023-06-27 18:25:51,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:25:51,888] [INFO] Task started: Prodigal
[2023-06-27 18:25:51,888] [INFO] Running command: gunzip -c /var/lib/cwl/stgb99e3805-779c-4b76-89af-061022068e1a/GCA_026992315.1_ASM2699231v1_genomic.fna.gz | prodigal -d GCA_026992315.1_ASM2699231v1_genomic.fna/cds.fna -a GCA_026992315.1_ASM2699231v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:25:59,842] [INFO] Task succeeded: Prodigal
[2023-06-27 18:25:59,842] [INFO] Task started: HMMsearch
[2023-06-27 18:25:59,843] [INFO] Running command: hmmsearch --tblout GCA_026992315.1_ASM2699231v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg019b9f90-ce3e-4861-9a79-fb9fc45fcee7/dqc_reference/reference_markers.hmm GCA_026992315.1_ASM2699231v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:26:00,126] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:26:00,127] [INFO] Found 6/6 markers.
[2023-06-27 18:26:00,160] [INFO] Query marker FASTA was written to GCA_026992315.1_ASM2699231v1_genomic.fna/markers.fasta
[2023-06-27 18:26:00,160] [INFO] Task started: Blastn
[2023-06-27 18:26:00,161] [INFO] Running command: blastn -query GCA_026992315.1_ASM2699231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg019b9f90-ce3e-4861-9a79-fb9fc45fcee7/dqc_reference/reference_markers.fasta -out GCA_026992315.1_ASM2699231v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:26:00,997] [INFO] Task succeeded: Blastn
[2023-06-27 18:26:01,001] [INFO] Selected 33 target genomes.
[2023-06-27 18:26:01,002] [INFO] Target genome list was writen to GCA_026992315.1_ASM2699231v1_genomic.fna/target_genomes.txt
[2023-06-27 18:26:01,054] [INFO] Task started: fastANI
[2023-06-27 18:26:01,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgb99e3805-779c-4b76-89af-061022068e1a/GCA_026992315.1_ASM2699231v1_genomic.fna.gz --refList GCA_026992315.1_ASM2699231v1_genomic.fna/target_genomes.txt --output GCA_026992315.1_ASM2699231v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:26:24,593] [INFO] Task succeeded: fastANI
[2023-06-27 18:26:24,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg019b9f90-ce3e-4861-9a79-fb9fc45fcee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:26:24,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg019b9f90-ce3e-4861-9a79-fb9fc45fcee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:26:24,617] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:26:24,617] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:26:24,617] [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
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	76.8242	87	900	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.767	146	900	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.6725	124	900	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	76.568	152	900	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.4473	107	900	95	below_threshold
Magnetospirillum molischianum	strain=DSM 120	GCA_000294655.1	1083	1083	type	True	76.3909	74	900	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	76.3545	92	900	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.3288	143	900	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.2918	59	900	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.2845	125	900	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_004341375.1	1086	1086	type	True	76.2734	99	900	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	76.2153	105	900	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.173	96	900	95	below_threshold
Camelimonas lactis	strain=DSM 22958	GCA_004342915.1	659006	659006	type	True	76.172	87	900	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	76.0892	117	900	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.0696	164	900	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.0373	143	900	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.0246	144	900	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	75.9897	61	900	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.9384	94	900	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.9104	108	900	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.8961	102	900	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	75.887	112	900	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	75.8456	107	900	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	75.8165	104	900	95	below_threshold
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	75.8107	55	900	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	75.7879	106	900	95	below_threshold
Roseomonas aerophila	strain=NBRC 108923	GCA_014490485.1	1224513	1224513	type	True	75.7254	91	900	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	75.6547	59	900	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	75.6259	64	900	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	75.6085	65	900	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	75.5027	55	900	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:26:24,620] [INFO] DFAST Taxonomy check result was written to GCA_026992315.1_ASM2699231v1_genomic.fna/tc_result.tsv
[2023-06-27 18:26:24,620] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:26:24,620] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:26:24,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg019b9f90-ce3e-4861-9a79-fb9fc45fcee7/dqc_reference/checkm_data
[2023-06-27 18:26:24,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:26:24,658] [INFO] Task started: CheckM
[2023-06-27 18:26:24,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026992315.1_ASM2699231v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026992315.1_ASM2699231v1_genomic.fna/checkm_input GCA_026992315.1_ASM2699231v1_genomic.fna/checkm_result
[2023-06-27 18:26:53,002] [INFO] Task succeeded: CheckM
[2023-06-27 18:26:53,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:26:53,026] [INFO] ===== Completeness check finished =====
[2023-06-27 18:26:53,027] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:26:53,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026992315.1_ASM2699231v1_genomic.fna/markers.fasta)
[2023-06-27 18:26:53,027] [INFO] Task started: Blastn
[2023-06-27 18:26:53,028] [INFO] Running command: blastn -query GCA_026992315.1_ASM2699231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg019b9f90-ce3e-4861-9a79-fb9fc45fcee7/dqc_reference/reference_markers_gtdb.fasta -out GCA_026992315.1_ASM2699231v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:26:54,523] [INFO] Task succeeded: Blastn
[2023-06-27 18:26:54,528] [INFO] Selected 34 target genomes.
