[2023-06-30 05:04:27,660] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:04:27,665] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:04:27,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ba551e8-f03e-4586-9a3f-07146ffb3cc8/dqc_reference
[2023-06-30 05:04:29,847] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:04:29,848] [INFO] Task started: Prodigal
[2023-06-30 05:04:29,848] [INFO] Running command: gunzip -c /var/lib/cwl/stg23649d90-2229-4f35-a085-b797ded3aef1/GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna.gz | prodigal -d GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/cds.fna -a GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:04:32,254] [INFO] Task succeeded: Prodigal
[2023-06-30 05:04:32,255] [INFO] Task started: HMMsearch
[2023-06-30 05:04:32,255] [INFO] Running command: hmmsearch --tblout GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ba551e8-f03e-4586-9a3f-07146ffb3cc8/dqc_reference/reference_markers.hmm GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:04:32,464] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:04:32,466] [INFO] Found 6/6 markers.
[2023-06-30 05:04:32,486] [INFO] Query marker FASTA was written to GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/markers.fasta
[2023-06-30 05:04:32,486] [INFO] Task started: Blastn
[2023-06-30 05:04:32,486] [INFO] Running command: blastn -query GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ba551e8-f03e-4586-9a3f-07146ffb3cc8/dqc_reference/reference_markers.fasta -out GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:04:34,170] [INFO] Task succeeded: Blastn
[2023-06-30 05:04:34,175] [INFO] Selected 25 target genomes.
[2023-06-30 05:04:34,176] [INFO] Target genome list was writen to GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/target_genomes.txt
[2023-06-30 05:04:34,182] [INFO] Task started: fastANI
[2023-06-30 05:04:34,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg23649d90-2229-4f35-a085-b797ded3aef1/GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna.gz --refList GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/target_genomes.txt --output GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:04:44,197] [INFO] Task succeeded: fastANI
[2023-06-30 05:04:44,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ba551e8-f03e-4586-9a3f-07146ffb3cc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:04:44,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ba551e8-f03e-4586-9a3f-07146ffb3cc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:04:44,201] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:04:44,201] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 05:04:44,201] [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 05:04:44,204] [INFO] DFAST Taxonomy check result was written to GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/tc_result.tsv
[2023-06-30 05:04:44,204] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:04:44,204] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:04:44,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ba551e8-f03e-4586-9a3f-07146ffb3cc8/dqc_reference/checkm_data
[2023-06-30 05:04:44,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:04:44,228] [INFO] Task started: CheckM
[2023-06-30 05:04:44,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/checkm_input GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/checkm_result
[2023-06-30 05:04:59,806] [INFO] Task succeeded: CheckM
[2023-06-30 05:04:59,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 05:04:59,828] [INFO] ===== Completeness check finished =====
[2023-06-30 05:04:59,828] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:04:59,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/markers.fasta)
[2023-06-30 05:04:59,829] [INFO] Task started: Blastn
[2023-06-30 05:04:59,829] [INFO] Running command: blastn -query GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ba551e8-f03e-4586-9a3f-07146ffb3cc8/dqc_reference/reference_markers_gtdb.fasta -out GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:05:00,777] [INFO] Task succeeded: Blastn
[2023-06-30 05:05:00,783] [INFO] Selected 11 target genomes.
[2023-06-30 05:05:00,783] [INFO] Target genome list was writen to GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:05:00,791] [INFO] Task started: fastANI
[2023-06-30 05:05:00,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg23649d90-2229-4f35-a085-b797ded3aef1/GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna.gz --refList GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/target_genomes_gtdb.txt --output GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:05:02,841] [INFO] Task succeeded: fastANI
[2023-06-30 05:05:02,855] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:05:02,855] [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
GCA_903842675.1	s__AAA044-D11 sp903842675	98.7419	219	257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.43	97.97	0.83	0.78	19	conclusive
GCA_000485495.1	s__AAA044-D11 sp000485495	79.9723	81	257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871555.1	s__AAA044-D11 sp903871555	79.4215	110	257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.45	99.05	0.90	0.84	22	-
GCA_007280395.1	s__AAA044-D11 sp007280395	79.3319	79	257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903836945.1	s__AAA044-D11 sp903836945	78.5661	88	257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.73	99.63	0.93	0.90	11	-
GCA_009701525.1	s__AAA044-D11 sp009701525	78.2144	58	257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009726125.1	s__AAA044-D11 sp009726125	78.0369	91	257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.98	99.96	0.97	0.96	6	-
GCA_002340925.1	s__AAA044-D11 sp002340925	77.9162	63	257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009701575.1	s__AAA044-D11 sp009701575	77.7494	84	257	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 05:05:02,857] [INFO] GTDB search result was written to GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/result_gtdb.tsv
[2023-06-30 05:05:02,858] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:05:02,861] [INFO] DFAST_QC result json was written to GCA_903852065.1_freshwater_MAG_---_YR3_bin-0656_genomic.fna/dqc_result.json
[2023-06-30 05:05:02,861] [INFO] DFAST_QC completed!
[2023-06-30 05:05:02,861] [INFO] Total running time: 0h0m35s