[2023-06-29 22:30:31,749] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:30:31,751] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:30:31,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ee54e81-46ec-4c11-979e-3658194c9c9b/dqc_reference
[2023-06-29 22:30:32,936] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:30:32,937] [INFO] Task started: Prodigal
[2023-06-29 22:30:32,937] [INFO] Running command: gunzip -c /var/lib/cwl/stg347f212e-0536-4a50-bff4-3dc33ccaf8ad/GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna.gz | prodigal -d GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/cds.fna -a GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:30:43,272] [INFO] Task succeeded: Prodigal
[2023-06-29 22:30:43,272] [INFO] Task started: HMMsearch
[2023-06-29 22:30:43,273] [INFO] Running command: hmmsearch --tblout GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ee54e81-46ec-4c11-979e-3658194c9c9b/dqc_reference/reference_markers.hmm GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:30:43,464] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:30:43,465] [INFO] Found 6/6 markers.
[2023-06-29 22:30:43,496] [INFO] Query marker FASTA was written to GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/markers.fasta
[2023-06-29 22:30:43,497] [INFO] Task started: Blastn
[2023-06-29 22:30:43,497] [INFO] Running command: blastn -query GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ee54e81-46ec-4c11-979e-3658194c9c9b/dqc_reference/reference_markers.fasta -out GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:30:44,132] [INFO] Task succeeded: Blastn
[2023-06-29 22:30:44,136] [INFO] Selected 36 target genomes.
[2023-06-29 22:30:44,136] [INFO] Target genome list was writen to GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/target_genomes.txt
[2023-06-29 22:30:44,142] [INFO] Task started: fastANI
[2023-06-29 22:30:44,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg347f212e-0536-4a50-bff4-3dc33ccaf8ad/GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna.gz --refList GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/target_genomes.txt --output GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:31:10,078] [INFO] Task succeeded: fastANI
[2023-06-29 22:31:10,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ee54e81-46ec-4c11-979e-3658194c9c9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:31:10,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ee54e81-46ec-4c11-979e-3658194c9c9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:31:10,086] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:31:10,086] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:31:10,087] [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
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	76.2032	52	1112	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	75.9689	51	1112	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	75.8631	64	1112	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	75.7875	55	1112	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	75.7373	68	1112	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	75.6226	60	1112	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:31:10,089] [INFO] DFAST Taxonomy check result was written to GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/tc_result.tsv
[2023-06-29 22:31:10,089] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:31:10,089] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:31:10,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ee54e81-46ec-4c11-979e-3658194c9c9b/dqc_reference/checkm_data
[2023-06-29 22:31:10,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:31:10,125] [INFO] Task started: CheckM
[2023-06-29 22:31:10,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/checkm_input GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/checkm_result
[2023-06-29 22:31:43,095] [INFO] Task succeeded: CheckM
[2023-06-29 22:31:43,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:31:43,114] [INFO] ===== Completeness check finished =====
[2023-06-29 22:31:43,114] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:31:43,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/markers.fasta)
[2023-06-29 22:31:43,114] [INFO] Task started: Blastn
[2023-06-29 22:31:43,115] [INFO] Running command: blastn -query GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ee54e81-46ec-4c11-979e-3658194c9c9b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:31:44,046] [INFO] Task succeeded: Blastn
[2023-06-29 22:31:44,050] [INFO] Selected 27 target genomes.
[2023-06-29 22:31:44,050] [INFO] Target genome list was writen to GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:31:44,067] [INFO] Task started: fastANI
[2023-06-29 22:31:44,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg347f212e-0536-4a50-bff4-3dc33ccaf8ad/GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna.gz --refList GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/target_genomes_gtdb.txt --output GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:31:59,262] [INFO] Task succeeded: fastANI
[2023-06-29 22:31:59,271] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:31:59,271] [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_903908265.1	s__CAIYLH01 sp903908265	99.5284	943	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.59	99.26	0.90	0.86	35	conclusive
GCA_903879335.1	s__CAIYLH01 sp903879335	78.4617	222	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.91	99.87	0.98	0.96	13	-
GCA_903927005.1	s__CAIYLH01 sp903927005	78.2803	165	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.60	99.60	0.92	0.92	2	-
GCA_903884235.1	s__CAIYLH01 sp903884235	77.2066	149	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.42	99.08	0.95	0.88	22	-
GCA_018241525.1	s__SZAS-83 sp018241525	76.3947	149	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138335.1	s__Steroidobacter_A agariperforans	75.9689	51	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297335.1	s__SCUD01 sp004297335	75.9328	62	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SCUD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241545.1	s__SZAS-83 sp018241545	75.8846	94	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138485.1	s__Steroidobacter_A soli	75.7373	68	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241425.1	s__13-2-20CM-66-19 sp018241425	75.595	62	1112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:31:59,274] [INFO] GTDB search result was written to GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/result_gtdb.tsv
[2023-06-29 22:31:59,274] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:31:59,277] [INFO] DFAST_QC result json was written to GCA_903856305.1_freshwater_MAG_---_VK3_bin-1644_genomic.fna/dqc_result.json
[2023-06-29 22:31:59,277] [INFO] DFAST_QC completed!
[2023-06-29 22:31:59,277] [INFO] Total running time: 0h1m28s