[2023-06-30 02:08:02,900] [INFO] DFAST_QC pipeline started.
[2023-06-30 02:08:02,902] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 02:08:02,902] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4fd6654-48e2-4a0e-83b3-d045068f5613/dqc_reference
[2023-06-30 02:08:04,221] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 02:08:04,222] [INFO] Task started: Prodigal
[2023-06-30 02:08:04,223] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5f8f0db-a12e-43ba-bf68-2f23d3c00df9/GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna.gz | prodigal -d GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/cds.fna -a GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 02:08:07,002] [INFO] Task succeeded: Prodigal
[2023-06-30 02:08:07,002] [INFO] Task started: HMMsearch
[2023-06-30 02:08:07,003] [INFO] Running command: hmmsearch --tblout GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4fd6654-48e2-4a0e-83b3-d045068f5613/dqc_reference/reference_markers.hmm GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/protein.faa > /dev/null
[2023-06-30 02:08:07,353] [INFO] Task succeeded: HMMsearch
[2023-06-30 02:08:07,355] [INFO] Found 6/6 markers.
[2023-06-30 02:08:07,382] [INFO] Query marker FASTA was written to GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/markers.fasta
[2023-06-30 02:08:07,382] [INFO] Task started: Blastn
[2023-06-30 02:08:07,382] [INFO] Running command: blastn -query GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4fd6654-48e2-4a0e-83b3-d045068f5613/dqc_reference/reference_markers.fasta -out GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:08:08,736] [INFO] Task succeeded: Blastn
[2023-06-30 02:08:08,739] [INFO] Selected 27 target genomes.
[2023-06-30 02:08:08,740] [INFO] Target genome list was writen to GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/target_genomes.txt
[2023-06-30 02:08:08,770] [INFO] Task started: fastANI
[2023-06-30 02:08:08,770] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5f8f0db-a12e-43ba-bf68-2f23d3c00df9/GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna.gz --refList GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/target_genomes.txt --output GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 02:08:23,336] [INFO] Task succeeded: fastANI
[2023-06-30 02:08:23,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4fd6654-48e2-4a0e-83b3-d045068f5613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 02:08:23,337] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4fd6654-48e2-4a0e-83b3-d045068f5613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 02:08:23,339] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 02:08:23,339] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 02:08:23,339] [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
--------------------------------------------------------------------------------
[2023-06-30 02:08:23,342] [INFO] DFAST Taxonomy check result was written to GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/tc_result.tsv
[2023-06-30 02:08:23,343] [INFO] ===== Taxonomy check completed =====
[2023-06-30 02:08:23,343] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 02:08:23,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4fd6654-48e2-4a0e-83b3-d045068f5613/dqc_reference/checkm_data
[2023-06-30 02:08:23,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 02:08:23,387] [INFO] Task started: CheckM
[2023-06-30 02:08:23,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/checkm_input GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/checkm_result
[2023-06-30 02:08:41,043] [INFO] Task succeeded: CheckM
[2023-06-30 02:08:41,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 02:08:41,067] [INFO] ===== Completeness check finished =====
[2023-06-30 02:08:41,067] [INFO] ===== Start GTDB Search =====
[2023-06-30 02:08:41,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/markers.fasta)
[2023-06-30 02:08:41,068] [INFO] Task started: Blastn
[2023-06-30 02:08:41,068] [INFO] Running command: blastn -query GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4fd6654-48e2-4a0e-83b3-d045068f5613/dqc_reference/reference_markers_gtdb.fasta -out GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:08:42,047] [INFO] Task succeeded: Blastn
[2023-06-30 02:08:42,052] [INFO] Selected 16 target genomes.
[2023-06-30 02:08:42,052] [INFO] Target genome list was writen to GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 02:08:42,062] [INFO] Task started: fastANI
[2023-06-30 02:08:42,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5f8f0db-a12e-43ba-bf68-2f23d3c00df9/GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna.gz --refList GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/target_genomes_gtdb.txt --output GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 02:08:49,139] [INFO] Task succeeded: fastANI
[2023-06-30 02:08:49,148] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 02:08:49,149] [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_903822055.1	s__UBA6186 sp903822055	100.0	531	537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6186;f__UBA6186;g__UBA6186	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002422785.1	s__UBA6186 sp002422785	79.0006	205	537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6186;f__UBA6186;g__UBA6186	95.0	98.01	97.66	0.76	0.68	5	-
GCA_903907935.1	s__UBA6186 sp903907935	78.2666	191	537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6186;f__UBA6186;g__UBA6186	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903827925.1	s__UBA6186 sp903827925	77.3447	113	537	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6186;f__UBA6186;g__UBA6186	95.0	99.82	99.82	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-30 02:08:49,151] [INFO] GTDB search result was written to GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/result_gtdb.tsv
[2023-06-30 02:08:49,151] [INFO] ===== GTDB Search completed =====
[2023-06-30 02:08:49,155] [INFO] DFAST_QC result json was written to GCA_903822055.1_freshwater_MAG_---_AlinenLipids_bin-5883_genomic.fna/dqc_result.json
[2023-06-30 02:08:49,155] [INFO] DFAST_QC completed!
[2023-06-30 02:08:49,156] [INFO] Total running time: 0h0m46s