[2023-06-30 16:53:38,588] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:53:38,591] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:53:38,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg99195eb0-924b-4922-8b53-3b199f1af91f/dqc_reference
[2023-06-30 16:53:41,353] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:53:41,355] [INFO] Task started: Prodigal
[2023-06-30 16:53:41,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b0d8d76-9d0b-44e8-a380-a5a1a8423fc0/GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna.gz | prodigal -d GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/cds.fna -a GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:54:00,692] [INFO] Task succeeded: Prodigal
[2023-06-30 16:54:00,692] [INFO] Task started: HMMsearch
[2023-06-30 16:54:00,692] [INFO] Running command: hmmsearch --tblout GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99195eb0-924b-4922-8b53-3b199f1af91f/dqc_reference/reference_markers.hmm GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:54:01,031] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:54:01,032] [INFO] Found 6/6 markers.
[2023-06-30 16:54:01,086] [INFO] Query marker FASTA was written to GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/markers.fasta
[2023-06-30 16:54:01,087] [INFO] Task started: Blastn
[2023-06-30 16:54:01,087] [INFO] Running command: blastn -query GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/markers.fasta -db /var/lib/cwl/stg99195eb0-924b-4922-8b53-3b199f1af91f/dqc_reference/reference_markers.fasta -out GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:54:01,697] [INFO] Task succeeded: Blastn
[2023-06-30 16:54:01,702] [INFO] Selected 24 target genomes.
[2023-06-30 16:54:01,703] [INFO] Target genome list was writen to GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/target_genomes.txt
[2023-06-30 16:54:01,714] [INFO] Task started: fastANI
[2023-06-30 16:54:01,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b0d8d76-9d0b-44e8-a380-a5a1a8423fc0/GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna.gz --refList GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/target_genomes.txt --output GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:54:25,436] [INFO] Task succeeded: fastANI
[2023-06-30 16:54:25,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99195eb0-924b-4922-8b53-3b199f1af91f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:54:25,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99195eb0-924b-4922-8b53-3b199f1af91f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:54:25,455] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:54:25,456] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:54:25,456] [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
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	76.0995	98	1986	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.1063	57	1986	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.0457	50	1986	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.9689	51	1986	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.8954	70	1986	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	74.6986	57	1986	95	below_threshold
Nocardia yamanashiensis	strain=NBRC 100130	GCA_001613325.1	209247	209247	type	True	74.6979	57	1986	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:54:25,459] [INFO] DFAST Taxonomy check result was written to GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/tc_result.tsv
[2023-06-30 16:54:25,459] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:54:25,460] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:54:25,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99195eb0-924b-4922-8b53-3b199f1af91f/dqc_reference/checkm_data
[2023-06-30 16:54:25,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:54:25,527] [INFO] Task started: CheckM
[2023-06-30 16:54:25,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/checkm_input GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/checkm_result
[2023-06-30 16:55:22,516] [INFO] Task succeeded: CheckM
[2023-06-30 16:55:22,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:55:22,544] [INFO] ===== Completeness check finished =====
[2023-06-30 16:55:22,544] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:55:22,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/markers.fasta)
[2023-06-30 16:55:22,545] [INFO] Task started: Blastn
[2023-06-30 16:55:22,546] [INFO] Running command: blastn -query GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/markers.fasta -db /var/lib/cwl/stg99195eb0-924b-4922-8b53-3b199f1af91f/dqc_reference/reference_markers_gtdb.fasta -out GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:55:23,377] [INFO] Task succeeded: Blastn
[2023-06-30 16:55:23,382] [INFO] Selected 24 target genomes.
[2023-06-30 16:55:23,383] [INFO] Target genome list was writen to GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:55:23,399] [INFO] Task started: fastANI
[2023-06-30 16:55:23,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b0d8d76-9d0b-44e8-a380-a5a1a8423fc0/GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna.gz --refList GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/target_genomes_gtdb.txt --output GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:55:40,258] [INFO] Task succeeded: fastANI
[2023-06-30 16:55:40,270] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:55:40,270] [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_903871935.1	s__CAIQIQ01 sp903871935	99.9081	1894	1986	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__CAIQIQ01	95.0	99.93	99.88	0.97	0.95	13	conclusive
GCF_015169395.1	s__Humisphaera borealis	76.0995	98	1986	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__Humisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367345.1	s__DSYW01 sp011367345	76.04	131	1986	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__DSYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380825.1	s__JACMJD01 sp014380825	75.2958	52	1986	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__JACMJD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002071695.1	s__MWDR01 sp002071695	74.8981	62	1986	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__SM23-33;f__SM23-33;g__MWDR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613325.1	s__Nocardia yamanashiensis	74.6961	58	1986	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:55:40,272] [INFO] GTDB search result was written to GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/result_gtdb.tsv
[2023-06-30 16:55:40,273] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:55:40,276] [INFO] DFAST_QC result json was written to GCA_903839015.1_freshwater_MAG_---_AM-lipid-01-D8_bin-1392_genomic.fna/dqc_result.json
[2023-06-30 16:55:40,276] [INFO] DFAST_QC completed!
[2023-06-30 16:55:40,276] [INFO] Total running time: 0h2m2s