[2023-07-01 03:15:00,428] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:15:00,430] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:15:00,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fc15948-1918-4d68-ac39-ca906f6e0ece/dqc_reference
[2023-07-01 03:15:01,669] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:15:01,670] [INFO] Task started: Prodigal
[2023-07-01 03:15:01,670] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c3d74f8-2470-4842-8958-8ea4195c59de/GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna.gz | prodigal -d GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/cds.fna -a GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:15:10,516] [INFO] Task succeeded: Prodigal
[2023-07-01 03:15:10,516] [INFO] Task started: HMMsearch
[2023-07-01 03:15:10,516] [INFO] Running command: hmmsearch --tblout GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fc15948-1918-4d68-ac39-ca906f6e0ece/dqc_reference/reference_markers.hmm GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:15:10,775] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:15:10,776] [INFO] Found 6/6 markers.
[2023-07-01 03:15:10,811] [INFO] Query marker FASTA was written to GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/markers.fasta
[2023-07-01 03:15:10,811] [INFO] Task started: Blastn
[2023-07-01 03:15:10,811] [INFO] Running command: blastn -query GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc15948-1918-4d68-ac39-ca906f6e0ece/dqc_reference/reference_markers.fasta -out GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:15:11,376] [INFO] Task succeeded: Blastn
[2023-07-01 03:15:11,381] [INFO] Selected 22 target genomes.
[2023-07-01 03:15:11,382] [INFO] Target genome list was writen to GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/target_genomes.txt
[2023-07-01 03:15:11,383] [INFO] Task started: fastANI
[2023-07-01 03:15:11,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c3d74f8-2470-4842-8958-8ea4195c59de/GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna.gz --refList GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/target_genomes.txt --output GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:15:22,610] [INFO] Task succeeded: fastANI
[2023-07-01 03:15:22,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fc15948-1918-4d68-ac39-ca906f6e0ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:15:22,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fc15948-1918-4d68-ac39-ca906f6e0ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:15:22,613] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:15:22,614] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 03:15:22,614] [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 03:15:22,616] [INFO] DFAST Taxonomy check result was written to GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/tc_result.tsv
[2023-07-01 03:15:22,617] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:15:22,617] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:15:22,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fc15948-1918-4d68-ac39-ca906f6e0ece/dqc_reference/checkm_data
[2023-07-01 03:15:22,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:15:22,670] [INFO] Task started: CheckM
[2023-07-01 03:15:22,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/checkm_input GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/checkm_result
[2023-07-01 03:15:54,844] [INFO] Task succeeded: CheckM
[2023-07-01 03:15:54,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:15:54,872] [INFO] ===== Completeness check finished =====
[2023-07-01 03:15:54,873] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:15:54,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/markers.fasta)
[2023-07-01 03:15:54,874] [INFO] Task started: Blastn
[2023-07-01 03:15:54,874] [INFO] Running command: blastn -query GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc15948-1918-4d68-ac39-ca906f6e0ece/dqc_reference/reference_markers_gtdb.fasta -out GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:15:55,608] [INFO] Task succeeded: Blastn
[2023-07-01 03:15:55,614] [INFO] Selected 20 target genomes.
[2023-07-01 03:15:55,614] [INFO] Target genome list was writen to GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:15:55,615] [INFO] Task started: fastANI
[2023-07-01 03:15:55,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c3d74f8-2470-4842-8958-8ea4195c59de/GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna.gz --refList GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/target_genomes_gtdb.txt --output GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:16:04,649] [INFO] Task succeeded: fastANI
[2023-07-01 03:16:04,658] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:16:04,658] [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_903885795.1	s__UBA8958 sp903885795	99.9351	1052	1075	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA8958;g__UBA8958	95.0	99.96	99.94	0.98	0.97	6	conclusive
GCA_003451635.1	s__UBA8958 sp003451635	86.2911	454	1075	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA8958;g__UBA8958	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056545.1	s__UBA8958 sp018056545	78.1511	144	1075	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA8958;g__UBA8958	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873745.1	s__UBA5619 sp001873745	76.9091	70	1075	d__Bacteria;p__Desulfobacterota;c__Syntrophia;o__Syntrophales;f__UBA5619;g__UBA5619	95.0	99.43	99.33	0.83	0.81	3	-
--------------------------------------------------------------------------------
[2023-07-01 03:16:04,660] [INFO] GTDB search result was written to GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/result_gtdb.tsv
[2023-07-01 03:16:04,661] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:16:04,664] [INFO] DFAST_QC result json was written to GCA_903855685.1_freshwater_MAG_---_AM-lipid-01-D10_bin-0019_genomic.fna/dqc_result.json
[2023-07-01 03:16:04,664] [INFO] DFAST_QC completed!
[2023-07-01 03:16:04,664] [INFO] Total running time: 0h1m4s