[2023-06-08 01:49:09,802] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:49:09,805] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:49:09,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b2bc6ee-d76e-4282-bacc-9335f044cfe2/dqc_reference
[2023-06-08 01:49:11,146] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:49:11,147] [INFO] Task started: Prodigal
[2023-06-08 01:49:11,147] [INFO] Running command: gunzip -c /var/lib/cwl/stga32ec63d-684d-4788-9acb-4675f76ea70d/GCA_945902735.1_TH-08apr19-148_genomic.fna.gz | prodigal -d GCA_945902735.1_TH-08apr19-148_genomic.fna/cds.fna -a GCA_945902735.1_TH-08apr19-148_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:49:19,173] [INFO] Task succeeded: Prodigal
[2023-06-08 01:49:19,173] [INFO] Task started: HMMsearch
[2023-06-08 01:49:19,173] [INFO] Running command: hmmsearch --tblout GCA_945902735.1_TH-08apr19-148_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b2bc6ee-d76e-4282-bacc-9335f044cfe2/dqc_reference/reference_markers.hmm GCA_945902735.1_TH-08apr19-148_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:49:19,395] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:49:19,397] [INFO] Found 6/6 markers.
[2023-06-08 01:49:19,440] [INFO] Query marker FASTA was written to GCA_945902735.1_TH-08apr19-148_genomic.fna/markers.fasta
[2023-06-08 01:49:19,440] [INFO] Task started: Blastn
[2023-06-08 01:49:19,441] [INFO] Running command: blastn -query GCA_945902735.1_TH-08apr19-148_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2bc6ee-d76e-4282-bacc-9335f044cfe2/dqc_reference/reference_markers.fasta -out GCA_945902735.1_TH-08apr19-148_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:49:20,299] [INFO] Task succeeded: Blastn
[2023-06-08 01:49:20,304] [INFO] Selected 32 target genomes.
[2023-06-08 01:49:20,304] [INFO] Target genome list was writen to GCA_945902735.1_TH-08apr19-148_genomic.fna/target_genomes.txt
[2023-06-08 01:49:20,310] [INFO] Task started: fastANI
[2023-06-08 01:49:20,310] [INFO] Running command: fastANI --query /var/lib/cwl/stga32ec63d-684d-4788-9acb-4675f76ea70d/GCA_945902735.1_TH-08apr19-148_genomic.fna.gz --refList GCA_945902735.1_TH-08apr19-148_genomic.fna/target_genomes.txt --output GCA_945902735.1_TH-08apr19-148_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:49:44,082] [INFO] Task succeeded: fastANI
[2023-06-08 01:49:44,083] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b2bc6ee-d76e-4282-bacc-9335f044cfe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:49:44,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b2bc6ee-d76e-4282-bacc-9335f044cfe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:49:44,102] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 01:49:44,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 01:49:44,102] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.1096	85	854	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.9675	54	854	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	75.9215	69	854	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.9169	75	854	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	75.7339	93	854	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	75.7247	63	854	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.7202	107	854	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	75.6971	92	854	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.6859	103	854	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.6353	65	854	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.5801	107	854	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.56	73	854	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	75.5592	61	854	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.5566	90	854	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.5371	83	854	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	75.5032	120	854	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.5008	72	854	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	75.4766	66	854	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	75.4603	67	854	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	75.4549	69	854	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.4423	80	854	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	75.4381	66	854	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	75.4369	66	854	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.2534	69	854	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.2011	51	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 01:49:44,104] [INFO] DFAST Taxonomy check result was written to GCA_945902735.1_TH-08apr19-148_genomic.fna/tc_result.tsv
[2023-06-08 01:49:44,104] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:49:44,104] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:49:44,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b2bc6ee-d76e-4282-bacc-9335f044cfe2/dqc_reference/checkm_data
[2023-06-08 01:49:44,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:49:44,136] [INFO] Task started: CheckM
[2023-06-08 01:49:44,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945902735.1_TH-08apr19-148_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945902735.1_TH-08apr19-148_genomic.fna/checkm_input GCA_945902735.1_TH-08apr19-148_genomic.fna/checkm_result
[2023-06-08 01:50:12,719] [INFO] Task succeeded: CheckM
[2023-06-08 01:50:12,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.80%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 01:50:12,742] [INFO] ===== Completeness check finished =====
[2023-06-08 01:50:12,742] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:50:12,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945902735.1_TH-08apr19-148_genomic.fna/markers.fasta)
[2023-06-08 01:50:12,743] [INFO] Task started: Blastn
[2023-06-08 01:50:12,744] [INFO] Running command: blastn -query GCA_945902735.1_TH-08apr19-148_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2bc6ee-d76e-4282-bacc-9335f044cfe2/dqc_reference/reference_markers_gtdb.fasta -out GCA_945902735.1_TH-08apr19-148_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:50:14,157] [INFO] Task succeeded: Blastn
[2023-06-08 01:50:14,162] [INFO] Selected 22 target genomes.
[2023-06-08 01:50:14,162] [INFO] Target genome list was writen to GCA_945902735.1_TH-08apr19-148_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:50:14,187] [INFO] Task started: fastANI
[2023-06-08 01:50:14,187] [INFO] Running command: fastANI --query /var/lib/cwl/stga32ec63d-684d-4788-9acb-4675f76ea70d/GCA_945902735.1_TH-08apr19-148_genomic.fna.gz --refList GCA_945902735.1_TH-08apr19-148_genomic.fna/target_genomes_gtdb.txt --output GCA_945902735.1_TH-08apr19-148_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:50:28,998] [INFO] Task succeeded: fastANI
[2023-06-08 01:50:29,017] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 01:50:29,017] [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_009691045.1	s__SHWC01 sp009691045	95.2499	500	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__SHWC01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016869195.1	s__SHWC01 sp016869195	78.9602	409	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__SHWC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666805.1	s__PTKB01 sp018666805	76.4712	157	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
GCA_002937555.1	s__PTKB01 sp002937555	76.2114	86	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523425.1	s__WTGU01 sp011523425	76.204	123	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284725.1	s__Phaeospirillum kuznetsovii	75.9675	54	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305635.1	s__Bauldia sp017305635	75.8469	69	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	75.8092	74	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	75.7967	73	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_900113835.1	s__Bosea sp900113835	75.7713	86	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.7325	106	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016792765.1	s__SBBV01 sp016792765	75.7312	112	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__SBBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858635.1	s__Telmatospirillum sp903858635	75.6941	64	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
GCF_000164635.1	s__Roseomonas cervicalis	75.6338	88	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574785.1	s__Nordella sp003574785	75.6239	108	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002845745.1	s__Telmatospirillum siberiense	75.6019	67	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	75.5046	61	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869435.1	s__Methylocystis sp016869435	75.466	58	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 01:50:29,019] [INFO] GTDB search result was written to GCA_945902735.1_TH-08apr19-148_genomic.fna/result_gtdb.tsv
[2023-06-08 01:50:29,020] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:50:29,024] [INFO] DFAST_QC result json was written to GCA_945902735.1_TH-08apr19-148_genomic.fna/dqc_result.json
[2023-06-08 01:50:29,024] [INFO] DFAST_QC completed!
[2023-06-08 01:50:29,024] [INFO] Total running time: 0h1m19s