[2023-06-29 11:31:35,775] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:31:35,789] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:31:35,789] [INFO] DQC Reference Directory: /var/lib/cwl/stga93078f5-2f2e-46f3-873c-f3061960c6b4/dqc_reference
[2023-06-29 11:31:38,708] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:31:38,711] [INFO] Task started: Prodigal
[2023-06-29 11:31:38,711] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f30a482-341b-4052-bef4-86274c74f57f/GCA_020442165.1_ASM2044216v1_genomic.fna.gz | prodigal -d GCA_020442165.1_ASM2044216v1_genomic.fna/cds.fna -a GCA_020442165.1_ASM2044216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:31:51,943] [INFO] Task succeeded: Prodigal
[2023-06-29 11:31:51,944] [INFO] Task started: HMMsearch
[2023-06-29 11:31:51,944] [INFO] Running command: hmmsearch --tblout GCA_020442165.1_ASM2044216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga93078f5-2f2e-46f3-873c-f3061960c6b4/dqc_reference/reference_markers.hmm GCA_020442165.1_ASM2044216v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:31:52,164] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:31:52,166] [INFO] Found 6/6 markers.
[2023-06-29 11:31:52,204] [INFO] Query marker FASTA was written to GCA_020442165.1_ASM2044216v1_genomic.fna/markers.fasta
[2023-06-29 11:31:52,205] [INFO] Task started: Blastn
[2023-06-29 11:31:52,205] [INFO] Running command: blastn -query GCA_020442165.1_ASM2044216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga93078f5-2f2e-46f3-873c-f3061960c6b4/dqc_reference/reference_markers.fasta -out GCA_020442165.1_ASM2044216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:31:52,960] [INFO] Task succeeded: Blastn
[2023-06-29 11:31:52,964] [INFO] Selected 24 target genomes.
[2023-06-29 11:31:52,965] [INFO] Target genome list was writen to GCA_020442165.1_ASM2044216v1_genomic.fna/target_genomes.txt
[2023-06-29 11:31:52,973] [INFO] Task started: fastANI
[2023-06-29 11:31:52,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f30a482-341b-4052-bef4-86274c74f57f/GCA_020442165.1_ASM2044216v1_genomic.fna.gz --refList GCA_020442165.1_ASM2044216v1_genomic.fna/target_genomes.txt --output GCA_020442165.1_ASM2044216v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:32:10,078] [INFO] Task succeeded: fastANI
[2023-06-29 11:32:10,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga93078f5-2f2e-46f3-873c-f3061960c6b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:32:10,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga93078f5-2f2e-46f3-873c-f3061960c6b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:32:10,097] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 11:32:10,097] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 11:32:10,097] [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
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	77.4917	215	1392	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	77.2032	133	1392	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	77.1359	184	1392	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	77.0516	224	1392	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	76.9979	166	1392	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	76.9881	168	1392	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.9201	117	1392	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.9103	132	1392	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.8187	134	1392	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.7785	144	1392	95	below_threshold
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	76.7421	144	1392	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	76.7169	98	1392	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	76.6601	128	1392	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	76.6543	127	1392	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.5914	125	1392	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	76.4076	149	1392	95	below_threshold
Filomicrobium insigne	strain=CGMCC 1.6497	GCA_900104305.1	418854	418854	type	True	76.3645	93	1392	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.3527	110	1392	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	76.3213	98	1392	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	76.1206	85	1392	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	76.017	98	1392	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	75.9845	89	1392	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	75.8182	62	1392	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.6182	59	1392	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:32:10,099] [INFO] DFAST Taxonomy check result was written to GCA_020442165.1_ASM2044216v1_genomic.fna/tc_result.tsv
[2023-06-29 11:32:10,100] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:32:10,100] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:32:10,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga93078f5-2f2e-46f3-873c-f3061960c6b4/dqc_reference/checkm_data
[2023-06-29 11:32:10,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:32:10,143] [INFO] Task started: CheckM
[2023-06-29 11:32:10,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020442165.1_ASM2044216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020442165.1_ASM2044216v1_genomic.fna/checkm_input GCA_020442165.1_ASM2044216v1_genomic.fna/checkm_result
[2023-06-29 11:32:50,916] [INFO] Task succeeded: CheckM
[2023-06-29 11:32:50,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 11:32:50,937] [INFO] ===== Completeness check finished =====
[2023-06-29 11:32:50,937] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:32:50,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020442165.1_ASM2044216v1_genomic.fna/markers.fasta)
[2023-06-29 11:32:50,937] [INFO] Task started: Blastn
[2023-06-29 11:32:50,938] [INFO] Running command: blastn -query GCA_020442165.1_ASM2044216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga93078f5-2f2e-46f3-873c-f3061960c6b4/dqc_reference/reference_markers_gtdb.fasta -out GCA_020442165.1_ASM2044216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:32:52,115] [INFO] Task succeeded: Blastn
[2023-06-29 11:32:52,118] [INFO] Selected 27 target genomes.
