[2023-06-17 16:58:57,118] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:58:57,121] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:58:57,122] [INFO] DQC Reference Directory: /var/lib/cwl/stg067f0deb-9598-48e0-929b-18c0a5c75bba/dqc_reference
[2023-06-17 16:58:58,443] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:58:58,444] [INFO] Task started: Prodigal
[2023-06-17 16:58:58,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a3d9d39-e5f3-404e-a38f-c69bf9f077cb/GCA_028277795.1_ASM2827779v1_genomic.fna.gz | prodigal -d GCA_028277795.1_ASM2827779v1_genomic.fna/cds.fna -a GCA_028277795.1_ASM2827779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:59:11,145] [INFO] Task succeeded: Prodigal
[2023-06-17 16:59:11,146] [INFO] Task started: HMMsearch
[2023-06-17 16:59:11,146] [INFO] Running command: hmmsearch --tblout GCA_028277795.1_ASM2827779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg067f0deb-9598-48e0-929b-18c0a5c75bba/dqc_reference/reference_markers.hmm GCA_028277795.1_ASM2827779v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:59:11,476] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:59:11,477] [INFO] Found 6/6 markers.
[2023-06-17 16:59:11,519] [INFO] Query marker FASTA was written to GCA_028277795.1_ASM2827779v1_genomic.fna/markers.fasta
[2023-06-17 16:59:11,519] [INFO] Task started: Blastn
[2023-06-17 16:59:11,520] [INFO] Running command: blastn -query GCA_028277795.1_ASM2827779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg067f0deb-9598-48e0-929b-18c0a5c75bba/dqc_reference/reference_markers.fasta -out GCA_028277795.1_ASM2827779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:59:12,582] [INFO] Task succeeded: Blastn
[2023-06-17 16:59:12,587] [INFO] Selected 22 target genomes.
[2023-06-17 16:59:12,587] [INFO] Target genome list was writen to GCA_028277795.1_ASM2827779v1_genomic.fna/target_genomes.txt
[2023-06-17 16:59:12,591] [INFO] Task started: fastANI
[2023-06-17 16:59:12,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a3d9d39-e5f3-404e-a38f-c69bf9f077cb/GCA_028277795.1_ASM2827779v1_genomic.fna.gz --refList GCA_028277795.1_ASM2827779v1_genomic.fna/target_genomes.txt --output GCA_028277795.1_ASM2827779v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:59:35,932] [INFO] Task succeeded: fastANI
[2023-06-17 16:59:35,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg067f0deb-9598-48e0-929b-18c0a5c75bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:59:35,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg067f0deb-9598-48e0-929b-18c0a5c75bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:59:35,950] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:59:35,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 16:59:35,951] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	77.6634	369	1333	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	77.5123	350	1333	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	77.4651	306	1333	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.3467	358	1333	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	77.1715	352	1333	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	77.1677	259	1333	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	77.0487	407	1333	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.926	359	1333	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.8982	402	1333	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.8726	408	1333	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.7882	359	1333	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.7841	349	1333	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.6978	291	1333	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.6878	313	1333	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.6234	298	1333	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.5761	328	1333	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.4924	162	1333	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.4637	285	1333	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.3226	160	1333	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.28	143	1333	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	75.8776	259	1333	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.7717	186	1333	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 16:59:35,953] [INFO] DFAST Taxonomy check result was written to GCA_028277795.1_ASM2827779v1_genomic.fna/tc_result.tsv
[2023-06-17 16:59:35,954] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:59:35,954] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:59:35,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg067f0deb-9598-48e0-929b-18c0a5c75bba/dqc_reference/checkm_data
[2023-06-17 16:59:35,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:59:36,003] [INFO] Task started: CheckM
[2023-06-17 16:59:36,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028277795.1_ASM2827779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028277795.1_ASM2827779v1_genomic.fna/checkm_input GCA_028277795.1_ASM2827779v1_genomic.fna/checkm_result
[2023-06-17 17:00:16,624] [INFO] Task succeeded: CheckM
[2023-06-17 17:00:16,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-17 17:00:16,654] [INFO] ===== Completeness check finished =====
[2023-06-17 17:00:16,654] [INFO] ===== Start GTDB Search =====
[2023-06-17 17:00:16,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028277795.1_ASM2827779v1_genomic.fna/markers.fasta)
[2023-06-17 17:00:16,655] [INFO] Task started: Blastn
[2023-06-17 17:00:16,655] [INFO] Running command: blastn -query GCA_028277795.1_ASM2827779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg067f0deb-9598-48e0-929b-18c0a5c75bba/dqc_reference/reference_markers_gtdb.fasta -out GCA_028277795.1_ASM2827779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 17:00:18,463] [INFO] Task succeeded: Blastn
[2023-06-17 17:00:18,469] [INFO] Selected 24 target genomes.
[2023-06-17 17:00:18,469] [INFO] Target genome list was writen to GCA_028277795.1_ASM2827779v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 17:00:18,488] [INFO] Task started: fastANI
[2023-06-17 17:00:18,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a3d9d39-e5f3-404e-a38f-c69bf9f077cb/GCA_028277795.1_ASM2827779v1_genomic.fna.gz --refList GCA_028277795.1_ASM2827779v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028277795.1_ASM2827779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 17:00:35,511] [INFO] Task succeeded: fastANI
[2023-06-17 17:00:35,543] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 17:00:35,543] [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_002686255.1	s__Casp-alpha2 sp002686255	77.6402	247	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCF_900100455.1	s__Roseospirillum parvum	77.6285	373	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	77.6056	313	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187325.1	s__JACPJY01 sp016187325	77.5673	261	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	77.5589	344	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	77.533	351	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	77.5082	327	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601025.1	s__Rhodospira navarrensis	77.4448	308	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853455.1	s__Phaeospirillum sp903853455	77.4293	321	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.97	99.97	0.98	0.98	2	-
GCA_018432935.1	s__JAHDSF01 sp018432935	77.3948	323	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694935.1	s__REEP01 sp007694935	77.3588	267	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__REEP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	77.345	189	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_013349695.1	s__GCA-2686765 sp013349695	77.2287	179	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__GCA-2686765	95.0	98.27	95.45	0.83	0.65	4	-
GCA_003354135.1	s__GLO-3 sp003354135	77.216	211	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__GLO-3;g__GLO-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	77.1917	233	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	77.1672	428	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016776525.1	s__JADHTD01 sp016776525	76.9692	153	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JADHTD01;g__JADHTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	76.848	340	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.8143	190	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695045.1	s__REEP01 sp007695045	76.7556	236	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__REEP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.5958	270	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869915.1	s__CAIOSQ01 sp016869915	76.4085	171	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	97.96	97.96	0.75	0.75	2	-
GCA_000518365.1	s__URHD0088 sp000518365	76.3409	264	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793045.1	s__JAEUKZ01 sp016793045	76.3271	231	1333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JAEUKZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 17:00:35,546] [INFO] GTDB search result was written to GCA_028277795.1_ASM2827779v1_genomic.fna/result_gtdb.tsv
[2023-06-17 17:00:35,547] [INFO] ===== GTDB Search completed =====
[2023-06-17 17:00:35,556] [INFO] DFAST_QC result json was written to GCA_028277795.1_ASM2827779v1_genomic.fna/dqc_result.json
[2023-06-17 17:00:35,556] [INFO] DFAST_QC completed!
[2023-06-17 17:00:35,556] [INFO] Total running time: 0h1m38s