[2023-06-30 13:24:28,694] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:24:28,726] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:24:28,726] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfafb19e-e898-49b3-816d-8044baf7f08c/dqc_reference
[2023-06-30 13:24:30,135] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:24:30,136] [INFO] Task started: Prodigal
[2023-06-30 13:24:30,136] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfe18d5d-a2cf-491a-99b2-11316d878300/GCA_016934455.1_ASM1693445v1_genomic.fna.gz | prodigal -d GCA_016934455.1_ASM1693445v1_genomic.fna/cds.fna -a GCA_016934455.1_ASM1693445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:24:43,196] [INFO] Task succeeded: Prodigal
[2023-06-30 13:24:43,196] [INFO] Task started: HMMsearch
[2023-06-30 13:24:43,196] [INFO] Running command: hmmsearch --tblout GCA_016934455.1_ASM1693445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfafb19e-e898-49b3-816d-8044baf7f08c/dqc_reference/reference_markers.hmm GCA_016934455.1_ASM1693445v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:24:43,508] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:24:43,510] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdfe18d5d-a2cf-491a-99b2-11316d878300/GCA_016934455.1_ASM1693445v1_genomic.fna.gz]
[2023-06-30 13:24:43,560] [INFO] Query marker FASTA was written to GCA_016934455.1_ASM1693445v1_genomic.fna/markers.fasta
[2023-06-30 13:24:43,560] [INFO] Task started: Blastn
[2023-06-30 13:24:43,561] [INFO] Running command: blastn -query GCA_016934455.1_ASM1693445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfafb19e-e898-49b3-816d-8044baf7f08c/dqc_reference/reference_markers.fasta -out GCA_016934455.1_ASM1693445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:44,321] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:44,325] [INFO] Selected 26 target genomes.
[2023-06-30 13:24:44,326] [INFO] Target genome list was writen to GCA_016934455.1_ASM1693445v1_genomic.fna/target_genomes.txt
[2023-06-30 13:24:44,328] [INFO] Task started: fastANI
[2023-06-30 13:24:44,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfe18d5d-a2cf-491a-99b2-11316d878300/GCA_016934455.1_ASM1693445v1_genomic.fna.gz --refList GCA_016934455.1_ASM1693445v1_genomic.fna/target_genomes.txt --output GCA_016934455.1_ASM1693445v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:25:06,313] [INFO] Task succeeded: fastANI
[2023-06-30 13:25:06,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfafb19e-e898-49b3-816d-8044baf7f08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:25:06,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfafb19e-e898-49b3-816d-8044baf7f08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:25:06,338] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:25:06,338] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 13:25:06,338] [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
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.4589	112	1566	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1959	265	1566	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.1715	165	1566	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	75.1123	163	1566	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.1017	220	1566	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	75.0843	151	1566	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	75.0771	204	1566	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.0424	135	1566	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	75.0423	84	1566	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	75.0206	200	1566	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	74.9432	211	1566	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	74.9238	167	1566	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	74.9202	67	1566	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	74.9113	91	1566	95	below_threshold
Halomonas daqiaonensis	strain=CGMCC 1.9150	GCA_900109725.1	650850	650850	type	True	74.9015	57	1566	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	74.8613	119	1566	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	74.8559	119	1566	95	below_threshold
Deinobacterium chartae	strain=DSM 21458	GCA_014202645.1	521158	521158	type	True	74.8512	75	1566	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	74.8456	97	1566	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8446	448	1566	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	74.8286	160	1566	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	74.7771	127	1566	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	74.7373	69	1566	95	below_threshold
Agrococcus jejuensis	strain=DSM 22002	GCA_900099705.1	399736	399736	type	True	74.6675	165	1566	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	74.6598	157	1566	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 13:25:06,340] [INFO] DFAST Taxonomy check result was written to GCA_016934455.1_ASM1693445v1_genomic.fna/tc_result.tsv
[2023-06-30 13:25:06,341] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:25:06,341] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:25:06,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfafb19e-e898-49b3-816d-8044baf7f08c/dqc_reference/checkm_data
[2023-06-30 13:25:06,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:25:06,398] [INFO] Task started: CheckM
[2023-06-30 13:25:06,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016934455.1_ASM1693445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016934455.1_ASM1693445v1_genomic.fna/checkm_input GCA_016934455.1_ASM1693445v1_genomic.fna/checkm_result
[2023-06-30 13:25:46,374] [INFO] Task succeeded: CheckM
[2023-06-30 13:25:46,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.38%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:25:46,403] [INFO] ===== Completeness check finished =====
[2023-06-30 13:25:46,404] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:25:46,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016934455.1_ASM1693445v1_genomic.fna/markers.fasta)
[2023-06-30 13:25:46,405] [INFO] Task started: Blastn
[2023-06-30 13:25:46,405] [INFO] Running command: blastn -query GCA_016934455.1_ASM1693445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfafb19e-e898-49b3-816d-8044baf7f08c/dqc_reference/reference_markers_gtdb.fasta -out GCA_016934455.1_ASM1693445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:25:47,661] [INFO] Task succeeded: Blastn
[2023-06-30 13:25:47,666] [INFO] Selected 25 target genomes.
