[2023-06-30 15:09:16,172] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:09:16,174] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:09:16,174] [INFO] DQC Reference Directory: /var/lib/cwl/stga2c44283-6fe9-4221-aa2f-64a5cd4d7bd6/dqc_reference
[2023-06-30 15:09:17,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:09:17,564] [INFO] Task started: Prodigal
[2023-06-30 15:09:17,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg288d875f-70fe-40b8-9c1b-54502cbc26bf/GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna.gz | prodigal -d GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/cds.fna -a GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:09:36,874] [INFO] Task succeeded: Prodigal
[2023-06-30 15:09:36,874] [INFO] Task started: HMMsearch
[2023-06-30 15:09:36,875] [INFO] Running command: hmmsearch --tblout GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2c44283-6fe9-4221-aa2f-64a5cd4d7bd6/dqc_reference/reference_markers.hmm GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:09:37,266] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:09:37,267] [INFO] Found 6/6 markers.
[2023-06-30 15:09:37,323] [INFO] Query marker FASTA was written to GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/markers.fasta
[2023-06-30 15:09:37,323] [INFO] Task started: Blastn
[2023-06-30 15:09:37,323] [INFO] Running command: blastn -query GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/markers.fasta -db /var/lib/cwl/stga2c44283-6fe9-4221-aa2f-64a5cd4d7bd6/dqc_reference/reference_markers.fasta -out GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:09:37,968] [INFO] Task succeeded: Blastn
[2023-06-30 15:09:37,972] [INFO] Selected 33 target genomes.
[2023-06-30 15:09:37,972] [INFO] Target genome list was writen to GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/target_genomes.txt
[2023-06-30 15:09:37,982] [INFO] Task started: fastANI
[2023-06-30 15:09:37,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg288d875f-70fe-40b8-9c1b-54502cbc26bf/GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna.gz --refList GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/target_genomes.txt --output GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:10:00,148] [INFO] Task succeeded: fastANI
[2023-06-30 15:10:00,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2c44283-6fe9-4221-aa2f-64a5cd4d7bd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:10:00,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2c44283-6fe9-4221-aa2f-64a5cd4d7bd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:10:00,158] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:10:00,158] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:10:00,158] [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
Methylococcus capsulatus	strain=Texas	GCA_000297615.1	414	414	type	True	75.8983	53	1700	95	below_threshold
Methylococcus capsulatus	strain=ATCC 19069	GCA_000424685.1	414	414	type	True	75.8732	54	1700	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:10:00,160] [INFO] DFAST Taxonomy check result was written to GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/tc_result.tsv
[2023-06-30 15:10:00,161] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:10:00,161] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:10:00,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2c44283-6fe9-4221-aa2f-64a5cd4d7bd6/dqc_reference/checkm_data
[2023-06-30 15:10:00,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:10:00,227] [INFO] Task started: CheckM
[2023-06-30 15:10:00,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/checkm_input GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/checkm_result
[2023-06-30 15:10:55,921] [INFO] Task succeeded: CheckM
[2023-06-30 15:10:55,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:10:55,947] [INFO] ===== Completeness check finished =====
[2023-06-30 15:10:55,947] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:10:55,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/markers.fasta)
[2023-06-30 15:10:55,948] [INFO] Task started: Blastn
[2023-06-30 15:10:55,948] [INFO] Running command: blastn -query GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/markers.fasta -db /var/lib/cwl/stga2c44283-6fe9-4221-aa2f-64a5cd4d7bd6/dqc_reference/reference_markers_gtdb.fasta -out GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:10:56,800] [INFO] Task succeeded: Blastn
[2023-06-30 15:10:56,805] [INFO] Selected 15 target genomes.
[2023-06-30 15:10:56,805] [INFO] Target genome list was writen to GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:10:56,871] [INFO] Task started: fastANI
[2023-06-30 15:10:56,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg288d875f-70fe-40b8-9c1b-54502cbc26bf/GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna.gz --refList GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/target_genomes_gtdb.txt --output GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:11:14,069] [INFO] Task succeeded: fastANI
[2023-06-30 15:11:14,080] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:11:14,081] [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_003242955.1	s__Methyloumidiphilus alinensis	98.4441	1363	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus	95.0	99.27	95.17	0.87	0.73	31	conclusive
GCA_903934875.1	s__Methyloumidiphilus sp903934875	81.1382	794	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus	95.0	99.88	99.86	0.93	0.91	5	-
GCA_903857165.1	s__Methyloumidiphilus sp903857165	79.5941	591	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930145.1	s__Methyloumidiphilus sp903930145	79.2898	441	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903911305.1	s__Methyloumidiphilus sp903911305	78.9327	403	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus	95.0	99.43	99.36	0.87	0.86	3	-
GCA_903859815.1	s__Methyloumidiphilus sp903859815	78.7806	432	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloumidiphilus	95.0	99.87	99.84	0.92	0.89	4	-
GCA_012026715.1	s__VEPB01 sp012026715	75.7286	62	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__VEPB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:11:14,083] [INFO] GTDB search result was written to GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/result_gtdb.tsv
[2023-06-30 15:11:14,084] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:11:14,088] [INFO] DFAST_QC result json was written to GCA_903893045.1_freshwater_MAG_---_Ki2-D3_bin-0447_genomic.fna/dqc_result.json
[2023-06-30 15:11:14,089] [INFO] DFAST_QC completed!
[2023-06-30 15:11:14,089] [INFO] Total running time: 0h1m58s