[2023-06-30 09:06:29,361] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:06:29,362] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:06:29,363] [INFO] DQC Reference Directory: /var/lib/cwl/stga2abedd5-7153-4e5d-814b-a3e165cf2fc8/dqc_reference
[2023-06-30 09:06:30,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:06:30,555] [INFO] Task started: Prodigal
[2023-06-30 09:06:30,555] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fbe75b4-8ce3-4191-a7bf-a2d750d6462f/GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna.gz | prodigal -d GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/cds.fna -a GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:06:52,927] [INFO] Task succeeded: Prodigal
[2023-06-30 09:06:52,927] [INFO] Task started: HMMsearch
[2023-06-30 09:06:52,927] [INFO] Running command: hmmsearch --tblout GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2abedd5-7153-4e5d-814b-a3e165cf2fc8/dqc_reference/reference_markers.hmm GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:06:53,194] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:06:53,196] [INFO] Found 6/6 markers.
[2023-06-30 09:06:53,245] [INFO] Query marker FASTA was written to GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/markers.fasta
[2023-06-30 09:06:53,245] [INFO] Task started: Blastn
[2023-06-30 09:06:53,245] [INFO] Running command: blastn -query GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/markers.fasta -db /var/lib/cwl/stga2abedd5-7153-4e5d-814b-a3e165cf2fc8/dqc_reference/reference_markers.fasta -out GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:06:53,833] [INFO] Task succeeded: Blastn
[2023-06-30 09:06:53,837] [INFO] Selected 25 target genomes.
[2023-06-30 09:06:53,837] [INFO] Target genome list was writen to GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/target_genomes.txt
[2023-06-30 09:06:53,863] [INFO] Task started: fastANI
[2023-06-30 09:06:53,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fbe75b4-8ce3-4191-a7bf-a2d750d6462f/GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna.gz --refList GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/target_genomes.txt --output GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:07:09,928] [INFO] Task succeeded: fastANI
[2023-06-30 09:07:09,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2abedd5-7153-4e5d-814b-a3e165cf2fc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:07:09,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2abedd5-7153-4e5d-814b-a3e165cf2fc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:07:09,930] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:07:09,931] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 09:07:09,931] [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
--------------------------------------------------------------------------------
[2023-06-30 09:07:09,933] [INFO] DFAST Taxonomy check result was written to GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/tc_result.tsv
[2023-06-30 09:07:09,933] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:07:09,934] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:07:09,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2abedd5-7153-4e5d-814b-a3e165cf2fc8/dqc_reference/checkm_data
[2023-06-30 09:07:09,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:07:09,994] [INFO] Task started: CheckM
[2023-06-30 09:07:09,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/checkm_input GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/checkm_result
[2023-06-30 09:08:15,768] [INFO] Task succeeded: CheckM
[2023-06-30 09:08:15,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.49%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-30 09:08:15,787] [INFO] ===== Completeness check finished =====
[2023-06-30 09:08:15,787] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:08:15,787] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/markers.fasta)
[2023-06-30 09:08:15,787] [INFO] Task started: Blastn
[2023-06-30 09:08:15,788] [INFO] Running command: blastn -query GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/markers.fasta -db /var/lib/cwl/stga2abedd5-7153-4e5d-814b-a3e165cf2fc8/dqc_reference/reference_markers_gtdb.fasta -out GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:08:16,594] [INFO] Task succeeded: Blastn
[2023-06-30 09:08:16,597] [INFO] Selected 23 target genomes.
[2023-06-30 09:08:16,598] [INFO] Target genome list was writen to GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:08:16,634] [INFO] Task started: fastANI
[2023-06-30 09:08:16,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fbe75b4-8ce3-4191-a7bf-a2d750d6462f/GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna.gz --refList GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/target_genomes_gtdb.txt --output GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:08:30,503] [INFO] Task succeeded: fastANI
[2023-06-30 09:08:30,519] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 09:08:30,520] [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_903844815.1	s__LD21 sp903844815	100.0	1885	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903824785.1	s__LD21 sp903824785	77.6143	189	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.94	99.93	0.97	0.96	4	-
GCA_016709865.1	s__LD21 sp016709865	77.5689	194	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.60	98.60	0.94	0.94	2	-
GCA_001768195.1	s__LD21 sp001768195	76.8666	134	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.84	99.74	0.96	0.95	8	-
GCA_003157015.1	s__LD21 sp003157015	76.6539	133	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.74	99.74	0.96	0.96	2	-
GCA_003162595.1	s__LD21 sp003162595	76.6173	116	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520925.1	s__LD21 sp003520925	76.5435	96	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.68	99.68	0.93	0.93	2	-
GCA_003141715.1	s__LD21 sp003141715	76.4754	121	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141495.1	s__LD21 sp003141495	76.4541	115	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002319885.1	s__LD21 sp002319885	76.3935	131	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517605.1	s__LD21 sp012517605	76.1328	89	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.39	99.39	0.94	0.94	2	-
GCA_003152835.1	s__LD21 sp003152835	76.0142	80	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	99.43	99.38	0.90	0.89	3	-
GCA_017882305.1	s__LD21 sp017882305	75.9234	117	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519515.1	s__LD21 sp012519515	75.5066	60	1902	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__VadinHA17;g__LD21	95.0	98.49	98.12	0.85	0.77	6	-
--------------------------------------------------------------------------------
[2023-06-30 09:08:30,521] [INFO] GTDB search result was written to GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/result_gtdb.tsv
[2023-06-30 09:08:30,522] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:08:30,524] [INFO] DFAST_QC result json was written to GCA_903844815.1_freshwater_MAG_---_Loclat_bin-20678_genomic.fna/dqc_result.json
[2023-06-30 09:08:30,525] [INFO] DFAST_QC completed!
[2023-06-30 09:08:30,525] [INFO] Total running time: 0h2m1s