[2023-06-29 21:51:21,231] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:51:21,234] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:51:21,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f028bcd-6e88-4184-b2bb-2510ae9ee99f/dqc_reference
[2023-06-29 21:51:22,420] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:51:22,421] [INFO] Task started: Prodigal
[2023-06-29 21:51:22,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg96afcaa4-eb22-4452-b08b-1a45e652b941/GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna.gz | prodigal -d GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/cds.fna -a GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:51:28,596] [INFO] Task succeeded: Prodigal
[2023-06-29 21:51:28,597] [INFO] Task started: HMMsearch
[2023-06-29 21:51:28,597] [INFO] Running command: hmmsearch --tblout GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f028bcd-6e88-4184-b2bb-2510ae9ee99f/dqc_reference/reference_markers.hmm GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:51:28,793] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:51:28,794] [INFO] Found 6/6 markers.
[2023-06-29 21:51:28,826] [INFO] Query marker FASTA was written to GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/markers.fasta
[2023-06-29 21:51:28,826] [INFO] Task started: Blastn
[2023-06-29 21:51:28,826] [INFO] Running command: blastn -query GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f028bcd-6e88-4184-b2bb-2510ae9ee99f/dqc_reference/reference_markers.fasta -out GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:51:29,620] [INFO] Task succeeded: Blastn
[2023-06-29 21:51:29,624] [INFO] Selected 15 target genomes.
[2023-06-29 21:51:29,625] [INFO] Target genome list was writen to GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/target_genomes.txt
[2023-06-29 21:51:29,629] [INFO] Task started: fastANI
[2023-06-29 21:51:29,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg96afcaa4-eb22-4452-b08b-1a45e652b941/GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna.gz --refList GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/target_genomes.txt --output GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:51:40,607] [INFO] Task succeeded: fastANI
[2023-06-29 21:51:40,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f028bcd-6e88-4184-b2bb-2510ae9ee99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:51:40,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f028bcd-6e88-4184-b2bb-2510ae9ee99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:51:40,621] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:51:40,622] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:51:40,622] [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
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	84.9925	660	759	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.4917	396	759	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	79.2637	341	759	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.1089	384	759	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	78.8387	347	759	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	78.687	352	759	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	78.5195	325	759	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	78.3455	246	759	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	78.3192	323	759	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	78.0487	287	759	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.0485	285	759	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	77.3311	155	759	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.5509	85	759	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.4128	96	759	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.9819	147	759	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:51:40,624] [INFO] DFAST Taxonomy check result was written to GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/tc_result.tsv
[2023-06-29 21:51:40,625] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:51:40,625] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:51:40,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f028bcd-6e88-4184-b2bb-2510ae9ee99f/dqc_reference/checkm_data
[2023-06-29 21:51:40,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:51:40,657] [INFO] Task started: CheckM
[2023-06-29 21:51:40,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/checkm_input GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/checkm_result
[2023-06-29 21:52:03,628] [INFO] Task succeeded: CheckM
[2023-06-29 21:52:03,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:52:03,648] [INFO] ===== Completeness check finished =====
[2023-06-29 21:52:03,649] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:52:03,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/markers.fasta)
[2023-06-29 21:52:03,649] [INFO] Task started: Blastn
[2023-06-29 21:52:03,649] [INFO] Running command: blastn -query GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f028bcd-6e88-4184-b2bb-2510ae9ee99f/dqc_reference/reference_markers_gtdb.fasta -out GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:52:05,134] [INFO] Task succeeded: Blastn
[2023-06-29 21:52:05,142] [INFO] Selected 14 target genomes.
[2023-06-29 21:52:05,143] [INFO] Target genome list was writen to GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:52:05,167] [INFO] Task started: fastANI
[2023-06-29 21:52:05,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg96afcaa4-eb22-4452-b08b-1a45e652b941/GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna.gz --refList GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/target_genomes_gtdb.txt --output GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:52:14,049] [INFO] Task succeeded: fastANI
[2023-06-29 21:52:14,060] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:52:14,060] [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_903933475.1	s__Phenylobacterium sp903933475	99.9999	748	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.29	99.29	0.84	0.84	2	conclusive
GCA_903912465.1	s__Phenylobacterium sp903912465	93.6927	543	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842425.1	s__Phenylobacterium sp903842425	85.2163	490	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003150835.1	s__Phenylobacterium parvum	84.961	662	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256425.1	s__Phenylobacterium sp002256425	79.0659	357	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911965.1	s__Phenylobacterium sp013911965	78.9667	344	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_018001015.1	s__Phenylobacterium sp018001015	78.8606	378	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCA_002363865.1	s__Phenylobacterium sp002363865	78.8532	322	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.98	99.98	0.95	0.91	3	-
GCA_001824475.1	s__Phenylobacterium sp001824475	78.6151	315	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	96.46	96.46	0.87	0.87	2	-
GCF_014196295.1	s__Phenylobacterium haematophilum	78.5072	326	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254525.1	s__Phenylobacterium kunshanense	78.3306	322	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793225.1	s__Phenylobacterium sp016793225	78.1636	322	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795885.1	s__Brevundimonas sp017795885	77.0874	157	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463485.1	s__Brevundimonas sp016463485	76.648	143	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:52:14,063] [INFO] GTDB search result was written to GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/result_gtdb.tsv
[2023-06-29 21:52:14,063] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:52:14,067] [INFO] DFAST_QC result json was written to GCA_903933475.1_freshwater_MAG_---_Loc090907-4m_bin-335_genomic.fna/dqc_result.json
[2023-06-29 21:52:14,067] [INFO] DFAST_QC completed!
[2023-06-29 21:52:14,067] [INFO] Total running time: 0h0m53s