[2023-06-13 19:29:48,803] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:29:48,805] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:29:48,806] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb5f9e73-dcab-4af8-b4a3-b362b13f88e6/dqc_reference
[2023-06-13 19:29:50,180] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:29:50,181] [INFO] Task started: Prodigal
[2023-06-13 19:29:50,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg333c500f-39c1-4eeb-9df3-4c06e27d3f5b/GCA_022562195.1_ASM2256219v1_genomic.fna.gz | prodigal -d GCA_022562195.1_ASM2256219v1_genomic.fna/cds.fna -a GCA_022562195.1_ASM2256219v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:29:56,979] [INFO] Task succeeded: Prodigal
[2023-06-13 19:29:56,979] [INFO] Task started: HMMsearch
[2023-06-13 19:29:56,979] [INFO] Running command: hmmsearch --tblout GCA_022562195.1_ASM2256219v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb5f9e73-dcab-4af8-b4a3-b362b13f88e6/dqc_reference/reference_markers.hmm GCA_022562195.1_ASM2256219v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:29:57,154] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:29:57,155] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg333c500f-39c1-4eeb-9df3-4c06e27d3f5b/GCA_022562195.1_ASM2256219v1_genomic.fna.gz]
[2023-06-13 19:29:57,181] [INFO] Query marker FASTA was written to GCA_022562195.1_ASM2256219v1_genomic.fna/markers.fasta
[2023-06-13 19:29:57,181] [INFO] Task started: Blastn
[2023-06-13 19:29:57,182] [INFO] Running command: blastn -query GCA_022562195.1_ASM2256219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb5f9e73-dcab-4af8-b4a3-b362b13f88e6/dqc_reference/reference_markers.fasta -out GCA_022562195.1_ASM2256219v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:29:57,887] [INFO] Task succeeded: Blastn
[2023-06-13 19:29:57,891] [INFO] Selected 22 target genomes.
[2023-06-13 19:29:57,891] [INFO] Target genome list was writen to GCA_022562195.1_ASM2256219v1_genomic.fna/target_genomes.txt
[2023-06-13 19:29:57,892] [INFO] Task started: fastANI
[2023-06-13 19:29:57,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg333c500f-39c1-4eeb-9df3-4c06e27d3f5b/GCA_022562195.1_ASM2256219v1_genomic.fna.gz --refList GCA_022562195.1_ASM2256219v1_genomic.fna/target_genomes.txt --output GCA_022562195.1_ASM2256219v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:30:14,884] [INFO] Task succeeded: fastANI
[2023-06-13 19:30:14,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb5f9e73-dcab-4af8-b4a3-b362b13f88e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:30:14,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb5f9e73-dcab-4af8-b4a3-b362b13f88e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:30:14,900] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:30:14,900] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 19:30:14,901] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	77.151	161	734	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.879	139	734	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.8315	190	734	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.6684	111	734	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.6134	143	734	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.6022	215	734	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.5573	197	734	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.5399	200	734	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.4912	135	734	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.4569	154	734	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.4493	156	734	95	below_threshold
Algihabitans albus	strain=HHTR 118	GCA_003572205.1	2164067	2164067	type	True	76.299	74	734	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.292	137	734	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.2882	139	734	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.2108	184	734	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.1956	148	734	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.9009	116	734	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	75.8933	77	734	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	75.807	86	734	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	75.5829	57	734	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:30:14,902] [INFO] DFAST Taxonomy check result was written to GCA_022562195.1_ASM2256219v1_genomic.fna/tc_result.tsv
[2023-06-13 19:30:14,903] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:30:14,903] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:30:14,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb5f9e73-dcab-4af8-b4a3-b362b13f88e6/dqc_reference/checkm_data
[2023-06-13 19:30:14,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:30:14,933] [INFO] Task started: CheckM
[2023-06-13 19:30:14,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022562195.1_ASM2256219v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022562195.1_ASM2256219v1_genomic.fna/checkm_input GCA_022562195.1_ASM2256219v1_genomic.fna/checkm_result
[2023-06-13 19:30:39,605] [INFO] Task succeeded: CheckM
[2023-06-13 19:30:39,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 8.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 19:30:39,625] [INFO] ===== Completeness check finished =====
[2023-06-13 19:30:39,625] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:30:39,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022562195.1_ASM2256219v1_genomic.fna/markers.fasta)
[2023-06-13 19:30:39,626] [INFO] Task started: Blastn
[2023-06-13 19:30:39,626] [INFO] Running command: blastn -query GCA_022562195.1_ASM2256219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb5f9e73-dcab-4af8-b4a3-b362b13f88e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_022562195.1_ASM2256219v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:30:40,777] [INFO] Task succeeded: Blastn
[2023-06-13 19:30:40,781] [INFO] Selected 14 target genomes.
[2023-06-13 19:30:40,781] [INFO] Target genome list was writen to GCA_022562195.1_ASM2256219v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:30:40,783] [INFO] Task started: fastANI
[2023-06-13 19:30:40,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg333c500f-39c1-4eeb-9df3-4c06e27d3f5b/GCA_022562195.1_ASM2256219v1_genomic.fna.gz --refList GCA_022562195.1_ASM2256219v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022562195.1_ASM2256219v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:30:48,878] [INFO] Task succeeded: fastANI
[2023-06-13 19:30:48,890] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 19:30:48,890] [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_002938075.1	s__Casp-alpha2 sp002938075	78.059	152	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	77.9681	211	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_013349695.1	s__GCA-2686765 sp013349695	77.4981	145	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__GCA-2686765	95.0	98.27	95.45	0.83	0.65	4	-
GCA_016187325.1	s__JACPJY01 sp016187325	77.4352	195	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	77.233	181	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214125.1	s__JACRPC01 sp016214125	77.2285	135	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__WMHbin7;g__JACRPC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693905.1	s__2-12-FULL-67-15 sp009693905	77.2237	96	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	99.79	99.79	0.72	0.72	2	-
GCA_001830425.1	s__2-02-FULL-58-16 sp001830425	77.2002	124	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__2-02-FULL-58-16	95.0	99.96	99.96	0.97	0.97	2	-
GCA_016202695.1	s__JACQOE01 sp016202695	77.1371	141	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710335.1	s__JADJXQ01 sp016710335	77.005	130	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__JADJXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.7081	165	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364825.1	s__Azospirillum sp008364825	76.5442	142	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.23	95.23	0.77	0.77	2	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.3721	110	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240745.1	s__Reyranella sp018240745	76.1081	122	734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 19:30:48,893] [INFO] GTDB search result was written to GCA_022562195.1_ASM2256219v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:30:48,893] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:30:48,898] [INFO] DFAST_QC result json was written to GCA_022562195.1_ASM2256219v1_genomic.fna/dqc_result.json
[2023-06-13 19:30:48,898] [INFO] DFAST_QC completed!
[2023-06-13 19:30:48,898] [INFO] Total running time: 0h1m0s