[2023-06-05 04:28:21,200] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:28:21,202] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:28:21,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg516d3cdb-9745-4f73-9ffc-2d33ca30df52/dqc_reference
[2023-06-05 04:28:22,715] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:28:22,716] [INFO] Task started: Prodigal
[2023-06-05 04:28:22,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg79c1614d-5673-4ea3-a306-ccdbad326c7c/GCA_934086485.1_ERR7738266_bin.234_genomic.fna.gz | prodigal -d GCA_934086485.1_ERR7738266_bin.234_genomic.fna/cds.fna -a GCA_934086485.1_ERR7738266_bin.234_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:28:24,643] [INFO] Task succeeded: Prodigal
[2023-06-05 04:28:24,644] [INFO] Task started: HMMsearch
[2023-06-05 04:28:24,644] [INFO] Running command: hmmsearch --tblout GCA_934086485.1_ERR7738266_bin.234_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg516d3cdb-9745-4f73-9ffc-2d33ca30df52/dqc_reference/reference_markers.hmm GCA_934086485.1_ERR7738266_bin.234_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:28:24,891] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:28:24,892] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg79c1614d-5673-4ea3-a306-ccdbad326c7c/GCA_934086485.1_ERR7738266_bin.234_genomic.fna.gz]
[2023-06-05 04:28:24,912] [INFO] Query marker FASTA was written to GCA_934086485.1_ERR7738266_bin.234_genomic.fna/markers.fasta
[2023-06-05 04:28:24,912] [INFO] Task started: Blastn
[2023-06-05 04:28:24,912] [INFO] Running command: blastn -query GCA_934086485.1_ERR7738266_bin.234_genomic.fna/markers.fasta -db /var/lib/cwl/stg516d3cdb-9745-4f73-9ffc-2d33ca30df52/dqc_reference/reference_markers.fasta -out GCA_934086485.1_ERR7738266_bin.234_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:28:25,539] [INFO] Task succeeded: Blastn
[2023-06-05 04:28:25,544] [INFO] Selected 20 target genomes.
[2023-06-05 04:28:25,544] [INFO] Target genome list was writen to GCA_934086485.1_ERR7738266_bin.234_genomic.fna/target_genomes.txt
[2023-06-05 04:28:25,548] [INFO] Task started: fastANI
[2023-06-05 04:28:25,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg79c1614d-5673-4ea3-a306-ccdbad326c7c/GCA_934086485.1_ERR7738266_bin.234_genomic.fna.gz --refList GCA_934086485.1_ERR7738266_bin.234_genomic.fna/target_genomes.txt --output GCA_934086485.1_ERR7738266_bin.234_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:28:34,811] [INFO] Task succeeded: fastANI
[2023-06-05 04:28:34,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg516d3cdb-9745-4f73-9ffc-2d33ca30df52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:28:34,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg516d3cdb-9745-4f73-9ffc-2d33ca30df52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:28:34,814] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:28:34,814] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 04:28:34,814] [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
--------------------------------------------------------------------------------
[2023-06-05 04:28:34,817] [INFO] DFAST Taxonomy check result was written to GCA_934086485.1_ERR7738266_bin.234_genomic.fna/tc_result.tsv
[2023-06-05 04:28:34,818] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:28:34,818] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:28:34,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg516d3cdb-9745-4f73-9ffc-2d33ca30df52/dqc_reference/checkm_data
[2023-06-05 04:28:34,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:28:34,840] [INFO] Task started: CheckM
[2023-06-05 04:28:34,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934086485.1_ERR7738266_bin.234_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934086485.1_ERR7738266_bin.234_genomic.fna/checkm_input GCA_934086485.1_ERR7738266_bin.234_genomic.fna/checkm_result
[2023-06-05 04:28:49,163] [INFO] Task succeeded: CheckM
[2023-06-05 04:28:49,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:28:49,183] [INFO] ===== Completeness check finished =====
[2023-06-05 04:28:49,184] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:28:49,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934086485.1_ERR7738266_bin.234_genomic.fna/markers.fasta)
[2023-06-05 04:28:49,184] [INFO] Task started: Blastn
[2023-06-05 04:28:49,185] [INFO] Running command: blastn -query GCA_934086485.1_ERR7738266_bin.234_genomic.fna/markers.fasta -db /var/lib/cwl/stg516d3cdb-9745-4f73-9ffc-2d33ca30df52/dqc_reference/reference_markers_gtdb.fasta -out GCA_934086485.1_ERR7738266_bin.234_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:28:49,951] [INFO] Task succeeded: Blastn
[2023-06-05 04:28:49,965] [INFO] Selected 17 target genomes.
[2023-06-05 04:28:49,965] [INFO] Target genome list was writen to GCA_934086485.1_ERR7738266_bin.234_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:28:49,969] [INFO] Task started: fastANI
[2023-06-05 04:28:49,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg79c1614d-5673-4ea3-a306-ccdbad326c7c/GCA_934086485.1_ERR7738266_bin.234_genomic.fna.gz --refList GCA_934086485.1_ERR7738266_bin.234_genomic.fna/target_genomes_gtdb.txt --output GCA_934086485.1_ERR7738266_bin.234_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:28:53,834] [INFO] Task succeeded: fastANI
[2023-06-05 04:28:53,844] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 04:28:53,844] [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_000437315.1	s__UBA6448 sp000437315	93.8907	324	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA6448	95.0	97.51	97.25	0.86	0.85	3	-
GCA_002439555.1	s__UBA6448 sp002439555	91.997	293	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA6448	95.0	99.37	99.14	0.89	0.87	3	-
GCA_900553855.1	s__CAG-533 sp900553855	81.8461	75	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-533	95.0	98.35	98.32	0.85	0.81	3	-
GCA_017544165.1	s__UBA6448 sp017544165	77.6992	94	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA6448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017434825.1	s__UBA6448 sp017434825	77.1573	81	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA6448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059305.1	s__UBA6448 sp015059305	77.1204	92	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA6448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438075.1	s__Onthocola_B sp000438075	76.2047	63	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthocola_B	95.0	98.04	97.73	0.84	0.82	3	-
GCA_016297695.1	s__RUG14121 sp016297695	75.8584	71	430	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14121	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 04:28:53,846] [INFO] GTDB search result was written to GCA_934086485.1_ERR7738266_bin.234_genomic.fna/result_gtdb.tsv
[2023-06-05 04:28:53,846] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:28:53,849] [INFO] DFAST_QC result json was written to GCA_934086485.1_ERR7738266_bin.234_genomic.fna/dqc_result.json
[2023-06-05 04:28:53,849] [INFO] DFAST_QC completed!
[2023-06-05 04:28:53,849] [INFO] Total running time: 0h0m33s