[2023-06-30 09:11:55,330] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:11:55,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:11:55,333] [INFO] DQC Reference Directory: /var/lib/cwl/stge4fc71f6-0691-45ce-9d3c-8dec1aee150c/dqc_reference
[2023-06-30 09:11:56,559] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:11:56,560] [INFO] Task started: Prodigal
[2023-06-30 09:11:56,561] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5b8a3ec-8e56-4f9d-a88f-c38ca50ab8e1/GCA_016792865.1_ASM1679286v1_genomic.fna.gz | prodigal -d GCA_016792865.1_ASM1679286v1_genomic.fna/cds.fna -a GCA_016792865.1_ASM1679286v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:12:06,991] [INFO] Task succeeded: Prodigal
[2023-06-30 09:12:06,992] [INFO] Task started: HMMsearch
[2023-06-30 09:12:06,992] [INFO] Running command: hmmsearch --tblout GCA_016792865.1_ASM1679286v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4fc71f6-0691-45ce-9d3c-8dec1aee150c/dqc_reference/reference_markers.hmm GCA_016792865.1_ASM1679286v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:12:07,246] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:12:07,248] [INFO] Found 6/6 markers.
[2023-06-30 09:12:07,298] [INFO] Query marker FASTA was written to GCA_016792865.1_ASM1679286v1_genomic.fna/markers.fasta
[2023-06-30 09:12:07,298] [INFO] Task started: Blastn
[2023-06-30 09:12:07,298] [INFO] Running command: blastn -query GCA_016792865.1_ASM1679286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4fc71f6-0691-45ce-9d3c-8dec1aee150c/dqc_reference/reference_markers.fasta -out GCA_016792865.1_ASM1679286v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:12:08,156] [INFO] Task succeeded: Blastn
[2023-06-30 09:12:08,162] [INFO] Selected 33 target genomes.
[2023-06-30 09:12:08,163] [INFO] Target genome list was writen to GCA_016792865.1_ASM1679286v1_genomic.fna/target_genomes.txt
[2023-06-30 09:12:08,172] [INFO] Task started: fastANI
[2023-06-30 09:12:08,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b8a3ec-8e56-4f9d-a88f-c38ca50ab8e1/GCA_016792865.1_ASM1679286v1_genomic.fna.gz --refList GCA_016792865.1_ASM1679286v1_genomic.fna/target_genomes.txt --output GCA_016792865.1_ASM1679286v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:12:34,484] [INFO] Task succeeded: fastANI
[2023-06-30 09:12:34,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4fc71f6-0691-45ce-9d3c-8dec1aee150c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:12:34,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4fc71f6-0691-45ce-9d3c-8dec1aee150c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:12:34,520] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:12:34,520] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 09:12:34,520] [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
Aestuariivirga litoralis	strain=KCTC 52945	GCA_003234965.1	2650924	2650924	type	True	78.5198	396	1014	95	below_threshold
Microvirga flavescens	strain=c27j1	GCA_003290125.1	2249811	2249811	type	True	77.107	108	1014	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	77.0914	118	1014	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	76.9653	134	1014	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	76.9256	108	1014	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	76.8832	144	1014	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	76.8073	157	1014	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	76.7967	118	1014	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	76.7768	128	1014	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	76.7538	132	1014	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.733	132	1014	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.6906	118	1014	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.6774	89	1014	95	below_threshold
Microvirga pudoricolor	strain=BT291	GCA_016892705.1	2778729	2778729	type	True	76.6578	103	1014	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	76.6464	110	1014	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	76.6355	150	1014	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	76.6252	112	1014	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	76.6136	111	1014	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.5956	121	1014	95	below_threshold
