[2023-06-30 21:55:16,098] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:55:16,101] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:55:16,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg4278fd89-1b76-405e-8399-904bab08220d/dqc_reference
[2023-06-30 21:55:18,122] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:55:18,123] [INFO] Task started: Prodigal
[2023-06-30 21:55:18,123] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe8a43c5-cab6-45a4-b862-6a064f34bcd9/GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna.gz | prodigal -d GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/cds.fna -a GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:55:31,168] [INFO] Task succeeded: Prodigal
[2023-06-30 21:55:31,168] [INFO] Task started: HMMsearch
[2023-06-30 21:55:31,168] [INFO] Running command: hmmsearch --tblout GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4278fd89-1b76-405e-8399-904bab08220d/dqc_reference/reference_markers.hmm GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:55:31,397] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:55:31,398] [INFO] Found 6/6 markers.
[2023-06-30 21:55:31,427] [INFO] Query marker FASTA was written to GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/markers.fasta
[2023-06-30 21:55:31,427] [INFO] Task started: Blastn
[2023-06-30 21:55:31,428] [INFO] Running command: blastn -query GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/markers.fasta -db /var/lib/cwl/stg4278fd89-1b76-405e-8399-904bab08220d/dqc_reference/reference_markers.fasta -out GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:55:31,978] [INFO] Task succeeded: Blastn
[2023-06-30 21:55:31,983] [INFO] Selected 28 target genomes.
[2023-06-30 21:55:31,983] [INFO] Target genome list was writen to GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/target_genomes.txt
[2023-06-30 21:55:31,985] [INFO] Task started: fastANI
[2023-06-30 21:55:31,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe8a43c5-cab6-45a4-b862-6a064f34bcd9/GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna.gz --refList GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/target_genomes.txt --output GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:55:56,633] [INFO] Task succeeded: fastANI
[2023-06-30 21:55:56,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4278fd89-1b76-405e-8399-904bab08220d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:55:56,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4278fd89-1b76-405e-8399-904bab08220d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:55:56,639] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:55:56,639] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 21:55:56,639] [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
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.4455	71	883	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.7094	53	883	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.2778	53	883	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 21:55:56,641] [INFO] DFAST Taxonomy check result was written to GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/tc_result.tsv
[2023-06-30 21:55:56,641] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:55:56,641] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:55:56,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4278fd89-1b76-405e-8399-904bab08220d/dqc_reference/checkm_data
[2023-06-30 21:55:56,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:55:56,677] [INFO] Task started: CheckM
[2023-06-30 21:55:56,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/checkm_input GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/checkm_result
[2023-06-30 21:56:36,631] [INFO] Task succeeded: CheckM
[2023-06-30 21:56:36,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.07%
Contamintation: 9.72%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:56:36,652] [INFO] ===== Completeness check finished =====
[2023-06-30 21:56:36,652] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:56:36,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/markers.fasta)
[2023-06-30 21:56:36,653] [INFO] Task started: Blastn
[2023-06-30 21:56:36,653] [INFO] Running command: blastn -query GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/markers.fasta -db /var/lib/cwl/stg4278fd89-1b76-405e-8399-904bab08220d/dqc_reference/reference_markers_gtdb.fasta -out GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:56:37,419] [INFO] Task succeeded: Blastn
[2023-06-30 21:56:37,422] [INFO] Selected 26 target genomes.
[2023-06-30 21:56:37,423] [INFO] Target genome list was writen to GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:56:37,427] [INFO] Task started: fastANI
[2023-06-30 21:56:37,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe8a43c5-cab6-45a4-b862-6a064f34bcd9/GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna.gz --refList GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/target_genomes_gtdb.txt --output GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:56:51,168] [INFO] Task succeeded: fastANI
[2023-06-30 21:56:51,180] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:56:51,180] [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_903858475.1	s__Ferruginibacter sp903858475	99.3449	743	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.60	99.32	0.91	0.84	6	conclusive
GCA_016710935.1	s__Ferruginibacter sp016710935	76.5156	110	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141115.1	s__Ferruginibacter sp013141115	76.4818	145	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268155.1	s__Ferruginibacter sp018268155	76.4431	84	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983695.1	s__Ferruginibacter sp017983695	76.3767	129	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266775.1	s__Ferruginibacter sp018266775	76.3532	98	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786725.1	s__Ferruginibacter sp016786725	76.2508	90	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268135.1	s__Ferruginibacter sp018268135	76.1131	77	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.79	99.79	0.93	0.93	2	-
GCA_016713965.1	s__Ferruginibacter sp016713965	76.074	76	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017988335.1	s__Ferruginibacter sp017988335	76.0738	99	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721385.1	s__Ferruginibacter sp016721385	76.0197	112	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885535.1	s__Ferruginibacter sp009885535	75.975	60	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837525.1	s__Ferruginibacter sp903837525	75.9397	81	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001623405.1	s__Hydrotalea flava	75.7094	53	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	95.88	95.18	0.90	0.86	13	-
GCA_014377975.1	s__Ferruginibacter sp014377975	75.6085	71	883	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 21:56:51,182] [INFO] GTDB search result was written to GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/result_gtdb.tsv
[2023-06-30 21:56:51,183] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:56:51,186] [INFO] DFAST_QC result json was written to GCA_903895025.1_freshwater_MAG_---_Kiruna3_bin-1608_genomic.fna/dqc_result.json
[2023-06-30 21:56:51,186] [INFO] DFAST_QC completed!
[2023-06-30 21:56:51,186] [INFO] Total running time: 0h1m35s