[2023-06-26 23:45:12,068] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:45:12,071] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:45:12,071] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4bc540f-af21-481f-a5d1-6f3c134d3644/dqc_reference
[2023-06-26 23:45:13,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:45:13,369] [INFO] Task started: Prodigal
[2023-06-26 23:45:13,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg27187d6a-4e9f-4e01-9660-96bc3c3d252f/GCA_027293365.1_ASM2729336v1_genomic.fna.gz | prodigal -d GCA_027293365.1_ASM2729336v1_genomic.fna/cds.fna -a GCA_027293365.1_ASM2729336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:45:18,804] [INFO] Task succeeded: Prodigal
[2023-06-26 23:45:18,804] [INFO] Task started: HMMsearch
[2023-06-26 23:45:18,804] [INFO] Running command: hmmsearch --tblout GCA_027293365.1_ASM2729336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4bc540f-af21-481f-a5d1-6f3c134d3644/dqc_reference/reference_markers.hmm GCA_027293365.1_ASM2729336v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:45:19,037] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:45:19,038] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg27187d6a-4e9f-4e01-9660-96bc3c3d252f/GCA_027293365.1_ASM2729336v1_genomic.fna.gz]
[2023-06-26 23:45:19,131] [INFO] Query marker FASTA was written to GCA_027293365.1_ASM2729336v1_genomic.fna/markers.fasta
[2023-06-26 23:45:19,132] [INFO] Task started: Blastn
[2023-06-26 23:45:19,132] [INFO] Running command: blastn -query GCA_027293365.1_ASM2729336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4bc540f-af21-481f-a5d1-6f3c134d3644/dqc_reference/reference_markers.fasta -out GCA_027293365.1_ASM2729336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:45:19,838] [INFO] Task succeeded: Blastn
[2023-06-26 23:45:19,842] [INFO] Selected 23 target genomes.
[2023-06-26 23:45:19,843] [INFO] Target genome list was writen to GCA_027293365.1_ASM2729336v1_genomic.fna/target_genomes.txt
[2023-06-26 23:45:19,853] [INFO] Task started: fastANI
[2023-06-26 23:45:19,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg27187d6a-4e9f-4e01-9660-96bc3c3d252f/GCA_027293365.1_ASM2729336v1_genomic.fna.gz --refList GCA_027293365.1_ASM2729336v1_genomic.fna/target_genomes.txt --output GCA_027293365.1_ASM2729336v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:45:38,734] [INFO] Task succeeded: fastANI
[2023-06-26 23:45:38,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4bc540f-af21-481f-a5d1-6f3c134d3644/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:45:38,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4bc540f-af21-481f-a5d1-6f3c134d3644/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:45:38,752] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:45:38,752] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:45:38,752] [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
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	77.4889	73	539	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	77.2548	69	539	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	77.1178	84	539	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.9778	102	539	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.8394	85	539	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.8381	113	539	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.8196	114	539	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.7139	85	539	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.6876	137	539	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.6443	99	539	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.6022	98	539	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	76.5972	113	539	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.5723	67	539	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.555	119	539	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.4349	95	539	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.3083	88	539	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.3009	112	539	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.3007	78	539	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.2905	110	539	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	76.0748	62	539	95	below_threshold
Bradyrhizobium betae	strain=PL7HG1	GCA_008932115.1	244734	244734	type	True	76.0365	61	539	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.0365	61	539	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	75.815	69	539	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:45:38,754] [INFO] DFAST Taxonomy check result was written to GCA_027293365.1_ASM2729336v1_genomic.fna/tc_result.tsv
[2023-06-26 23:45:38,755] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:45:38,755] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:45:38,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4bc540f-af21-481f-a5d1-6f3c134d3644/dqc_reference/checkm_data
[2023-06-26 23:45:38,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:45:38,788] [INFO] Task started: CheckM
[2023-06-26 23:45:38,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027293365.1_ASM2729336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027293365.1_ASM2729336v1_genomic.fna/checkm_input GCA_027293365.1_ASM2729336v1_genomic.fna/checkm_result
[2023-06-26 23:46:01,435] [INFO] Task succeeded: CheckM
[2023-06-26 23:46:01,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 23.73%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-26 23:46:01,468] [INFO] ===== Completeness check finished =====
[2023-06-26 23:46:01,468] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:46:01,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027293365.1_ASM2729336v1_genomic.fna/markers.fasta)
[2023-06-26 23:46:01,469] [INFO] Task started: Blastn
[2023-06-26 23:46:01,469] [INFO] Running command: blastn -query GCA_027293365.1_ASM2729336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4bc540f-af21-481f-a5d1-6f3c134d3644/dqc_reference/reference_markers_gtdb.fasta -out GCA_027293365.1_ASM2729336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:46:02,590] [INFO] Task succeeded: Blastn
[2023-06-26 23:46:02,595] [INFO] Selected 24 target genomes.
[2023-06-26 23:46:02,596] [INFO] Target genome list was writen to GCA_027293365.1_ASM2729336v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:46:02,637] [INFO] Task started: fastANI
[2023-06-26 23:46:02,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg27187d6a-4e9f-4e01-9660-96bc3c3d252f/GCA_027293365.1_ASM2729336v1_genomic.fna.gz --refList GCA_027293365.1_ASM2729336v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027293365.1_ASM2729336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:46:19,259] [INFO] Task succeeded: fastANI
[2023-06-26 23:46:19,281] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:46:19,281] [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_004356985.1	s__SMXQ01 sp004356985	77.5059	114	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009380075.1	s__WHSO01 sp009380075	77.3467	129	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__WHSO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.9949	128	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.8402	123	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187325.1	s__JACPJY01 sp016187325	76.7928	94	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202695.1	s__JACQOE01 sp016202695	76.7902	119	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794165.1	s__Dongia sp016794165	76.7584	53	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765655.1	s__Skermanella mucosa	76.6221	97	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	76.6194	102	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.501	81	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_006738865.1	s__Stella sp006738865	76.4708	116	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	76.459	112	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	76.3851	97	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792765.1	s__SBBV01 sp016792765	76.3607	93	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__SBBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843145.1	s__Skermanella pratensis	76.3271	87	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.3222	101	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	76.2765	79	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.2373	64	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826885.1	s__CADEGL01 sp902826885	76.2227	68	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CADEGL01;f__CADEGL01;g__CADEGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171835.1	s__Thalassobaculum_A sp000171835	76.1553	77	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590795.1	s__Bradyrhizobium sp001590795	75.9448	58	539	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:46:19,292] [INFO] GTDB search result was written to GCA_027293365.1_ASM2729336v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:46:19,292] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:46:19,302] [INFO] DFAST_QC result json was written to GCA_027293365.1_ASM2729336v1_genomic.fna/dqc_result.json
[2023-06-26 23:46:19,303] [INFO] DFAST_QC completed!
[2023-06-26 23:46:19,303] [INFO] Total running time: 0h1m7s