[2023-06-30 10:21:41,135] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:21:41,136] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:21:41,137] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cb67b61-1da5-4397-a908-e95bc39224d9/dqc_reference
[2023-06-30 10:21:43,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:21:43,888] [INFO] Task started: Prodigal
[2023-06-30 10:21:43,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg749ec9cc-1e72-4aa9-8584-40b6c54f1bef/GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna.gz | prodigal -d GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/cds.fna -a GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:21:50,510] [INFO] Task succeeded: Prodigal
[2023-06-30 10:21:50,510] [INFO] Task started: HMMsearch
[2023-06-30 10:21:50,511] [INFO] Running command: hmmsearch --tblout GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cb67b61-1da5-4397-a908-e95bc39224d9/dqc_reference/reference_markers.hmm GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:21:50,763] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:21:50,765] [INFO] Found 6/6 markers.
[2023-06-30 10:21:50,794] [INFO] Query marker FASTA was written to GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/markers.fasta
[2023-06-30 10:21:50,794] [INFO] Task started: Blastn
[2023-06-30 10:21:50,795] [INFO] Running command: blastn -query GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cb67b61-1da5-4397-a908-e95bc39224d9/dqc_reference/reference_markers.fasta -out GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:21:51,423] [INFO] Task succeeded: Blastn
[2023-06-30 10:21:51,441] [INFO] Selected 20 target genomes.
[2023-06-30 10:21:51,442] [INFO] Target genome list was writen to GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/target_genomes.txt
[2023-06-30 10:21:51,448] [INFO] Task started: fastANI
[2023-06-30 10:21:51,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg749ec9cc-1e72-4aa9-8584-40b6c54f1bef/GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna.gz --refList GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/target_genomes.txt --output GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:22:05,198] [INFO] Task succeeded: fastANI
[2023-06-30 10:22:05,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cb67b61-1da5-4397-a908-e95bc39224d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:22:05,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cb67b61-1da5-4397-a908-e95bc39224d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:22:05,207] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:22:05,208] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:22:05,208] [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
Solimicrobium silvestre	strain=S20-91	GCA_002976435.1	2099400	2099400	type	True	76.936	69	386	95	below_threshold
Sapientia aquatica	strain=SA-152	GCA_004358105.1	1549640	1549640	type	True	76.8579	52	386	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:22:05,215] [INFO] DFAST Taxonomy check result was written to GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/tc_result.tsv
[2023-06-30 10:22:05,216] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:22:05,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:22:05,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cb67b61-1da5-4397-a908-e95bc39224d9/dqc_reference/checkm_data
[2023-06-30 10:22:05,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:22:05,256] [INFO] Task started: CheckM
[2023-06-30 10:22:05,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/checkm_input GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/checkm_result
[2023-06-30 10:22:31,189] [INFO] Task succeeded: CheckM
[2023-06-30 10:22:31,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:22:31,216] [INFO] ===== Completeness check finished =====
[2023-06-30 10:22:31,216] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:22:31,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/markers.fasta)
[2023-06-30 10:22:31,217] [INFO] Task started: Blastn
[2023-06-30 10:22:31,217] [INFO] Running command: blastn -query GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cb67b61-1da5-4397-a908-e95bc39224d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:22:32,159] [INFO] Task succeeded: Blastn
[2023-06-30 10:22:32,164] [INFO] Selected 22 target genomes.
[2023-06-30 10:22:32,164] [INFO] Target genome list was writen to GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:22:32,177] [INFO] Task started: fastANI
[2023-06-30 10:22:32,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg749ec9cc-1e72-4aa9-8584-40b6c54f1bef/GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna.gz --refList GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/target_genomes_gtdb.txt --output GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:22:47,013] [INFO] Task succeeded: fastANI
[2023-06-30 10:22:47,021] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 10:22:47,021] [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
GCF_002976435.1	s__Solimicrobium silvestre	76.9102	68	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358105.1	s__Solimicrobium aquaticum	76.8567	51	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893945.1	s__Solimicrobium sp903893945	76.3964	57	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium	95.0	99.85	99.85	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-30 10:22:47,023] [INFO] GTDB search result was written to GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/result_gtdb.tsv
[2023-06-30 10:22:47,024] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:22:47,027] [INFO] DFAST_QC result json was written to GCA_903845335.1_freshwater_MAG_---_B4coas_bin-0688_genomic.fna/dqc_result.json
[2023-06-30 10:22:47,027] [INFO] DFAST_QC completed!
[2023-06-30 10:22:47,028] [INFO] Total running time: 0h1m6s