[2023-06-30 07:19:04,828] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:19:04,832] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:19:04,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg36da1f9b-dbaa-4ba7-a3ce-ddc557bab5ab/dqc_reference
[2023-06-30 07:19:07,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:19:07,275] [INFO] Task started: Prodigal
[2023-06-30 07:19:07,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg54ef93db-485a-4b11-8327-41713928c4b7/GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna.gz | prodigal -d GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/cds.fna -a GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:19:18,714] [INFO] Task succeeded: Prodigal
[2023-06-30 07:19:18,714] [INFO] Task started: HMMsearch
[2023-06-30 07:19:18,715] [INFO] Running command: hmmsearch --tblout GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36da1f9b-dbaa-4ba7-a3ce-ddc557bab5ab/dqc_reference/reference_markers.hmm GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:19:18,942] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:19:18,944] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg54ef93db-485a-4b11-8327-41713928c4b7/GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna.gz]
[2023-06-30 07:19:18,973] [INFO] Query marker FASTA was written to GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/markers.fasta
[2023-06-30 07:19:18,973] [INFO] Task started: Blastn
[2023-06-30 07:19:18,973] [INFO] Running command: blastn -query GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/markers.fasta -db /var/lib/cwl/stg36da1f9b-dbaa-4ba7-a3ce-ddc557bab5ab/dqc_reference/reference_markers.fasta -out GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:19:19,537] [INFO] Task succeeded: Blastn
[2023-06-30 07:19:19,542] [INFO] Selected 15 target genomes.
[2023-06-30 07:19:19,543] [INFO] Target genome list was writen to GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/target_genomes.txt
[2023-06-30 07:19:19,544] [INFO] Task started: fastANI
[2023-06-30 07:19:19,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg54ef93db-485a-4b11-8327-41713928c4b7/GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna.gz --refList GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/target_genomes.txt --output GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:19:27,977] [INFO] Task succeeded: fastANI
[2023-06-30 07:19:27,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36da1f9b-dbaa-4ba7-a3ce-ddc557bab5ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:19:27,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36da1f9b-dbaa-4ba7-a3ce-ddc557bab5ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:19:27,982] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:19:27,982] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 07:19:27,983] [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 07:19:27,986] [INFO] DFAST Taxonomy check result was written to GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/tc_result.tsv
[2023-06-30 07:19:27,987] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:19:27,987] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:19:27,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36da1f9b-dbaa-4ba7-a3ce-ddc557bab5ab/dqc_reference/checkm_data
[2023-06-30 07:19:27,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:19:28,066] [INFO] Task started: CheckM
[2023-06-30 07:19:28,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/checkm_input GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/checkm_result
[2023-06-30 07:20:06,917] [INFO] Task succeeded: CheckM
[2023-06-30 07:20:06,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.87%
Contamintation: 1.50%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 07:20:06,944] [INFO] ===== Completeness check finished =====
[2023-06-30 07:20:06,945] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:20:06,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/markers.fasta)
[2023-06-30 07:20:06,946] [INFO] Task started: Blastn
[2023-06-30 07:20:06,946] [INFO] Running command: blastn -query GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/markers.fasta -db /var/lib/cwl/stg36da1f9b-dbaa-4ba7-a3ce-ddc557bab5ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:20:07,719] [INFO] Task succeeded: Blastn
[2023-06-30 07:20:07,726] [INFO] Selected 12 target genomes.
[2023-06-30 07:20:07,726] [INFO] Target genome list was writen to GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:20:07,729] [INFO] Task started: fastANI
[2023-06-30 07:20:07,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg54ef93db-485a-4b11-8327-41713928c4b7/GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna.gz --refList GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/target_genomes_gtdb.txt --output GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:20:13,812] [INFO] Task succeeded: fastANI
[2023-06-30 07:20:13,822] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:20:13,823] [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_903945495.1	s__M0103 sp903945495	99.7836	468	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	conclusive
GCA_017984635.1	s__M0103 sp017984635	78.0435	107	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930085.1	s__M0103 sp903930085	77.4939	68	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885545.1	s__M0103 sp009885545	77.0073	122	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887095.1	s__M0103 sp903887095	76.8051	59	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178305.1	s__CAIUKX01 sp016178305	76.7417	58	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 07:20:13,825] [INFO] GTDB search result was written to GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/result_gtdb.tsv
[2023-06-30 07:20:13,826] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:20:13,830] [INFO] DFAST_QC result json was written to GCA_903944435.1_freshwater_MAG_---_Loc081215-4m_bin-1207_genomic.fna/dqc_result.json
[2023-06-30 07:20:13,830] [INFO] DFAST_QC completed!
[2023-06-30 07:20:13,830] [INFO] Total running time: 0h1m9s