[2023-07-01 04:39:49,319] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:39:49,322] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:39:49,322] [INFO] DQC Reference Directory: /var/lib/cwl/stge2d1dcdf-c3f8-4501-b8dd-16d041d503ba/dqc_reference
[2023-07-01 04:39:50,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:39:50,645] [INFO] Task started: Prodigal
[2023-07-01 04:39:50,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f92520c-a9dc-462f-8061-df7fca6013b2/GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna.gz | prodigal -d GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/cds.fna -a GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:40:10,616] [INFO] Task succeeded: Prodigal
[2023-07-01 04:40:10,617] [INFO] Task started: HMMsearch
[2023-07-01 04:40:10,617] [INFO] Running command: hmmsearch --tblout GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2d1dcdf-c3f8-4501-b8dd-16d041d503ba/dqc_reference/reference_markers.hmm GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:40:10,908] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:40:10,910] [INFO] Found 6/6 markers.
[2023-07-01 04:40:10,949] [INFO] Query marker FASTA was written to GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/markers.fasta
[2023-07-01 04:40:10,949] [INFO] Task started: Blastn
[2023-07-01 04:40:10,949] [INFO] Running command: blastn -query GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d1dcdf-c3f8-4501-b8dd-16d041d503ba/dqc_reference/reference_markers.fasta -out GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:40:11,518] [INFO] Task succeeded: Blastn
[2023-07-01 04:40:11,523] [INFO] Selected 31 target genomes.
[2023-07-01 04:40:11,523] [INFO] Target genome list was writen to GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/target_genomes.txt
[2023-07-01 04:40:11,524] [INFO] Task started: fastANI
[2023-07-01 04:40:11,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f92520c-a9dc-462f-8061-df7fca6013b2/GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna.gz --refList GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/target_genomes.txt --output GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:40:28,672] [INFO] Task succeeded: fastANI
[2023-07-01 04:40:28,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2d1dcdf-c3f8-4501-b8dd-16d041d503ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:40:28,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2d1dcdf-c3f8-4501-b8dd-16d041d503ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:40:28,675] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:40:28,675] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 04:40:28,676] [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
--------------------------------------------------------------------------------
[2023-07-01 04:40:28,678] [INFO] DFAST Taxonomy check result was written to GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/tc_result.tsv
[2023-07-01 04:40:28,679] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:40:28,679] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:40:28,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2d1dcdf-c3f8-4501-b8dd-16d041d503ba/dqc_reference/checkm_data
[2023-07-01 04:40:28,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:40:28,724] [INFO] Task started: CheckM
[2023-07-01 04:40:28,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/checkm_input GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/checkm_result
[2023-07-01 04:41:28,959] [INFO] Task succeeded: CheckM
[2023-07-01 04:41:28,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 04:41:28,984] [INFO] ===== Completeness check finished =====
[2023-07-01 04:41:28,984] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:41:28,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/markers.fasta)
[2023-07-01 04:41:28,985] [INFO] Task started: Blastn
[2023-07-01 04:41:28,985] [INFO] Running command: blastn -query GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/markers.fasta -db /var/lib/cwl/stge2d1dcdf-c3f8-4501-b8dd-16d041d503ba/dqc_reference/reference_markers_gtdb.fasta -out GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:41:29,750] [INFO] Task succeeded: Blastn
[2023-07-01 04:41:29,757] [INFO] Selected 21 target genomes.
[2023-07-01 04:41:29,757] [INFO] Target genome list was writen to GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:41:29,759] [INFO] Task started: fastANI
[2023-07-01 04:41:29,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f92520c-a9dc-462f-8061-df7fca6013b2/GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna.gz --refList GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/target_genomes_gtdb.txt --output GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:41:43,861] [INFO] Task succeeded: fastANI
[2023-07-01 04:41:43,878] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:41:43,879] [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_903945175.1	s__CAIVAT01 sp903945175	99.8693	1159	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.77	99.52	0.96	0.91	13	conclusive
GCA_903885595.1	s__CAIVAT01 sp903885595	79.7088	518	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.84	99.83	0.92	0.92	3	-
GCA_903903985.1	s__CAIVAT01 sp903903985	77.7999	321	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875045.1	s__CAIVAT01 sp903875045	77.7073	296	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925275.1	s__CAIVAT01 sp903925275	77.6843	284	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959905.1	s__CAIVAT01 sp903959905	77.6776	247	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.98	99.96	0.97	0.97	6	-
GCA_903828645.1	s__CAIVAT01 sp903828645	77.6422	278	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.44	99.32	0.88	0.87	3	-
GCA_903913885.1	s__CAIVAT01 sp903913885	77.5612	245	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.91	99.89	0.96	0.95	3	-
GCA_903845055.1	s__CAIVAT01 sp903845055	77.4238	220	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.64	99.58	0.94	0.93	3	-
GCA_009928665.1	s__SACF01 sp009928665	76.7359	122	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__SACF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882335.1	s__FEN-979 sp017882335	76.1731	74	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__FEN-979	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 04:41:43,881] [INFO] GTDB search result was written to GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/result_gtdb.tsv
[2023-07-01 04:41:43,882] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:41:43,886] [INFO] DFAST_QC result json was written to GCA_903942435.1_freshwater_MAG_---_Loc080925-7m_bin-0190_genomic.fna/dqc_result.json
[2023-07-01 04:41:43,887] [INFO] DFAST_QC completed!
[2023-07-01 04:41:43,887] [INFO] Total running time: 0h1m55s