[2023-07-01 05:37:47,758] [INFO] DFAST_QC pipeline started.
[2023-07-01 05:37:47,760] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 05:37:47,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg60354727-5ffa-4726-9b60-5cc87a20bf2b/dqc_reference
[2023-07-01 05:37:48,932] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 05:37:48,933] [INFO] Task started: Prodigal
[2023-07-01 05:37:48,933] [INFO] Running command: gunzip -c /var/lib/cwl/stga6d1ff82-8e57-449f-bf34-70124c287cc6/GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna.gz | prodigal -d GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/cds.fna -a GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 05:37:59,659] [INFO] Task succeeded: Prodigal
[2023-07-01 05:37:59,659] [INFO] Task started: HMMsearch
[2023-07-01 05:37:59,659] [INFO] Running command: hmmsearch --tblout GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60354727-5ffa-4726-9b60-5cc87a20bf2b/dqc_reference/reference_markers.hmm GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/protein.faa > /dev/null
[2023-07-01 05:37:59,939] [INFO] Task succeeded: HMMsearch
[2023-07-01 05:37:59,940] [INFO] Found 6/6 markers.
[2023-07-01 05:37:59,973] [INFO] Query marker FASTA was written to GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/markers.fasta
[2023-07-01 05:37:59,974] [INFO] Task started: Blastn
[2023-07-01 05:37:59,974] [INFO] Running command: blastn -query GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/markers.fasta -db /var/lib/cwl/stg60354727-5ffa-4726-9b60-5cc87a20bf2b/dqc_reference/reference_markers.fasta -out GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:38:00,985] [INFO] Task succeeded: Blastn
[2023-07-01 05:38:00,990] [INFO] Selected 27 target genomes.
[2023-07-01 05:38:00,990] [INFO] Target genome list was writen to GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/target_genomes.txt
[2023-07-01 05:38:00,991] [INFO] Task started: fastANI
[2023-07-01 05:38:00,992] [INFO] Running command: fastANI --query /var/lib/cwl/stga6d1ff82-8e57-449f-bf34-70124c287cc6/GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna.gz --refList GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/target_genomes.txt --output GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 05:38:18,169] [INFO] Task succeeded: fastANI
[2023-07-01 05:38:18,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60354727-5ffa-4726-9b60-5cc87a20bf2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 05:38:18,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60354727-5ffa-4726-9b60-5cc87a20bf2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 05:38:18,193] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 05:38:18,193] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 05:38:18,193] [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
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	78.5809	312	1118	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	78.5312	307	1118	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	77.6937	189	1118	95	below_threshold
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	77.6802	204	1118	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.2608	206	1118	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	77.2354	201	1118	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.0109	130	1118	95	below_threshold
Sulfuriferula multivorans	strain=TTN	GCA_003851125.1	1559896	1559896	type	True	76.8833	109	1118	95	below_threshold
Sulfuriferula plumbiphila	strain=Gro7	GCA_009938015.1	171865	171865	type	True	76.7558	139	1118	95	below_threshold
Sulfuriferula plumbiphila	strain=NBRC 107929	GCA_007992375.1	171865	171865	type	True	76.7368	140	1118	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	76.7118	120	1118	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	76.7109	144	1118	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	76.685	124	1118	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	76.6717	166	1118	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	76.653	129	1118	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	76.6374	173	1118	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	76.626	171	1118	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.444	149	1118	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.4392	145	1118	95	below_threshold
Stenotrophomonas terrae	strain=DSM 18941	GCA_001431465.1	405446	405446	type	True	76.1925	69	1118	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.1867	103	1118	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	76.0931	132	1118	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	75.9864	127	1118	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	75.9465	98	1118	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	75.932	99	1118	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	75.9272	73	1118	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	75.8006	69	1118	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 05:38:18,196] [INFO] DFAST Taxonomy check result was written to GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/tc_result.tsv
[2023-07-01 05:38:18,196] [INFO] ===== Taxonomy check completed =====
[2023-07-01 05:38:18,196] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 05:38:18,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60354727-5ffa-4726-9b60-5cc87a20bf2b/dqc_reference/checkm_data
[2023-07-01 05:38:18,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 05:38:18,233] [INFO] Task started: CheckM
[2023-07-01 05:38:18,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/checkm_input GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/checkm_result
[2023-07-01 05:38:52,710] [INFO] Task succeeded: CheckM
[2023-07-01 05:38:52,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 05:38:52,733] [INFO] ===== Completeness check finished =====
[2023-07-01 05:38:52,733] [INFO] ===== Start GTDB Search =====
[2023-07-01 05:38:52,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/markers.fasta)
[2023-07-01 05:38:52,734] [INFO] Task started: Blastn
[2023-07-01 05:38:52,734] [INFO] Running command: blastn -query GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/markers.fasta -db /var/lib/cwl/stg60354727-5ffa-4726-9b60-5cc87a20bf2b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:38:54,604] [INFO] Task succeeded: Blastn
[2023-07-01 05:38:54,620] [INFO] Selected 9 target genomes.
[2023-07-01 05:38:54,620] [INFO] Target genome list was writen to GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 05:38:54,621] [INFO] Task started: fastANI
[2023-07-01 05:38:54,622] [INFO] Running command: fastANI --query /var/lib/cwl/stga6d1ff82-8e57-449f-bf34-70124c287cc6/GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna.gz --refList GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/target_genomes_gtdb.txt --output GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 05:39:01,142] [INFO] Task succeeded: fastANI
[2023-07-01 05:39:01,153] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 05:39:01,154] [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_903835655.1	s__PFJX01 sp903835655	99.883	1078	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.87	99.69	0.96	0.90	25	conclusive
GCA_903883985.1	s__PFJX01 sp903883985	89.3945	615	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	98.94	98.94	0.77	0.77	2	-
GCA_002784045.1	s__PFJX01 sp002784045	81.4995	519	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.74	99.63	0.93	0.93	3	-
GCA_016719465.1	s__PFJX01 sp016719465	79.9347	415	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.31	99.27	0.95	0.94	3	-
GCA_903918705.1	s__PFJX01 sp903918705	79.5672	365	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873935.1	s__PFJX01 sp016873935	79.4957	391	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219425.1	s__PFJX01 sp016219425	79.4871	421	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772925.1	s__PFJX01 sp009772925	79.4511	443	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	99.99	99.98	1.00	0.99	4	-
GCA_002281555.1	s__PFJX01 sp002281555	79.2833	390	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__PFJX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 05:39:01,156] [INFO] GTDB search result was written to GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/result_gtdb.tsv
[2023-07-01 05:39:01,156] [INFO] ===== GTDB Search completed =====
[2023-07-01 05:39:01,161] [INFO] DFAST_QC result json was written to GCA_903834115.1_freshwater_MAG_---_MJ120620B_bin-457_genomic.fna/dqc_result.json
[2023-07-01 05:39:01,162] [INFO] DFAST_QC completed!
[2023-07-01 05:39:01,162] [INFO] Total running time: 0h1m13s