[2023-06-04 17:30:51,434] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:30:51,438] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:30:51,439] [INFO] DQC Reference Directory: /var/lib/cwl/stge03afab6-d781-4781-8655-31d4c2793b1a/dqc_reference
[2023-06-04 17:30:53,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:30:53,180] [INFO] Task started: Prodigal
[2023-06-04 17:30:53,180] [INFO] Running command: gunzip -c /var/lib/cwl/stgc929d1ff-e138-4888-beed-226f80ef3921/GCA_934149515.1_ERR7745914_bin.50_genomic.fna.gz | prodigal -d GCA_934149515.1_ERR7745914_bin.50_genomic.fna/cds.fna -a GCA_934149515.1_ERR7745914_bin.50_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:30:55,028] [INFO] Task succeeded: Prodigal
[2023-06-04 17:30:55,029] [INFO] Task started: HMMsearch
[2023-06-04 17:30:55,029] [INFO] Running command: hmmsearch --tblout GCA_934149515.1_ERR7745914_bin.50_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge03afab6-d781-4781-8655-31d4c2793b1a/dqc_reference/reference_markers.hmm GCA_934149515.1_ERR7745914_bin.50_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:30:55,252] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:30:55,254] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc929d1ff-e138-4888-beed-226f80ef3921/GCA_934149515.1_ERR7745914_bin.50_genomic.fna.gz]
[2023-06-04 17:30:55,271] [INFO] Query marker FASTA was written to GCA_934149515.1_ERR7745914_bin.50_genomic.fna/markers.fasta
[2023-06-04 17:30:55,272] [INFO] Task started: Blastn
[2023-06-04 17:30:55,272] [INFO] Running command: blastn -query GCA_934149515.1_ERR7745914_bin.50_genomic.fna/markers.fasta -db /var/lib/cwl/stge03afab6-d781-4781-8655-31d4c2793b1a/dqc_reference/reference_markers.fasta -out GCA_934149515.1_ERR7745914_bin.50_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:30:56,536] [INFO] Task succeeded: Blastn
[2023-06-04 17:30:56,541] [INFO] Selected 18 target genomes.
[2023-06-04 17:30:56,541] [INFO] Target genome list was writen to GCA_934149515.1_ERR7745914_bin.50_genomic.fna/target_genomes.txt
[2023-06-04 17:30:57,407] [INFO] Task started: fastANI
[2023-06-04 17:30:57,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgc929d1ff-e138-4888-beed-226f80ef3921/GCA_934149515.1_ERR7745914_bin.50_genomic.fna.gz --refList GCA_934149515.1_ERR7745914_bin.50_genomic.fna/target_genomes.txt --output GCA_934149515.1_ERR7745914_bin.50_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:31:02,958] [INFO] Task succeeded: fastANI
[2023-06-04 17:31:02,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge03afab6-d781-4781-8655-31d4c2793b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:31:02,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge03afab6-d781-4781-8655-31d4c2793b1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:31:02,960] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:31:02,960] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 17:31:02,961] [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
--------------------------------------------------------------------------------
[2023-06-04 17:31:02,962] [INFO] DFAST Taxonomy check result was written to GCA_934149515.1_ERR7745914_bin.50_genomic.fna/tc_result.tsv
[2023-06-04 17:31:02,963] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:31:02,963] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:31:02,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge03afab6-d781-4781-8655-31d4c2793b1a/dqc_reference/checkm_data
[2023-06-04 17:31:02,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:31:02,980] [INFO] Task started: CheckM
[2023-06-04 17:31:02,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934149515.1_ERR7745914_bin.50_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934149515.1_ERR7745914_bin.50_genomic.fna/checkm_input GCA_934149515.1_ERR7745914_bin.50_genomic.fna/checkm_result
[2023-06-04 17:31:17,919] [INFO] Task succeeded: CheckM
[2023-06-04 17:31:17,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:31:17,949] [INFO] ===== Completeness check finished =====
[2023-06-04 17:31:17,949] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:31:17,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934149515.1_ERR7745914_bin.50_genomic.fna/markers.fasta)
[2023-06-04 17:31:17,950] [INFO] Task started: Blastn
[2023-06-04 17:31:17,950] [INFO] Running command: blastn -query GCA_934149515.1_ERR7745914_bin.50_genomic.fna/markers.fasta -db /var/lib/cwl/stge03afab6-d781-4781-8655-31d4c2793b1a/dqc_reference/reference_markers_gtdb.fasta -out GCA_934149515.1_ERR7745914_bin.50_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:31:18,759] [INFO] Task succeeded: Blastn
[2023-06-04 17:31:18,766] [INFO] Selected 25 target genomes.
[2023-06-04 17:31:18,767] [INFO] Target genome list was writen to GCA_934149515.1_ERR7745914_bin.50_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:31:19,447] [INFO] Task started: fastANI
[2023-06-04 17:31:19,447] [INFO] Running command: fastANI --query /var/lib/cwl/stgc929d1ff-e138-4888-beed-226f80ef3921/GCA_934149515.1_ERR7745914_bin.50_genomic.fna.gz --refList GCA_934149515.1_ERR7745914_bin.50_genomic.fna/target_genomes_gtdb.txt --output GCA_934149515.1_ERR7745914_bin.50_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:31:25,621] [INFO] Task succeeded: fastANI
[2023-06-04 17:31:25,637] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 17:31:25,637] [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_900769695.1	s__UMGS995 sp900769695	77.681	65	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438295.1	s__Onthousia sp000438295	77.6557	93	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	96.69	96.41	0.79	0.73	4	-
GCA_904420615.1	s__Onthousia sp904420615	77.6017	89	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014846175.1	s__Onthousia sp014846175	77.2411	93	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716225.1	s__Onthousia faecigallinarum	77.1334	87	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712385.1	s__Onthousia excrementipullorum	76.8978	77	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	97.70	95.09	0.85	0.78	4	-
GCA_900760545.1	s__Onthousia sp900760545	76.8551	72	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543055.1	s__UBA3789 sp900543055	76.7902	54	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA3789	95.0	98.54	97.21	0.78	0.56	4	-
GCA_018711135.1	s__Onthousia faecavium	76.7666	98	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Onthousia	95.0	99.89	99.89	0.91	0.91	2	-
GCA_017886705.1	s__Faecimonas sp017886705	76.5574	60	347	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:31:25,639] [INFO] GTDB search result was written to GCA_934149515.1_ERR7745914_bin.50_genomic.fna/result_gtdb.tsv
[2023-06-04 17:31:25,639] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:31:25,642] [INFO] DFAST_QC result json was written to GCA_934149515.1_ERR7745914_bin.50_genomic.fna/dqc_result.json
[2023-06-04 17:31:25,642] [INFO] DFAST_QC completed!
[2023-06-04 17:31:25,642] [INFO] Total running time: 0h0m34s