[2023-07-01 07:17:20,902] [INFO] DFAST_QC pipeline started.
[2023-07-01 07:17:20,904] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 07:17:20,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg5aa61d81-254f-4afb-a55c-b2a546f7900f/dqc_reference
[2023-07-01 07:17:22,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 07:17:22,158] [INFO] Task started: Prodigal
[2023-07-01 07:17:22,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg50132522-7801-45a2-bc9d-4bf0e9e9a31e/GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna.gz | prodigal -d GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/cds.fna -a GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 07:17:51,654] [INFO] Task succeeded: Prodigal
[2023-07-01 07:17:51,655] [INFO] Task started: HMMsearch
[2023-07-01 07:17:51,655] [INFO] Running command: hmmsearch --tblout GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5aa61d81-254f-4afb-a55c-b2a546f7900f/dqc_reference/reference_markers.hmm GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/protein.faa > /dev/null
[2023-07-01 07:17:51,893] [INFO] Task succeeded: HMMsearch
[2023-07-01 07:17:51,895] [INFO] Found 6/6 markers.
[2023-07-01 07:17:51,937] [INFO] Query marker FASTA was written to GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/markers.fasta
[2023-07-01 07:17:51,937] [INFO] Task started: Blastn
[2023-07-01 07:17:51,937] [INFO] Running command: blastn -query GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aa61d81-254f-4afb-a55c-b2a546f7900f/dqc_reference/reference_markers.fasta -out GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:17:52,634] [INFO] Task succeeded: Blastn
[2023-07-01 07:17:52,638] [INFO] Selected 19 target genomes.
[2023-07-01 07:17:52,639] [INFO] Target genome list was writen to GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/target_genomes.txt
[2023-07-01 07:17:52,654] [INFO] Task started: fastANI
[2023-07-01 07:17:52,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg50132522-7801-45a2-bc9d-4bf0e9e9a31e/GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna.gz --refList GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/target_genomes.txt --output GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 07:18:06,804] [INFO] Task succeeded: fastANI
[2023-07-01 07:18:06,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5aa61d81-254f-4afb-a55c-b2a546f7900f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 07:18:06,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5aa61d81-254f-4afb-a55c-b2a546f7900f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 07:18:06,816] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 07:18:06,816] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 07:18:06,816] [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
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	83.0067	606	957	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	77.6184	239	957	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.7829	58	957	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	75.639	57	957	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	75.5271	66	957	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	75.2913	51	957	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.2842	78	957	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.1415	101	957	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	75.0728	108	957	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.0569	117	957	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	74.9586	65	957	95	below_threshold
Streptomyces daghestanicus	strain=JCM 4365	GCA_014649475.1	66885	66885	suspected-type	True	74.9499	66	957	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 07:18:06,819] [INFO] DFAST Taxonomy check result was written to GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/tc_result.tsv
[2023-07-01 07:18:06,819] [INFO] ===== Taxonomy check completed =====
[2023-07-01 07:18:06,820] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 07:18:06,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5aa61d81-254f-4afb-a55c-b2a546f7900f/dqc_reference/checkm_data
[2023-07-01 07:18:06,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 07:18:06,866] [INFO] Task started: CheckM
[2023-07-01 07:18:06,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/checkm_input GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/checkm_result
[2023-07-01 07:18:36,055] [INFO] Task succeeded: CheckM
[2023-07-01 07:18:36,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 07:18:36,097] [INFO] ===== Completeness check finished =====
[2023-07-01 07:18:36,097] [INFO] ===== Start GTDB Search =====
[2023-07-01 07:18:36,098] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/markers.fasta)
[2023-07-01 07:18:36,098] [INFO] Task started: Blastn
[2023-07-01 07:18:36,098] [INFO] Running command: blastn -query GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/markers.fasta -db /var/lib/cwl/stg5aa61d81-254f-4afb-a55c-b2a546f7900f/dqc_reference/reference_markers_gtdb.fasta -out GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:18:37,191] [INFO] Task succeeded: Blastn
[2023-07-01 07:18:37,199] [INFO] Selected 7 target genomes.
[2023-07-01 07:18:37,199] [INFO] Target genome list was writen to GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 07:18:37,204] [INFO] Task started: fastANI
[2023-07-01 07:18:37,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg50132522-7801-45a2-bc9d-4bf0e9e9a31e/GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna.gz --refList GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/target_genomes_gtdb.txt --output GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 07:18:43,185] [INFO] Task succeeded: fastANI
[2023-07-01 07:18:43,192] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 07:18:43,192] [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_903843705.1	s__Geothrix sp903843705	99.0916	828	957	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.09	98.86	0.88	0.85	6	conclusive
GCA_903876615.1	s__Geothrix sp903876615	93.8214	510	957	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903857495.1	s__Geothrix sp903857495	90.7775	854	957	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.99	99.97	0.99	0.98	50	-
GCA_903863195.1	s__Geothrix sp903863195	90.674	796	957	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.63	99.47	0.91	0.90	5	-
GCA_013334395.1	s__Geothrix sp013334395	90.4676	679	957	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903937385.1	s__Geothrix sp903937385	90.4478	846	957	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.84	98.90	0.96	0.91	10	-
GCA_903840385.1	s__Geothrix sp903840385	84.1117	660	957	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.80	99.80	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-07-01 07:18:43,195] [INFO] GTDB search result was written to GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/result_gtdb.tsv
[2023-07-01 07:18:43,195] [INFO] ===== GTDB Search completed =====
[2023-07-01 07:18:43,198] [INFO] DFAST_QC result json was written to GCA_903883145.1_freshwater_MAG_---_Ki2-D4_bin-0631_genomic.fna/dqc_result.json
[2023-07-01 07:18:43,199] [INFO] DFAST_QC completed!
[2023-07-01 07:18:43,199] [INFO] Total running time: 0h1m22s