[2023-06-30 15:09:24,869] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:09:24,872] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:09:24,872] [INFO] DQC Reference Directory: /var/lib/cwl/stg040df873-104f-4e63-82a3-32d7d1569a6f/dqc_reference
[2023-06-30 15:09:26,107] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:09:26,108] [INFO] Task started: Prodigal
[2023-06-30 15:09:26,109] [INFO] Running command: gunzip -c /var/lib/cwl/stg54c56a71-1ab3-482d-9d07-474be642c563/GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna.gz | prodigal -d GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/cds.fna -a GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:09:33,134] [INFO] Task succeeded: Prodigal
[2023-06-30 15:09:33,135] [INFO] Task started: HMMsearch
[2023-06-30 15:09:33,135] [INFO] Running command: hmmsearch --tblout GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg040df873-104f-4e63-82a3-32d7d1569a6f/dqc_reference/reference_markers.hmm GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:09:33,334] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:09:33,336] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg54c56a71-1ab3-482d-9d07-474be642c563/GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna.gz]
[2023-06-30 15:09:33,366] [INFO] Query marker FASTA was written to GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/markers.fasta
[2023-06-30 15:09:33,367] [INFO] Task started: Blastn
[2023-06-30 15:09:33,367] [INFO] Running command: blastn -query GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/markers.fasta -db /var/lib/cwl/stg040df873-104f-4e63-82a3-32d7d1569a6f/dqc_reference/reference_markers.fasta -out GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:09:33,892] [INFO] Task succeeded: Blastn
[2023-06-30 15:09:33,896] [INFO] Selected 6 target genomes.
[2023-06-30 15:09:33,897] [INFO] Target genome list was writen to GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/target_genomes.txt
[2023-06-30 15:09:33,898] [INFO] Task started: fastANI
[2023-06-30 15:09:33,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c56a71-1ab3-482d-9d07-474be642c563/GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna.gz --refList GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/target_genomes.txt --output GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:09:38,589] [INFO] Task succeeded: fastANI
[2023-06-30 15:09:38,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg040df873-104f-4e63-82a3-32d7d1569a6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:09:38,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg040df873-104f-4e63-82a3-32d7d1569a6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:09:38,597] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:09:38,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:09:38,597] [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
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	78.6634	101	234	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	78.6042	101	234	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	78.5945	107	234	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.472	110	234	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	78.4626	115	234	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.1739	105	234	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:09:38,599] [INFO] DFAST Taxonomy check result was written to GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/tc_result.tsv
[2023-06-30 15:09:38,600] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:09:38,600] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:09:38,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg040df873-104f-4e63-82a3-32d7d1569a6f/dqc_reference/checkm_data
[2023-06-30 15:09:38,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:09:38,630] [INFO] Task started: CheckM
[2023-06-30 15:09:38,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/checkm_input GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/checkm_result
[2023-06-30 15:10:04,315] [INFO] Task succeeded: CheckM
[2023-06-30 15:10:04,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 18.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:10:04,339] [INFO] ===== Completeness check finished =====
[2023-06-30 15:10:04,339] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:10:04,340] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/markers.fasta)
[2023-06-30 15:10:04,340] [INFO] Task started: Blastn
[2023-06-30 15:10:04,341] [INFO] Running command: blastn -query GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/markers.fasta -db /var/lib/cwl/stg040df873-104f-4e63-82a3-32d7d1569a6f/dqc_reference/reference_markers_gtdb.fasta -out GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:10:04,899] [INFO] Task succeeded: Blastn
[2023-06-30 15:10:04,903] [INFO] Selected 7 target genomes.
[2023-06-30 15:10:04,904] [INFO] Target genome list was writen to GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:10:04,924] [INFO] Task started: fastANI
[2023-06-30 15:10:04,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c56a71-1ab3-482d-9d07-474be642c563/GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna.gz --refList GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/target_genomes_gtdb.txt --output GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:10:10,844] [INFO] Task succeeded: fastANI
[2023-06-30 15:10:10,854] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 15:10:10,855] [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_005403045.1	s__Aquabacterium_A pictum	83.642	192	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770815.1	s__Aquabacterium_A sp001770815	83.4173	168	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999135.1	s__Aquabacterium_A sp017999135	82.4488	141	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790515.1	s__Aquabacterium_A sp016790515	81.4249	147	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	80.6014	154	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001295905.1	s__Rubrivivax sp001295905	79.3311	127	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266755.1	s__Aquabacterium_A terrae	78.6646	136	234	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:10:10,857] [INFO] GTDB search result was written to GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/result_gtdb.tsv
[2023-06-30 15:10:10,857] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:10:10,861] [INFO] DFAST_QC result json was written to GCA_903883535.1_freshwater_MAG_---_Ja1-D2_bin-0112_genomic.fna/dqc_result.json
[2023-06-30 15:10:10,861] [INFO] DFAST_QC completed!
[2023-06-30 15:10:10,861] [INFO] Total running time: 0h0m46s