[2023-06-30 13:25:47,666] [INFO] Target genome list was writen to GCA_016934455.1_ASM1693445v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:25:47,674] [INFO] Task started: fastANI
[2023-06-30 13:25:47,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfe18d5d-a2cf-491a-99b2-11316d878300/GCA_016934455.1_ASM1693445v1_genomic.fna.gz --refList GCA_016934455.1_ASM1693445v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016934455.1_ASM1693445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:26:08,130] [INFO] Task succeeded: fastANI
[2023-06-30 13:26:08,154] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:26:08,154] [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_016934455.1	s__JAFGSX01 sp016934455	100.0	1547	1566	d__Bacteria;p__Myxococcota;c__JAFGSX01;o__JAFGSX01;f__JAFGSX01;g__JAFGSX01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002408385.1	s__UBA10939 sp002408385	75.5455	256	1566	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__UBA5297;g__UBA10939	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903874275.1	s__CAIOAK01 sp903874275	75.4779	142	1566	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__CAIOAK01	95.0	99.83	99.81	0.95	0.94	3	-
GCA_903904005.1	s__CAIOAK01 sp903904005	75.3966	135	1566	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__CAIOAK01	95.0	99.78	99.64	0.94	0.92	4	-
GCF_013340205.1	s__R267 sp013340205	75.3838	268	1566	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718565.1	s__JADKCZ01 sp016718565	75.3035	289	1566	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JADKCZ01	95.0	99.81	99.81	0.97	0.97	2	-
GCA_016214955.1	s__JACRMN01 sp016214955	75.2846	256	1566	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JACRMN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	75.2752	241	1566	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696455.1	s__UBA2376 sp900696455	75.2228	468	1566	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_016707895.1	s__UBA2376 sp016707895	75.1738	557	1566	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCF_000013385.1	s__Anaeromyxobacter dehalogenans_B	75.1665	285	1566	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794525.1	s__UBA2376 sp016794525	75.1517	597	1566	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	75.0824	171	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133645.1	s__RBG-13-68-16 sp003133645	75.0767	115	1566	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	75.0655	527	1566	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	75.0604	157	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526565.1	s__WYBL01 sp011526565	74.9926	292	1566	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Fen-336;f__Fen-336;g__WYBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312895.1	s__Luteimonas sp008312895	74.9538	173	1566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141555.1	s__FEN-413 sp003141555	74.9522	53	1566	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__UBA4085;g__FEN-413	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179555.1	s__Solidesulfovibrio fructosivorans	74.8984	70	1566	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:26:08,156] [INFO] GTDB search result was written to GCA_016934455.1_ASM1693445v1_genomic.fna/result_gtdb.tsv
[2023-06-30 13:26:08,156] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:26:08,161] [INFO] DFAST_QC result json was written to GCA_016934455.1_ASM1693445v1_genomic.fna/dqc_result.json
[2023-06-30 13:26:08,161] [INFO] DFAST_QC completed!
[2023-06-30 13:26:08,162] [INFO] Total running time: 0h1m39s