[2023-06-17 08:06:50,083] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:06:50,087] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:06:50,087] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2a9a9f0-2e26-4461-9822-b7ffbac0debf/dqc_reference
[2023-06-17 08:06:51,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:06:51,744] [INFO] Task started: Prodigal
[2023-06-17 08:06:51,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg53f0d962-7ecb-4e9e-a8de-12ff0bff4ad6/GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna.gz | prodigal -d GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/cds.fna -a GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:06:56,003] [INFO] Task succeeded: Prodigal
[2023-06-17 08:06:56,003] [INFO] Task started: HMMsearch
[2023-06-17 08:06:56,003] [INFO] Running command: hmmsearch --tblout GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2a9a9f0-2e26-4461-9822-b7ffbac0debf/dqc_reference/reference_markers.hmm GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:06:56,220] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:06:56,222] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg53f0d962-7ecb-4e9e-a8de-12ff0bff4ad6/GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna.gz]
[2023-06-17 08:06:56,243] [INFO] Query marker FASTA was written to GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/markers.fasta
[2023-06-17 08:06:56,243] [INFO] Task started: Blastn
[2023-06-17 08:06:56,244] [INFO] Running command: blastn -query GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2a9a9f0-2e26-4461-9822-b7ffbac0debf/dqc_reference/reference_markers.fasta -out GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:06:56,944] [INFO] Task succeeded: Blastn
[2023-06-17 08:06:56,948] [INFO] Selected 23 target genomes.
[2023-06-17 08:06:56,949] [INFO] Target genome list was writen to GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/target_genomes.txt
[2023-06-17 08:06:56,959] [INFO] Task started: fastANI
[2023-06-17 08:06:56,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg53f0d962-7ecb-4e9e-a8de-12ff0bff4ad6/GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna.gz --refList GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/target_genomes.txt --output GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:07:10,716] [INFO] Task succeeded: fastANI
[2023-06-17 08:07:10,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2a9a9f0-2e26-4461-9822-b7ffbac0debf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:07:10,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2a9a9f0-2e26-4461-9822-b7ffbac0debf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:07:10,723] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:07:10,723] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 08:07:10,723] [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
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	76.947	54	630	95	below_threshold
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	76.8317	85	630	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	76.7409	78	630	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	76.36	58	630	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	76.2217	61	630	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 08:07:10,726] [INFO] DFAST Taxonomy check result was written to GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/tc_result.tsv
[2023-06-17 08:07:10,726] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:07:10,726] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:07:10,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2a9a9f0-2e26-4461-9822-b7ffbac0debf/dqc_reference/checkm_data
[2023-06-17 08:07:10,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:07:10,752] [INFO] Task started: CheckM
[2023-06-17 08:07:10,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/checkm_input GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/checkm_result
[2023-06-17 08:07:31,386] [INFO] Task succeeded: CheckM
[2023-06-17 08:07:31,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:07:31,412] [INFO] ===== Completeness check finished =====
[2023-06-17 08:07:31,412] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:07:31,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/markers.fasta)
[2023-06-17 08:07:31,413] [INFO] Task started: Blastn
[2023-06-17 08:07:31,413] [INFO] Running command: blastn -query GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2a9a9f0-2e26-4461-9822-b7ffbac0debf/dqc_reference/reference_markers_gtdb.fasta -out GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:07:32,439] [INFO] Task succeeded: Blastn
[2023-06-17 08:07:32,443] [INFO] Selected 14 target genomes.
[2023-06-17 08:07:32,443] [INFO] Target genome list was writen to GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:07:32,453] [INFO] Task started: fastANI
[2023-06-17 08:07:32,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg53f0d962-7ecb-4e9e-a8de-12ff0bff4ad6/GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna.gz --refList GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/target_genomes_gtdb.txt --output GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:07:38,037] [INFO] Task succeeded: fastANI
[2023-06-17 08:07:38,055] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:07:38,055] [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_905479075.1	s__GCA-002733105 sp905479075	100.0	628	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479985.1	s__GCA-002733105 sp905479985	78.347	173	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018646825.1	s__GCA-002733105 sp018646825	78.1228	128	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181885.1	s__GCA-002733105 sp905181885	77.713	112	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859375.1	s__GCA-002733105 sp014859375	77.5101	114	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733335.1	s__GCA-002733105 sp002733335	77.2649	99	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003645385.1	s__GCA-002733105 sp003645385	77.246	96	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	98.88	98.88	0.61	0.61	2	-
GCA_002733505.1	s__GCA-002733105 sp002733505	77.2209	100	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215775.1	s__GCA-002733105 sp013215775	77.2149	134	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163115.1	s__41-12-T18 sp002163115	77.0611	116	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400805.1	s__41-12-T18 sp002400805	76.8656	60	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053005.1	s__GCA-002733105 sp011053005	76.8156	108	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733715.2	s__GCA-002733105 sp002733715	76.7832	121	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214595.1	s__Methylophaga aminisulfidivorans	76.7409	78	630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.12	97.07	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-17 08:07:38,057] [INFO] GTDB search result was written to GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/result_gtdb.tsv
[2023-06-17 08:07:38,058] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:07:38,061] [INFO] DFAST_QC result json was written to GCA_905479075.1_0.2_20180517_Bin_72_sub_2_genomic.fna/dqc_result.json
[2023-06-17 08:07:38,061] [INFO] DFAST_QC completed!
[2023-06-17 08:07:38,061] [INFO] Total running time: 0h0m48s