[2023-06-30 16:29:08,575] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:29:08,578] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:29:08,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c9ac66e-1906-493c-b0de-248db5052a2e/dqc_reference
[2023-06-30 16:29:11,381] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:29:11,382] [INFO] Task started: Prodigal
[2023-06-30 16:29:11,383] [INFO] Running command: gunzip -c /var/lib/cwl/stga238aa5a-2e1d-41b9-961b-913d1be23935/GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna.gz | prodigal -d GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/cds.fna -a GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:29:17,944] [INFO] Task succeeded: Prodigal
[2023-06-30 16:29:17,944] [INFO] Task started: HMMsearch
[2023-06-30 16:29:17,944] [INFO] Running command: hmmsearch --tblout GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c9ac66e-1906-493c-b0de-248db5052a2e/dqc_reference/reference_markers.hmm GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:29:18,176] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:29:18,178] [INFO] Found 6/6 markers.
[2023-06-30 16:29:18,206] [INFO] Query marker FASTA was written to GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/markers.fasta
[2023-06-30 16:29:18,207] [INFO] Task started: Blastn
[2023-06-30 16:29:18,207] [INFO] Running command: blastn -query GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c9ac66e-1906-493c-b0de-248db5052a2e/dqc_reference/reference_markers.fasta -out GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:29:18,786] [INFO] Task succeeded: Blastn
[2023-06-30 16:29:18,790] [INFO] Selected 14 target genomes.
[2023-06-30 16:29:18,791] [INFO] Target genome list was writen to GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/target_genomes.txt
[2023-06-30 16:29:18,793] [INFO] Task started: fastANI
[2023-06-30 16:29:18,794] [INFO] Running command: fastANI --query /var/lib/cwl/stga238aa5a-2e1d-41b9-961b-913d1be23935/GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna.gz --refList GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/target_genomes.txt --output GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:29:25,474] [INFO] Task succeeded: fastANI
[2023-06-30 16:29:25,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c9ac66e-1906-493c-b0de-248db5052a2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:29:25,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c9ac66e-1906-493c-b0de-248db5052a2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:29:25,487] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:29:25,487] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:29:25,487] [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
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	79.6725	396	821	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	77.9749	237	821	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	77.5772	155	821	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.2466	116	821	95	below_threshold
Prosthecochloris aestuarii	strain=DSM 271	GCA_000020625.1	1102	1102	type	True	76.0171	57	821	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:29:25,490] [INFO] DFAST Taxonomy check result was written to GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/tc_result.tsv
[2023-06-30 16:29:25,491] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:29:25,491] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:29:25,491] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c9ac66e-1906-493c-b0de-248db5052a2e/dqc_reference/checkm_data
[2023-06-30 16:29:25,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:29:25,523] [INFO] Task started: CheckM
[2023-06-30 16:29:25,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/checkm_input GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/checkm_result
[2023-06-30 16:30:01,930] [INFO] Task succeeded: CheckM
[2023-06-30 16:30:01,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 16:30:01,952] [INFO] ===== Completeness check finished =====
[2023-06-30 16:30:01,953] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:30:01,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/markers.fasta)
[2023-06-30 16:30:01,953] [INFO] Task started: Blastn
[2023-06-30 16:30:01,954] [INFO] Running command: blastn -query GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c9ac66e-1906-493c-b0de-248db5052a2e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:30:02,784] [INFO] Task succeeded: Blastn
[2023-06-30 16:30:02,789] [INFO] Selected 10 target genomes.
[2023-06-30 16:30:02,789] [INFO] Target genome list was writen to GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:30:02,792] [INFO] Task started: fastANI
[2023-06-30 16:30:02,792] [INFO] Running command: fastANI --query /var/lib/cwl/stga238aa5a-2e1d-41b9-961b-913d1be23935/GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna.gz --refList GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/target_genomes_gtdb.txt --output GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:30:08,185] [INFO] Task succeeded: fastANI
[2023-06-30 16:30:08,199] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:30:08,199] [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_903843305.1	s__Chlorobium sp903843305	99.9434	805	821	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.98	96.88	0.93	0.82	17	conclusive
GCA_903887845.1	s__Chlorobium sp903887845	85.0084	587	821	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.96	99.96	0.95	0.95	2	-
GCA_903937835.1	s__Chlorobium sp903937835	84.7066	534	821	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.77	99.60	0.93	0.86	6	-
GCA_903836465.1	s__Chlorobium sp903836465	84.6926	576	821	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.30	97.63	0.95	0.90	12	-
GCA_903929845.1	s__Chlorobium sp903929845	84.4665	406	821	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.53	99.40	0.83	0.81	5	-
GCA_903994455.1	s__Chlorobium sp903994455	83.8458	506	821	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.65	99.40	0.86	0.85	13	-
GCA_005862225.1	s__Chlorobium sp005862225	82.342	524	821	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903915955.1	s__Chlorobium sp903915955	81.8639	428	821	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.74	96.45	0.88	0.78	5	-
GCA_903994525.1	s__Chlorobium sp903994525	81.0634	378	821	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.83	98.94	0.92	0.84	27	-
--------------------------------------------------------------------------------
[2023-06-30 16:30:08,201] [INFO] GTDB search result was written to GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/result_gtdb.tsv
[2023-06-30 16:30:08,202] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:30:08,239] [INFO] DFAST_QC result json was written to GCA_903883255.1_freshwater_MAG_---_AM-lipid-02-D8_bin-528_genomic.fna/dqc_result.json
[2023-06-30 16:30:08,240] [INFO] DFAST_QC completed!
[2023-06-30 16:30:08,240] [INFO] Total running time: 0h0m60s