[2023-06-27 15:55:08,335] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:55:08,337] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:55:08,338] [INFO] DQC Reference Directory: /var/lib/cwl/stgd21f5a33-e88d-4820-a626-d206d9a41f44/dqc_reference
[2023-06-27 15:55:10,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:55:10,767] [INFO] Task started: Prodigal
[2023-06-27 15:55:10,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b3b4cb2-a35b-4423-b066-ac9a2883e925/GCA_026708265.1_ASM2670826v1_genomic.fna.gz | prodigal -d GCA_026708265.1_ASM2670826v1_genomic.fna/cds.fna -a GCA_026708265.1_ASM2670826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:55:25,866] [INFO] Task succeeded: Prodigal
[2023-06-27 15:55:25,866] [INFO] Task started: HMMsearch
[2023-06-27 15:55:25,866] [INFO] Running command: hmmsearch --tblout GCA_026708265.1_ASM2670826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd21f5a33-e88d-4820-a626-d206d9a41f44/dqc_reference/reference_markers.hmm GCA_026708265.1_ASM2670826v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:55:26,134] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:55:26,135] [INFO] Found 6/6 markers.
[2023-06-27 15:55:26,184] [INFO] Query marker FASTA was written to GCA_026708265.1_ASM2670826v1_genomic.fna/markers.fasta
[2023-06-27 15:55:26,184] [INFO] Task started: Blastn
[2023-06-27 15:55:26,185] [INFO] Running command: blastn -query GCA_026708265.1_ASM2670826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd21f5a33-e88d-4820-a626-d206d9a41f44/dqc_reference/reference_markers.fasta -out GCA_026708265.1_ASM2670826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:55:26,857] [INFO] Task succeeded: Blastn
[2023-06-27 15:55:26,861] [INFO] Selected 32 target genomes.
[2023-06-27 15:55:26,862] [INFO] Target genome list was writen to GCA_026708265.1_ASM2670826v1_genomic.fna/target_genomes.txt
[2023-06-27 15:55:26,895] [INFO] Task started: fastANI
[2023-06-27 15:55:26,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b3b4cb2-a35b-4423-b066-ac9a2883e925/GCA_026708265.1_ASM2670826v1_genomic.fna.gz --refList GCA_026708265.1_ASM2670826v1_genomic.fna/target_genomes.txt --output GCA_026708265.1_ASM2670826v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:55:50,165] [INFO] Task succeeded: fastANI
[2023-06-27 15:55:50,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd21f5a33-e88d-4820-a626-d206d9a41f44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:55:50,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd21f5a33-e88d-4820-a626-d206d9a41f44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:55:50,184] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:55:50,184] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 15:55:50,185] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.8861	216	1951	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	74.9658	203	1951	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	74.9631	90	1951	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	74.9486	117	1951	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	74.9443	71	1951	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	74.9183	104	1951	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	74.8918	139	1951	95	below_threshold
Pseudoxanthomonas indica	strain=P15	GCA_900167565.1	428993	428993	type	True	74.8846	56	1951	95	below_threshold
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	74.8846	56	1951	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.8661	161	1951	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	74.824	97	1951	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	74.818	58	1951	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	74.8106	59	1951	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	74.7938	154	1951	95	below_threshold
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	74.7827	247	1951	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.7824	178	1951	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	74.7761	174	1951	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	74.7377	350	1951	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	74.7372	79	1951	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.6956	260	1951	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	74.6888	98	1951	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	74.6819	219	1951	95	below_threshold
Streptosporangium becharense	strain=DSM 46887	GCA_014204985.1	1816182	1816182	type	True	74.6777	223	1951	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	74.6101	116	1951	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	74.6058	138	1951	95	below_threshold
Haloferax prahovense	strain=DSM 18310	GCA_000336815.1	381852	381852	type	True	74.6016	108	1951	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 15:55:50,186] [INFO] DFAST Taxonomy check result was written to GCA_026708265.1_ASM2670826v1_genomic.fna/tc_result.tsv
