[2023-06-30 12:22:21,217] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:22:21,220] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:22:21,220] [INFO] DQC Reference Directory: /var/lib/cwl/stga92a0ac5-82d2-4eec-83df-7056431c3be0/dqc_reference
[2023-06-30 12:22:22,495] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:22:22,497] [INFO] Task started: Prodigal
[2023-06-30 12:22:22,497] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4397e52-440c-422d-808e-b132630ed6d8/GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna.gz | prodigal -d GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/cds.fna -a GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:22:32,038] [INFO] Task succeeded: Prodigal
[2023-06-30 12:22:32,039] [INFO] Task started: HMMsearch
[2023-06-30 12:22:32,039] [INFO] Running command: hmmsearch --tblout GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga92a0ac5-82d2-4eec-83df-7056431c3be0/dqc_reference/reference_markers.hmm GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:22:32,284] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:22:32,285] [INFO] Found 6/6 markers.
[2023-06-30 12:22:32,320] [INFO] Query marker FASTA was written to GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/markers.fasta
[2023-06-30 12:22:32,321] [INFO] Task started: Blastn
[2023-06-30 12:22:32,321] [INFO] Running command: blastn -query GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/markers.fasta -db /var/lib/cwl/stga92a0ac5-82d2-4eec-83df-7056431c3be0/dqc_reference/reference_markers.fasta -out GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:22:32,979] [INFO] Task succeeded: Blastn
[2023-06-30 12:22:32,983] [INFO] Selected 18 target genomes.
[2023-06-30 12:22:32,984] [INFO] Target genome list was writen to GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/target_genomes.txt
[2023-06-30 12:22:32,987] [INFO] Task started: fastANI
[2023-06-30 12:22:32,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4397e52-440c-422d-808e-b132630ed6d8/GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna.gz --refList GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/target_genomes.txt --output GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:22:47,243] [INFO] Task succeeded: fastANI
[2023-06-30 12:22:47,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga92a0ac5-82d2-4eec-83df-7056431c3be0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:22:47,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga92a0ac5-82d2-4eec-83df-7056431c3be0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:22:47,253] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:22:47,253] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:22:47,253] [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
Gemmatimonas phototrophica	strain=AP64	GCA_000695095.2	1379270	1379270	type	True	76.9149	86	1054	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	76.6779	124	1054	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	76.6757	94	1054	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	76.1707	257	1054	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.6275	65	1054	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	74.7895	164	1054	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:22:47,255] [INFO] DFAST Taxonomy check result was written to GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/tc_result.tsv
[2023-06-30 12:22:47,256] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:22:47,256] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:22:47,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga92a0ac5-82d2-4eec-83df-7056431c3be0/dqc_reference/checkm_data
[2023-06-30 12:22:47,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:22:47,289] [INFO] Task started: CheckM
[2023-06-30 12:22:47,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/checkm_input GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/checkm_result
[2023-06-30 12:23:19,793] [INFO] Task succeeded: CheckM
[2023-06-30 12:23:19,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:23:19,817] [INFO] ===== Completeness check finished =====
[2023-06-30 12:23:19,817] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:23:19,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/markers.fasta)
[2023-06-30 12:23:19,818] [INFO] Task started: Blastn
[2023-06-30 12:23:19,818] [INFO] Running command: blastn -query GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/markers.fasta -db /var/lib/cwl/stga92a0ac5-82d2-4eec-83df-7056431c3be0/dqc_reference/reference_markers_gtdb.fasta -out GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:23:20,817] [INFO] Task succeeded: Blastn
[2023-06-30 12:23:20,822] [INFO] Selected 14 target genomes.
[2023-06-30 12:23:20,822] [INFO] Target genome list was writen to GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:23:20,830] [INFO] Task started: fastANI
[2023-06-30 12:23:20,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4397e52-440c-422d-808e-b132630ed6d8/GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna.gz --refList GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/target_genomes_gtdb.txt --output GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:23:29,494] [INFO] Task succeeded: fastANI
[2023-06-30 12:23:29,510] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:23:29,511] [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_903910555.1	s__Fen-1231 sp903910555	99.9918	1051	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	99.81	99.24	0.99	0.96	5	conclusive
GCA_017881585.1	s__Fen-1231 sp017881585	81.2347	574	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003171215.1	s__Fen-1231 sp003171215	80.8291	669	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	97.59	95.49	0.88	0.84	3	-
GCA_016194585.1	s__Fen-1231 sp016194585	77.7789	299	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	99.33	99.33	0.81	0.81	2	-
GCA_903882745.1	s__Fen-1231 sp903882745	77.622	197	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	99.53	99.21	0.97	0.93	11	-
GCA_016218305.1	s__PNKL01 sp016218305	77.3535	124	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871915.1	s__PNKF01 sp016871915	77.1769	116	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	99.71	99.71	0.88	0.88	2	-
GCA_016182795.1	s__PNKL01 sp016182795	77.1073	161	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874035.1	s__Fen-1231 sp016874035	77.0758	154	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Fen-1231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714015.1	s__PNKF01 sp016714015	77.053	212	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871855.1	s__PNKL01 sp016871855	76.7795	149	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825965.1	s__PNKF01 sp902825965	76.7395	165	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__PNKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794835.1	s__SCN-70-22 sp016794835	76.5661	62	1054	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:23:29,514] [INFO] GTDB search result was written to GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/result_gtdb.tsv
[2023-06-30 12:23:29,514] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:23:29,519] [INFO] DFAST_QC result json was written to GCA_903867045.1_freshwater_MAG_---_Umea3p2_bin-0537_genomic.fna/dqc_result.json
[2023-06-30 12:23:29,519] [INFO] DFAST_QC completed!
[2023-06-30 12:23:29,519] [INFO] Total running time: 0h1m8s