[2023-06-27 18:26:54,528] [INFO] Target genome list was writen to GCA_026992315.1_ASM2699231v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:26:54,594] [INFO] Task started: fastANI
[2023-06-27 18:26:54,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgb99e3805-779c-4b76-89af-061022068e1a/GCA_026992315.1_ASM2699231v1_genomic.fna.gz --refList GCA_026992315.1_ASM2699231v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026992315.1_ASM2699231v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:27:18,131] [INFO] Task succeeded: fastANI
[2023-06-27 18:27:18,164] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 18:27:18,165] [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_003576705.1	s__SYSU-D60015 sp003576705	76.9953	140	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.8522	148	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	76.7983	88	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924445.1	s__Minwuia thermotolerans	76.7353	148	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCF_004363235.1	s__Dongia mobilis	76.674	124	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	76.6101	124	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.5273	154	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_018336035.1	s__Ferrovibrio sp018336035	76.4323	161	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108475.1	s__Phaeospirillum fulvum_A	76.4165	104	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712715.1	s__Dongia sp016712715	76.3449	110	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	76.3335	154	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	76.3168	144	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.2928	195	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	76.2007	106	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.1874	90	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.1293	114	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.1204	130	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_019084075.1	s__G192 sp019084075	76.1165	117	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	76.0992	119	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195085.1	s__JACQAG01 sp016195085	76.0969	90	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__JACQAG01	95.0	99.88	99.88	0.96	0.96	2	-
GCA_009694265.1	s__Pseudolabrys sp009694265	76.0841	64	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.66	99.66	0.83	0.83	2	-
GCA_011374735.1	s__Thermopetrobacter sp011374735	76.082	65	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Thermopetrobacteraceae;g__Thermopetrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011332665.1	s__Acidibrevibacterium sp011332665	75.977	70	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidibrevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018701215.1	s__GCA-2731375 sp018701215	75.9619	101	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.97	99.95	0.98	0.97	15	-
GCA_005884705.1	s__Reyranella sp005884705	75.9474	76	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238725.1	s__Bin65 sp002238725	75.8791	108	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882935.1	s__Sneathiella chungangensis	75.8456	107	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000164635.1	s__Roseomonas cervicalis	75.8341	104	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667855.1	s__GCA-2731375 sp018667855	75.8232	80	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCA_006227805.1	s__Aestuariivita sp006227805	75.7381	50	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001717955.1	s__Sphingomonas panacis	75.6757	58	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	75.6217	64	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018660265.1	s__GCA-2731375 sp018660265	75.3996	57	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.92	99.87	0.96	0.94	11	-
GCA_002706985.1	s__Sneathiella sp002706985	75.3286	51	900	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-27 18:27:18,167] [INFO] GTDB search result was written to GCA_026992315.1_ASM2699231v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:27:18,167] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:27:18,173] [INFO] DFAST_QC result json was written to GCA_026992315.1_ASM2699231v1_genomic.fna/dqc_result.json
[2023-06-27 18:27:18,173] [INFO] DFAST_QC completed!
[2023-06-27 18:27:18,173] [INFO] Total running time: 0h1m28s