[2023-06-08 06:29:51,890] [INFO] DFAST_QC pipeline started.
[2023-06-08 06:29:51,893] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 06:29:51,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b230975-502c-4dc8-8488-a852c7b5c39d/dqc_reference
[2023-06-08 06:29:55,291] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 06:29:55,292] [INFO] Task started: Prodigal
[2023-06-08 06:29:55,293] [INFO] Running command: gunzip -c /var/lib/cwl/stga3a90a64-1745-4c86-91ad-1c23905da4f2/GCA_945878895.1_TrH-03may19-36_genomic.fna.gz | prodigal -d GCA_945878895.1_TrH-03may19-36_genomic.fna/cds.fna -a GCA_945878895.1_TrH-03may19-36_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 06:30:06,766] [INFO] Task succeeded: Prodigal
[2023-06-08 06:30:06,766] [INFO] Task started: HMMsearch
[2023-06-08 06:30:06,766] [INFO] Running command: hmmsearch --tblout GCA_945878895.1_TrH-03may19-36_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b230975-502c-4dc8-8488-a852c7b5c39d/dqc_reference/reference_markers.hmm GCA_945878895.1_TrH-03may19-36_genomic.fna/protein.faa > /dev/null
[2023-06-08 06:30:07,056] [INFO] Task succeeded: HMMsearch
[2023-06-08 06:30:07,058] [INFO] Found 6/6 markers.
[2023-06-08 06:30:07,104] [INFO] Query marker FASTA was written to GCA_945878895.1_TrH-03may19-36_genomic.fna/markers.fasta
[2023-06-08 06:30:07,104] [INFO] Task started: Blastn
[2023-06-08 06:30:07,104] [INFO] Running command: blastn -query GCA_945878895.1_TrH-03may19-36_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b230975-502c-4dc8-8488-a852c7b5c39d/dqc_reference/reference_markers.fasta -out GCA_945878895.1_TrH-03may19-36_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:30:08,036] [INFO] Task succeeded: Blastn
[2023-06-08 06:30:08,041] [INFO] Selected 20 target genomes.
[2023-06-08 06:30:08,042] [INFO] Target genome list was writen to GCA_945878895.1_TrH-03may19-36_genomic.fna/target_genomes.txt
[2023-06-08 06:30:08,046] [INFO] Task started: fastANI
[2023-06-08 06:30:08,046] [INFO] Running command: fastANI --query /var/lib/cwl/stga3a90a64-1745-4c86-91ad-1c23905da4f2/GCA_945878895.1_TrH-03may19-36_genomic.fna.gz --refList GCA_945878895.1_TrH-03may19-36_genomic.fna/target_genomes.txt --output GCA_945878895.1_TrH-03may19-36_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 06:30:28,433] [INFO] Task succeeded: fastANI
[2023-06-08 06:30:28,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b230975-502c-4dc8-8488-a852c7b5c39d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 06:30:28,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b230975-502c-4dc8-8488-a852c7b5c39d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 06:30:28,452] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 06:30:28,452] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 06:30:28,453] [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
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	79.1338	717	1330	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	78.7191	552	1330	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	78.5659	647	1330	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	78.2929	530	1330	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.538	268	1330	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.4836	194	1330	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.4642	266	1330	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.4137	373	1330	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.3037	335	1330	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.2622	293	1330	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.2314	315	1330	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.2071	214	1330	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	76.0601	183	1330	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.9523	317	1330	95	below_threshold
Fodinicurvata fenggangensis	strain=DSM 21160	GCA_000686045.1	1121830	1121830	type	True	75.8655	78	1330	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.8434	194	1330	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	75.7434	163	1330	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	75.6863	140	1330	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	75.6515	143	1330	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	75.6387	143	1330	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 06:30:28,455] [INFO] DFAST Taxonomy check result was written to GCA_945878895.1_TrH-03may19-36_genomic.fna/tc_result.tsv
[2023-06-08 06:30:28,455] [INFO] ===== Taxonomy check completed =====
[2023-06-08 06:30:28,455] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 06:30:28,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b230975-502c-4dc8-8488-a852c7b5c39d/dqc_reference/checkm_data
[2023-06-08 06:30:28,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 06:30:28,502] [INFO] Task started: CheckM
[2023-06-08 06:30:28,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945878895.1_TrH-03may19-36_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945878895.1_TrH-03may19-36_genomic.fna/checkm_input GCA_945878895.1_TrH-03may19-36_genomic.fna/checkm_result
[2023-06-08 06:31:04,509] [INFO] Task succeeded: CheckM
[2023-06-08 06:31:04,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 06:31:04,541] [INFO] ===== Completeness check finished =====
[2023-06-08 06:31:04,541] [INFO] ===== Start GTDB Search =====
[2023-06-08 06:31:04,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945878895.1_TrH-03may19-36_genomic.fna/markers.fasta)
[2023-06-08 06:31:04,542] [INFO] Task started: Blastn
[2023-06-08 06:31:04,542] [INFO] Running command: blastn -query GCA_945878895.1_TrH-03may19-36_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b230975-502c-4dc8-8488-a852c7b5c39d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945878895.1_TrH-03may19-36_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:31:06,367] [INFO] Task succeeded: Blastn
[2023-06-08 06:31:06,372] [INFO] Selected 15 target genomes.
[2023-06-08 06:31:06,372] [INFO] Target genome list was writen to GCA_945878895.1_TrH-03may19-36_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 06:31:06,401] [INFO] Task started: fastANI
[2023-06-08 06:31:06,401] [INFO] Running command: fastANI --query /var/lib/cwl/stga3a90a64-1745-4c86-91ad-1c23905da4f2/GCA_945878895.1_TrH-03may19-36_genomic.fna.gz --refList GCA_945878895.1_TrH-03may19-36_genomic.fna/target_genomes_gtdb.txt --output GCA_945878895.1_TrH-03may19-36_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 06:31:21,817] [INFO] Task succeeded: fastANI
[2023-06-08 06:31:21,831] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 06:31:21,832] [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_016699855.1	s__GCA-016699855 sp016699855	80.3338	809	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869975.1	s__JAFAZJ01 sp016869975	79.9047	778	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239835.1	s__JAFAZJ01 sp019239835	79.377	458	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__JAFAZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	79.164	712	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305915.1	s__Reyranella sp017305915	79.1048	658	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296815.1	s__Reyranella sp004296815	78.8576	468	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296935.1	s__Reyranella sp004296935	78.7828	543	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	78.6928	650	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859315.1	s__SYSU-D60007 sp007859315	78.6076	670	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240695.1	s__Reyranella sp018240695	78.5858	502	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	96.90	96.90	0.84	0.84	2	-
GCA_003574685.1	s__SYSU-D60007 sp003574685	78.4317	536	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010032545.1	s__Reyranella sp010032545	78.3674	491	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	76.4599	195	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941095.1	s__Magnetospirillum sp903941095	76.1173	155	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.83	99.83	0.93	0.93	2	-
GCA_903858635.1	s__Telmatospirillum sp903858635	75.7979	147	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-08 06:31:21,834] [INFO] GTDB search result was written to GCA_945878895.1_TrH-03may19-36_genomic.fna/result_gtdb.tsv
[2023-06-08 06:31:21,834] [INFO] ===== GTDB Search completed =====
[2023-06-08 06:31:21,839] [INFO] DFAST_QC result json was written to GCA_945878895.1_TrH-03may19-36_genomic.fna/dqc_result.json
[2023-06-08 06:31:21,839] [INFO] DFAST_QC completed!
[2023-06-08 06:31:21,839] [INFO] Total running time: 0h1m30s