[2023-07-01 01:02:07,877] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:02:07,881] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:02:07,882] [INFO] DQC Reference Directory: /var/lib/cwl/stg81c0b917-c16d-46db-bc56-5359f07bc47b/dqc_reference
[2023-07-01 01:02:09,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:02:09,900] [INFO] Task started: Prodigal
[2023-07-01 01:02:09,901] [INFO] Running command: gunzip -c /var/lib/cwl/stg09d4c0b9-2f38-401d-b9c9-de6729ccb67d/GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna.gz | prodigal -d GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/cds.fna -a GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:02:11,623] [INFO] Task succeeded: Prodigal
[2023-07-01 01:02:11,624] [INFO] Task started: HMMsearch
[2023-07-01 01:02:11,624] [INFO] Running command: hmmsearch --tblout GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81c0b917-c16d-46db-bc56-5359f07bc47b/dqc_reference/reference_markers.hmm GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:02:11,891] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:02:11,892] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg09d4c0b9-2f38-401d-b9c9-de6729ccb67d/GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna.gz]
[2023-07-01 01:02:11,912] [INFO] Query marker FASTA was written to GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/markers.fasta
[2023-07-01 01:02:11,913] [INFO] Task started: Blastn
[2023-07-01 01:02:11,913] [INFO] Running command: blastn -query GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c0b917-c16d-46db-bc56-5359f07bc47b/dqc_reference/reference_markers.fasta -out GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:02:13,727] [INFO] Task succeeded: Blastn
[2023-07-01 01:02:13,731] [INFO] Selected 29 target genomes.
[2023-07-01 01:02:13,731] [INFO] Target genome list was writen to GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/target_genomes.txt
[2023-07-01 01:02:13,752] [INFO] Task started: fastANI
[2023-07-01 01:02:13,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d4c0b9-2f38-401d-b9c9-de6729ccb67d/GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna.gz --refList GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/target_genomes.txt --output GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:02:28,605] [INFO] Task succeeded: fastANI
[2023-07-01 01:02:28,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81c0b917-c16d-46db-bc56-5359f07bc47b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:02:28,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81c0b917-c16d-46db-bc56-5359f07bc47b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:02:28,607] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:02:28,608] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 01:02:28,608] [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 01:02:28,609] [INFO] DFAST Taxonomy check result was written to GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/tc_result.tsv
[2023-07-01 01:02:28,610] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:02:28,610] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:02:28,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81c0b917-c16d-46db-bc56-5359f07bc47b/dqc_reference/checkm_data
[2023-07-01 01:02:28,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:02:28,626] [INFO] Task started: CheckM
[2023-07-01 01:02:28,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/checkm_input GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/checkm_result
[2023-07-01 01:02:43,915] [INFO] Task succeeded: CheckM
[2023-07-01 01:02:43,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:02:43,945] [INFO] ===== Completeness check finished =====
[2023-07-01 01:02:43,945] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:02:43,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/markers.fasta)
[2023-07-01 01:02:43,946] [INFO] Task started: Blastn
[2023-07-01 01:02:43,946] [INFO] Running command: blastn -query GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c0b917-c16d-46db-bc56-5359f07bc47b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:02:44,761] [INFO] Task succeeded: Blastn
[2023-07-01 01:02:44,766] [INFO] Selected 9 target genomes.
[2023-07-01 01:02:44,766] [INFO] Target genome list was writen to GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:02:44,784] [INFO] Task started: fastANI
[2023-07-01 01:02:44,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d4c0b9-2f38-401d-b9c9-de6729ccb67d/GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna.gz --refList GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/target_genomes_gtdb.txt --output GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:02:47,132] [INFO] Task succeeded: fastANI
[2023-07-01 01:02:47,141] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:02:47,141] [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_903914945.1	s__Methylopumilus sp903914945	97.6583	168	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	98.58	97.76	0.86	0.81	18	conclusive
GCA_014190615.1	s__Methylopumilus sp014190615	91.6007	162	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981505.1	s__Methylopumilus planktonicus	84.9549	167	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	96.26	95.25	0.92	0.89	9	-
GCF_006365315.1	s__Methylopumilus universalis	84.6787	168	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	97.60	96.52	0.95	0.91	36	-
GCF_006364615.1	s__Methylopumilus rimovensis	83.6784	161	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	98.38	98.38	0.95	0.95	2	-
GCA_903849185.1	s__Methylopumilus sp903849185	83.0335	147	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	98.91	98.07	0.83	0.78	5	-
GCA_003533095.1	s__Methylopumilus sp003533095	82.4477	123	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	99.11	99.08	0.89	0.88	3	-
GCA_009693175.1	s__Methylopumilus sp009693175	82.3473	148	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926035.1	s__Methylopumilus sp009926035	82.0248	113	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:02:47,143] [INFO] GTDB search result was written to GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/result_gtdb.tsv
[2023-07-01 01:02:47,144] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:02:47,172] [INFO] DFAST_QC result json was written to GCA_903830295.1_freshwater_MAG_---_Ki3-D4_bin-147_genomic.fna/dqc_result.json
[2023-07-01 01:02:47,173] [INFO] DFAST_QC completed!
[2023-07-01 01:02:47,173] [INFO] Total running time: 0h0m39s