[2023-07-01 02:13:30,943] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:13:30,946] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:13:30,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f877a3d-1c6b-4bc4-ab2a-be9e5acd0063/dqc_reference
[2023-07-01 02:13:33,218] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:13:33,219] [INFO] Task started: Prodigal
[2023-07-01 02:13:33,219] [INFO] Running command: gunzip -c /var/lib/cwl/stgc132395b-1c7d-45b2-905d-d95a0c8aafd2/GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna.gz | prodigal -d GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/cds.fna -a GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:13:45,452] [INFO] Task succeeded: Prodigal
[2023-07-01 02:13:45,453] [INFO] Task started: HMMsearch
[2023-07-01 02:13:45,453] [INFO] Running command: hmmsearch --tblout GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f877a3d-1c6b-4bc4-ab2a-be9e5acd0063/dqc_reference/reference_markers.hmm GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:13:45,683] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:13:45,684] [INFO] Found 6/6 markers.
[2023-07-01 02:13:45,720] [INFO] Query marker FASTA was written to GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/markers.fasta
[2023-07-01 02:13:45,721] [INFO] Task started: Blastn
[2023-07-01 02:13:45,721] [INFO] Running command: blastn -query GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f877a3d-1c6b-4bc4-ab2a-be9e5acd0063/dqc_reference/reference_markers.fasta -out GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:13:46,303] [INFO] Task succeeded: Blastn
[2023-07-01 02:13:46,311] [INFO] Selected 17 target genomes.
[2023-07-01 02:13:46,311] [INFO] Target genome list was writen to GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/target_genomes.txt
[2023-07-01 02:13:46,314] [INFO] Task started: fastANI
[2023-07-01 02:13:46,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgc132395b-1c7d-45b2-905d-d95a0c8aafd2/GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna.gz --refList GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/target_genomes.txt --output GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:13:57,666] [INFO] Task succeeded: fastANI
[2023-07-01 02:13:57,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f877a3d-1c6b-4bc4-ab2a-be9e5acd0063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:13:57,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f877a3d-1c6b-4bc4-ab2a-be9e5acd0063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:13:57,669] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:13:57,670] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 02:13:57,670] [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
--------------------------------------------------------------------------------
[2023-07-01 02:13:57,672] [INFO] DFAST Taxonomy check result was written to GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/tc_result.tsv
[2023-07-01 02:13:57,673] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:13:57,673] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:13:57,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f877a3d-1c6b-4bc4-ab2a-be9e5acd0063/dqc_reference/checkm_data
[2023-07-01 02:13:57,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:13:57,704] [INFO] Task started: CheckM
[2023-07-01 02:13:57,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/checkm_input GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/checkm_result
[2023-07-01 02:14:35,204] [INFO] Task succeeded: CheckM
[2023-07-01 02:14:35,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:14:35,227] [INFO] ===== Completeness check finished =====
[2023-07-01 02:14:35,227] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:14:35,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/markers.fasta)
[2023-07-01 02:14:35,228] [INFO] Task started: Blastn
[2023-07-01 02:14:35,228] [INFO] Running command: blastn -query GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f877a3d-1c6b-4bc4-ab2a-be9e5acd0063/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:14:36,087] [INFO] Task succeeded: Blastn
[2023-07-01 02:14:36,107] [INFO] Selected 17 target genomes.
[2023-07-01 02:14:36,107] [INFO] Target genome list was writen to GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:14:36,116] [INFO] Task started: fastANI
[2023-07-01 02:14:36,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgc132395b-1c7d-45b2-905d-d95a0c8aafd2/GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna.gz --refList GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/target_genomes_gtdb.txt --output GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:14:41,938] [INFO] Task succeeded: fastANI
[2023-07-01 02:14:41,954] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:14:41,954] [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_903840355.1	s__UBA953 sp903840355	99.9771	716	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.98	99.95	0.99	0.98	15	conclusive
GCA_903925205.1	s__UBA953 sp903925205	77.2721	116	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293385.1	s__UBA953 sp004293385	77.1404	70	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903829855.1	s__UBA953 sp903829855	77.0796	118	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.27	99.00	0.85	0.74	14	-
GCA_903855995.1	s__UBA953 sp903855995	77.0618	139	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.61	99.32	0.98	0.94	20	-
GCA_003569165.1	s__UBA953 sp003569165	77.0138	119	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903895475.1	s__UBA953 sp903895475	76.9214	101	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	97.79	97.63	0.79	0.78	5	-
GCA_009924965.1	s__UBA953 sp009924965	76.8876	82	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280935.1	s__UBA953 sp007280935	76.8734	109	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569205.1	s__UBA953 sp003569205	76.8528	118	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470605.1	s__UBA953 sp002470605	76.8335	117	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	96.53	95.34	0.88	0.80	17	-
GCA_903919185.1	s__UBA953 sp903919185	76.8264	114	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.87	99.74	0.94	0.93	4	-
GCA_005798925.1	s__UBA953 sp005798925	76.4747	87	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691685.1	s__UBA953 sp002737185	76.4435	79	723	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	99.79	99.79	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-07-01 02:14:41,957] [INFO] GTDB search result was written to GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/result_gtdb.tsv
[2023-07-01 02:14:41,957] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:14:41,961] [INFO] DFAST_QC result json was written to GCA_903830045.1_freshwater_MAG_---_VK3_bin-0550_genomic.fna/dqc_result.json
[2023-07-01 02:14:41,961] [INFO] DFAST_QC completed!
[2023-07-01 02:14:41,961] [INFO] Total running time: 0h1m11s