Microvirga alba	strain=BT350	GCA_015694465.1	2791025	2791025	type	True	76.5826	103	1014	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	76.5396	149	1014	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	76.5133	102	1014	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	76.506	134	1014	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.4834	126	1014	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.4345	134	1014	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	76.412	172	1014	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	76.4038	131	1014	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_900102695.1	1080	1080	type	True	76.3588	96	1014	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_016584015.1	1080	1080	type	True	76.3585	96	1014	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_003258905.1	1080	1080	type	True	76.2869	94	1014	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	76.2364	92	1014	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	76.1047	112	1014	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8224	118	1014	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 09:12:34,522] [INFO] DFAST Taxonomy check result was written to GCA_016792865.1_ASM1679286v1_genomic.fna/tc_result.tsv
[2023-06-30 09:12:34,522] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:12:34,523] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:12:34,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4fc71f6-0691-45ce-9d3c-8dec1aee150c/dqc_reference/checkm_data
[2023-06-30 09:12:34,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:12:34,560] [INFO] Task started: CheckM
[2023-06-30 09:12:34,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016792865.1_ASM1679286v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016792865.1_ASM1679286v1_genomic.fna/checkm_input GCA_016792865.1_ASM1679286v1_genomic.fna/checkm_result
[2023-06-30 09:13:33,763] [INFO] Task succeeded: CheckM
[2023-06-30 09:13:33,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:13:33,787] [INFO] ===== Completeness check finished =====
[2023-06-30 09:13:33,787] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:13:33,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016792865.1_ASM1679286v1_genomic.fna/markers.fasta)
[2023-06-30 09:13:33,788] [INFO] Task started: Blastn
[2023-06-30 09:13:33,788] [INFO] Running command: blastn -query GCA_016792865.1_ASM1679286v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4fc71f6-0691-45ce-9d3c-8dec1aee150c/dqc_reference/reference_markers_gtdb.fasta -out GCA_016792865.1_ASM1679286v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:13:35,386] [INFO] Task succeeded: Blastn
[2023-06-30 09:13:35,393] [INFO] Selected 14 target genomes.
[2023-06-30 09:13:35,393] [INFO] Target genome list was writen to GCA_016792865.1_ASM1679286v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:13:35,399] [INFO] Task started: fastANI
[2023-06-30 09:13:35,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b8a3ec-8e56-4f9d-a88f-c38ca50ab8e1/GCA_016792865.1_ASM1679286v1_genomic.fna.gz --refList GCA_016792865.1_ASM1679286v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016792865.1_ASM1679286v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:13:46,821] [INFO] Task succeeded: fastANI
[2023-06-30 09:13:46,840] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 09:13:46,841] [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_016792865.1	s__Aestuariivirga sp016792865	100.0	998	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016710435.1	s__Aestuariivirga sp016710435	81.1613	715	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234965.1	s__Aestuariivirga litoralis	78.5094	397	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900298995.1	s__Aestuariivirga sp900298995	77.7663	273	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046735.1	s__Nordella sp011046735	77.3994	260	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576695.1	s__Nordella sp003576695	77.3536	317	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032065.1	s__Aestuariivirga sp012032065	77.35	220	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792825.1	s__Aestuariivirga sp016792825	77.2937	229	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574785.1	s__Nordella sp003574785	77.2417	307	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595235.1	s__Nordella sp016595235	77.2031	298	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015714715.1	s__Aestuariivirga litoralis_A	77.1303	250	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000017645.1	s__Xanthobacter autotrophicus	76.8773	138	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793355.1	s__JAEUMG01 sp016793355	76.8236	195	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__JAEUMG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242205.1	s__Pseudolabrys sp018242205	76.7344	113	1014	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 09:13:46,843] [INFO] GTDB search result was written to GCA_016792865.1_ASM1679286v1_genomic.fna/result_gtdb.tsv
[2023-06-30 09:13:46,844] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:13:46,849] [INFO] DFAST_QC result json was written to GCA_016792865.1_ASM1679286v1_genomic.fna/dqc_result.json
[2023-06-30 09:13:46,849] [INFO] DFAST_QC completed!
[2023-06-30 09:13:46,849] [INFO] Total running time: 0h1m52s