[2023-06-29 11:32:52,118] [INFO] Target genome list was writen to GCA_020442165.1_ASM2044216v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:32:52,151] [INFO] Task started: fastANI
[2023-06-29 11:32:52,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f30a482-341b-4052-bef4-86274c74f57f/GCA_020442165.1_ASM2044216v1_genomic.fna.gz --refList GCA_020442165.1_ASM2044216v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020442165.1_ASM2044216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:33:09,433] [INFO] Task succeeded: fastANI
[2023-06-29 11:33:09,453] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 11:33:09,454] [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_016793635.1	s__JAEUMD01 sp016793635	78.1239	351	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__JAEUMD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708035.1	s__Hyphomicrobium_A sp009708035	77.4789	216	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793445.1	s__Hyphomicrobium sp016793445	77.4283	177	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026145.1	s__Hyphomicrobium_A sp009026145	77.4205	239	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002928395.1	s__Hyphomicrobium sp002928395	77.3156	120	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018819265.1	s__Filomicrobium sp018819265	77.2358	216	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019137195.1	s__Hyphomicrobium sp019137195	77.2005	198	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304275.1	s__Hyphomicrobium sp017304275	77.0653	154	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117455.1	s__Hyphomicrobium sp900117455	77.0649	204	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826555.1	s__Hyphomicrobium sp902826555	77.0515	187	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383415.1	s__Hyphomicrobium zavarzinii	77.0406	225	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.69	98.69	0.95	0.95	2	-
GCA_018830445.1	s__Filomicrobium sp018830445	77.0392	191	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279935.1	s__Hyphomicrobium sp002279935	77.0165	160	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_013306565.1	s__Hyphomicrobium_A sulfonivorans	76.9979	166	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	98.55	97.10	0.95	0.91	3	-
GCF_900117445.1	s__Hyphomicrobium_A sp900117445	76.9568	203	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792465.1	s__Filomicrobium sp017792465	76.9501	159	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Filomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933705.1	s__AWTP1-13 sp008933705	76.8659	210	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046675.1	s__AWTP1-13 sp011046675	76.8294	201	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826715.1	s__CADEFX01 sp902826715	76.7955	147	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__CADEFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000253295.1	s__Hyphomicrobium sp000253295	76.7946	149	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.46	99.46	0.96	0.96	2	-
GCF_000293785.1	s__Rhodoplanes sp000293785	76.7539	112	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143145.1	s__Hyphomicrobium denitrificans	76.7421	144	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	95.20	95.20	0.90	0.90	2	-
GCF_017872635.1	s__Starkeya sp017872635	76.5996	129	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001464955.1	s__Ga0077555 sp001464955	76.3451	175	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Ga0077555	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295845.1	s__Rhodopseudomonas sp001295845	75.9713	134	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694985.1	s__Parvibaculum sp002694985	75.9099	62	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017642695.1	s__Parvibaculum sp017642695	75.6247	76	1392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
--------------------------------------------------------------------------------
[2023-06-29 11:33:09,456] [INFO] GTDB search result was written to GCA_020442165.1_ASM2044216v1_genomic.fna/result_gtdb.tsv
[2023-06-29 11:33:09,456] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:33:09,461] [INFO] DFAST_QC result json was written to GCA_020442165.1_ASM2044216v1_genomic.fna/dqc_result.json
[2023-06-29 11:33:09,461] [INFO] DFAST_QC completed!
[2023-06-29 11:33:09,462] [INFO] Total running time: 0h1m34s