[2023-06-29 21:28:14,866] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:28:14,868] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:28:14,868] [INFO] DQC Reference Directory: /var/lib/cwl/stgeef29693-5192-4c19-8fb1-c68c9fea6c80/dqc_reference
[2023-06-29 21:28:16,138] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:28:16,139] [INFO] Task started: Prodigal
[2023-06-29 21:28:16,140] [INFO] Running command: gunzip -c /var/lib/cwl/stg3077e176-b1a3-49ef-b993-055bacddf262/GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna.gz | prodigal -d GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/cds.fna -a GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:28:26,779] [INFO] Task succeeded: Prodigal
[2023-06-29 21:28:26,780] [INFO] Task started: HMMsearch
[2023-06-29 21:28:26,780] [INFO] Running command: hmmsearch --tblout GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeef29693-5192-4c19-8fb1-c68c9fea6c80/dqc_reference/reference_markers.hmm GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:28:27,080] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:28:27,082] [INFO] Found 6/6 markers.
[2023-06-29 21:28:27,126] [INFO] Query marker FASTA was written to GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/markers.fasta
[2023-06-29 21:28:27,127] [INFO] Task started: Blastn
[2023-06-29 21:28:27,127] [INFO] Running command: blastn -query GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/markers.fasta -db /var/lib/cwl/stgeef29693-5192-4c19-8fb1-c68c9fea6c80/dqc_reference/reference_markers.fasta -out GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:28:27,954] [INFO] Task succeeded: Blastn
[2023-06-29 21:28:27,958] [INFO] Selected 22 target genomes.
[2023-06-29 21:28:27,958] [INFO] Target genome list was writen to GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/target_genomes.txt
[2023-06-29 21:28:27,960] [INFO] Task started: fastANI
[2023-06-29 21:28:27,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg3077e176-b1a3-49ef-b993-055bacddf262/GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna.gz --refList GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/target_genomes.txt --output GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:28:42,804] [INFO] Task succeeded: fastANI
[2023-06-29 21:28:42,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeef29693-5192-4c19-8fb1-c68c9fea6c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:28:42,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeef29693-5192-4c19-8fb1-c68c9fea6c80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:28:42,825] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:28:42,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:28:42,825] [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
Pseudomethylobacillus aquaticus	strain=H-5	GCA_003730115.1	2676064	2676064	type	True	76.8096	127	1045	95	below_threshold
Novimethylophilus kurashikiensis	strain=La2-4	GCA_003112435.1	1825523	1825523	type	True	76.7903	141	1045	95	below_threshold
Methylovorus mays	strain=VKM B-2221	GCA_020531915.1	184077	184077	type	True	76.782	104	1045	95	below_threshold
Methylovorus glucosotrophus	strain=DSM 6874	GCA_009858335.1	266009	266009	type	True	76.7139	103	1045	95	below_threshold
Methylobacillus arboreus	strain=VKM B-2590	GCA_020532725.1	755170	755170	type	True	76.6185	97	1045	95	below_threshold
Methylovorus menthalis	strain=VKM B-2663	GCA_020523625.1	1002227	1002227	type	True	76.5686	88	1045	95	below_threshold
Methylobacillus flagellatus	strain=KT	GCA_000013705.1	405	405	type	True	76.4308	94	1045	95	below_threshold
Sulfuriferula multivorans	strain=TTN	GCA_003851125.1	1559896	1559896	type	True	76.4049	65	1045	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	76.3362	78	1045	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	76.3114	54	1045	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	76.3108	76	1045	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	76.2784	68	1045	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	76.2483	69	1045	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	76.2353	67	1045	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	76.0895	58	1045	95	below_threshold
Methylobacillus gramineus	strain=VKM B-2591	GCA_020532675.1	755169	755169	type	True	76.0458	72	1045	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	75.6015	54	1045	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:28:42,828] [INFO] DFAST Taxonomy check result was written to GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/tc_result.tsv
[2023-06-29 21:28:42,828] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:28:42,829] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:28:42,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeef29693-5192-4c19-8fb1-c68c9fea6c80/dqc_reference/checkm_data
[2023-06-29 21:28:42,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:28:42,874] [INFO] Task started: CheckM
[2023-06-29 21:28:42,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/checkm_input GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/checkm_result
[2023-06-29 21:29:19,000] [INFO] Task succeeded: CheckM
[2023-06-29 21:29:19,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.80%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-29 21:29:19,025] [INFO] ===== Completeness check finished =====
[2023-06-29 21:29:19,026] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:29:19,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/markers.fasta)
[2023-06-29 21:29:19,027] [INFO] Task started: Blastn
[2023-06-29 21:29:19,027] [INFO] Running command: blastn -query GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/markers.fasta -db /var/lib/cwl/stgeef29693-5192-4c19-8fb1-c68c9fea6c80/dqc_reference/reference_markers_gtdb.fasta -out GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:29:20,519] [INFO] Task succeeded: Blastn
[2023-06-29 21:29:20,524] [INFO] Selected 21 target genomes.
[2023-06-29 21:29:20,525] [INFO] Target genome list was writen to GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:29:20,535] [INFO] Task started: fastANI
[2023-06-29 21:29:20,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg3077e176-b1a3-49ef-b993-055bacddf262/GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna.gz --refList GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/target_genomes_gtdb.txt --output GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:29:30,318] [INFO] Task succeeded: fastANI
[2023-06-29 21:29:30,335] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:29:30,335] [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_903824575.1	s__CAIJXJ01 sp903824575	100.0	1038	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__CAIJXJ01	95.0	99.81	99.81	0.93	0.93	2	conclusive
GCF_001645185.1	s__MM2 sp001645185	77.4622	191	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__MM2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001704575.1	s__UBA6140 sp001704575	77.0468	106	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168195.1	s__CABHOJ01 sp902168195	77.0371	89	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__CABHOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842435.1	s__UBA6140 sp002842435	76.8566	138	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880825.1	s__JADGRN01 sp017880825	76.8478	77	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__JADGRN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730115.1	s__Pseudomethylobacillus aquaticus	76.8096	127	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502435.1	s__Pseudomethylobacillus flagellatus_A	76.8029	122	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Pseudomethylobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858335.1	s__Methylovorus glucosotrophus	76.7349	102	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylovorus	95.0	97.11	97.01	0.92	0.92	3	-
GCA_905339275.1	s__UBA6140 sp905339275	76.6287	116	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013705.1	s__Methylobacillus flagellatus	76.4308	94	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylobacillus	95.0	97.96	97.96	0.89	0.89	2	-
GCF_003851125.1	s__Sulfuriferula multivorans	76.3771	66	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938015.1	s__Sulfuriferula plumbiphila	76.2483	69	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuriferulaceae;g__Sulfuriferula	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002842135.1	s__UBA6140 sp002842135	76.1764	75	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__UBA6140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	75.989	68	1045	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-29 21:29:30,337] [INFO] GTDB search result was written to GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/result_gtdb.tsv
[2023-06-29 21:29:30,338] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:29:30,353] [INFO] DFAST_QC result json was written to GCA_903824575.1_freshwater_MAG_---_A14_bin-1995_genomic.fna/dqc_result.json
[2023-06-29 21:29:30,353] [INFO] DFAST_QC completed!
[2023-06-29 21:29:30,354] [INFO] Total running time: 0h1m15s