[2023-06-27 15:55:50,187] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:55:50,187] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:55:50,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd21f5a33-e88d-4820-a626-d206d9a41f44/dqc_reference/checkm_data
[2023-06-27 15:55:50,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:55:50,249] [INFO] Task started: CheckM
[2023-06-27 15:55:50,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708265.1_ASM2670826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708265.1_ASM2670826v1_genomic.fna/checkm_input GCA_026708265.1_ASM2670826v1_genomic.fna/checkm_result
[2023-06-27 15:56:34,857] [INFO] Task succeeded: CheckM
[2023-06-27 15:56:34,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 15:56:34,881] [INFO] ===== Completeness check finished =====
[2023-06-27 15:56:34,881] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:56:34,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708265.1_ASM2670826v1_genomic.fna/markers.fasta)
[2023-06-27 15:56:34,882] [INFO] Task started: Blastn
[2023-06-27 15:56:34,882] [INFO] Running command: blastn -query GCA_026708265.1_ASM2670826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd21f5a33-e88d-4820-a626-d206d9a41f44/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708265.1_ASM2670826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:56:36,077] [INFO] Task succeeded: Blastn
[2023-06-27 15:56:36,085] [INFO] Selected 19 target genomes.
[2023-06-27 15:56:36,085] [INFO] Target genome list was writen to GCA_026708265.1_ASM2670826v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:56:36,116] [INFO] Task started: fastANI
[2023-06-27 15:56:36,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b3b4cb2-a35b-4423-b066-ac9a2883e925/GCA_026708265.1_ASM2670826v1_genomic.fna.gz --refList GCA_026708265.1_ASM2670826v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708265.1_ASM2670826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:56:53,612] [INFO] Task succeeded: fastANI
[2023-06-27 15:56:53,627] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 15:56:53,627] [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_009861545.1	s__WTFV01 sp009861545	81.0324	982	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	96.15	96.15	0.82	0.82	2	-
GCA_011523845.1	s__WTFV01 sp011523845	80.9582	1034	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012271165.1	s__JAAXGX01 sp012271165	79.8229	607	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__JAAXGX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523485.1	s__WTFV01 sp011523485	79.5996	585	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009838525.1	s__VXRJ01 sp009838525	78.7551	632	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__VXRJ01	95.0	98.98	98.07	0.95	0.93	4	-
GCA_016192845.1	s__Gp6-AA40 sp016192845	76.6519	249	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328835.1	s__UBA2161 sp002328835	76.4804	219	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_016871375.1	s__Gp6-AA40 sp016871375	76.403	291	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767525.1	s__Gp6-AA40 sp001767525	76.3353	248	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	99.96	99.96	0.95	0.95	2	-
GCA_016184105.1	s__JACPDI01 sp016184105	76.2176	215	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__2-12-FULL-66-21;g__JACPDI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170135.1	s__Fen-181 sp003170135	76.1346	227	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__Fen-181	95.0	99.94	99.94	0.97	0.97	2	-
GCA_016865485.1	s__Luteitalea sp016865485	76.1055	288	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__Luteitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223775.1	s__Gp6-AA45 sp003223775	75.7604	269	1951	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136105.1	s__RPQJ01 sp019136105	75.1392	64	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167565.1	s__Pseudoxanthomonas_A indica	74.8846	56	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018780145.1	s__Ideonella sp018780145	74.8483	117	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	74.8161	97	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728675.1	s__GCA-002728675 sp002728675	74.7425	51	1951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__GCA-002728675	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 15:56:53,629] [INFO] GTDB search result was written to GCA_026708265.1_ASM2670826v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:56:53,630] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:56:53,635] [INFO] DFAST_QC result json was written to GCA_026708265.1_ASM2670826v1_genomic.fna/dqc_result.json
[2023-06-27 15:56:53,635] [INFO] DFAST_QC completed!
[2023-06-27 15:56:53,635] [INFO] Total running time: 0h1m45s