[2023-06-30 19:16:06,853] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:16:06,857] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:16:06,857] [INFO] DQC Reference Directory: /var/lib/cwl/stgd862517c-66c6-49bc-81dd-18ae3adbfb09/dqc_reference
[2023-06-30 19:16:09,193] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:16:09,195] [INFO] Task started: Prodigal
[2023-06-30 19:16:09,195] [INFO] Running command: gunzip -c /var/lib/cwl/stga9874245-b2c3-4706-b644-90ac07a410d7/GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna.gz | prodigal -d GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/cds.fna -a GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:16:15,380] [INFO] Task succeeded: Prodigal
[2023-06-30 19:16:15,380] [INFO] Task started: HMMsearch
[2023-06-30 19:16:15,381] [INFO] Running command: hmmsearch --tblout GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd862517c-66c6-49bc-81dd-18ae3adbfb09/dqc_reference/reference_markers.hmm GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:16:15,660] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:16:15,662] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga9874245-b2c3-4706-b644-90ac07a410d7/GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna.gz]
[2023-06-30 19:16:15,697] [INFO] Query marker FASTA was written to GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/markers.fasta
[2023-06-30 19:16:15,697] [INFO] Task started: Blastn
[2023-06-30 19:16:15,698] [INFO] Running command: blastn -query GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/markers.fasta -db /var/lib/cwl/stgd862517c-66c6-49bc-81dd-18ae3adbfb09/dqc_reference/reference_markers.fasta -out GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:16:16,390] [INFO] Task succeeded: Blastn
[2023-06-30 19:16:16,396] [INFO] Selected 20 target genomes.
[2023-06-30 19:16:16,397] [INFO] Target genome list was writen to GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/target_genomes.txt
[2023-06-30 19:16:16,402] [INFO] Task started: fastANI
[2023-06-30 19:16:16,402] [INFO] Running command: fastANI --query /var/lib/cwl/stga9874245-b2c3-4706-b644-90ac07a410d7/GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna.gz --refList GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/target_genomes.txt --output GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:16:30,181] [INFO] Task succeeded: fastANI
[2023-06-30 19:16:30,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd862517c-66c6-49bc-81dd-18ae3adbfb09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:16:30,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd862517c-66c6-49bc-81dd-18ae3adbfb09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:16:30,198] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:16:30,198] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:16:30,198] [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
Jatrophihabitans endophyticus	strain=DSM 45627	GCA_900129455.1	1206085	1206085	type	True	74.9089	71	493	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	74.8833	74	493	95	below_threshold
Pseudonocardia oceani	strain=KRD185	GCA_019263585.2	2792013	2792013	type	True	74.8496	102	493	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	74.8196	85	493	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	74.8104	75	493	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	74.8097	92	493	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	74.7628	97	493	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.7042	98	493	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	74.6657	93	493	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:16:30,201] [INFO] DFAST Taxonomy check result was written to GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/tc_result.tsv
[2023-06-30 19:16:30,202] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:16:30,203] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:16:30,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd862517c-66c6-49bc-81dd-18ae3adbfb09/dqc_reference/checkm_data
[2023-06-30 19:16:30,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:16:30,242] [INFO] Task started: CheckM
[2023-06-30 19:16:30,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/checkm_input GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/checkm_result
[2023-06-30 19:16:54,165] [INFO] Task succeeded: CheckM
[2023-06-30 19:16:54,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.24%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 19:16:54,191] [INFO] ===== Completeness check finished =====
[2023-06-30 19:16:54,191] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:16:54,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/markers.fasta)
[2023-06-30 19:16:54,196] [INFO] Task started: Blastn
[2023-06-30 19:16:54,197] [INFO] Running command: blastn -query GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/markers.fasta -db /var/lib/cwl/stgd862517c-66c6-49bc-81dd-18ae3adbfb09/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:16:55,275] [INFO] Task succeeded: Blastn
[2023-06-30 19:16:55,279] [INFO] Selected 20 target genomes.
[2023-06-30 19:16:55,279] [INFO] Target genome list was writen to GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:16:55,284] [INFO] Task started: fastANI
[2023-06-30 19:16:55,284] [INFO] Running command: fastANI --query /var/lib/cwl/stga9874245-b2c3-4706-b644-90ac07a410d7/GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna.gz --refList GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/target_genomes_gtdb.txt --output GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:17:03,884] [INFO] Task succeeded: fastANI
[2023-06-30 19:17:03,912] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 19:17:03,913] [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_903928275.1	s__CAIYQJ01 sp903928275	79.7511	234	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIYQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881055.1	s__C-114 sp005881055	77.5545	92	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__C-114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875645.1	s__VGPE01 sp016875645	77.3119	76	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__VGPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005880805.1	s__CF-16 sp005880805	77.2219	68	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CF-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250155.1	s__UBA5189 sp003250155	77.1236	81	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	99.47	99.47	0.88	0.88	2	-
GCA_903930745.1	s__CAIXZV01 sp903930745	77.0441	106	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIXZV01	95.0	99.19	99.11	0.83	0.82	3	-
GCA_017881905.1	s__Chersky-267 sp017881905	76.988	107	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Chersky-267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191395.1	s__UBA5189 sp016191395	76.945	88	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882635.1	s__CF-46 sp005882635	76.9131	105	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CF-46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200675.1	s__UBA5189 sp016200675	76.8636	80	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001795245.1	s__UBA5189 sp001795245	76.843	118	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026785.1	s__UBA5189 sp012026785	76.8202	96	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200745.1	s__SPCO01 sp016200745	76.8008	93	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__SPCO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881915.1	s__Palsa-1033 sp017881915	76.6821	86	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1033	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860675.1	s__CTSoil-043 sp017860675	76.6734	80	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CTSoil-043	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169655.1	s__Palsa-1033 sp003169655	76.4856	82	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1033	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001443375.1	s__CSP1-4 sp001443375	76.4634	100	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CSP1-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003171065.1	s__Fen-1039 sp003171065	76.3571	67	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	99.79	99.79	0.91	0.91	2	-
GCA_003171035.1	s__Fen-1039 sp003171035	76.1716	56	493	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 19:17:03,915] [INFO] GTDB search result was written to GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/result_gtdb.tsv
[2023-06-30 19:17:03,916] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:17:03,920] [INFO] DFAST_QC result json was written to GCA_903830355.1_freshwater_MAG_---_LaPlata-15m-b_bin-529_genomic.fna/dqc_result.json
[2023-06-30 19:17:03,921] [INFO] DFAST_QC completed!
[2023-06-30 19:17:03,921] [INFO] Total running time: 0h0m57s