[2023-06-29 21:41:49,531] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:41:49,535] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:41:49,536] [INFO] DQC Reference Directory: /var/lib/cwl/stgc69062e1-03be-407e-9f32-e1569e47e427/dqc_reference
[2023-06-29 21:41:50,755] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:41:50,756] [INFO] Task started: Prodigal
[2023-06-29 21:41:50,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ea34f06-c0bc-48c1-ad17-20e7c73813f4/GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna.gz | prodigal -d GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/cds.fna -a GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:41:52,327] [INFO] Task succeeded: Prodigal
[2023-06-29 21:41:52,327] [INFO] Task started: HMMsearch
[2023-06-29 21:41:52,328] [INFO] Running command: hmmsearch --tblout GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc69062e1-03be-407e-9f32-e1569e47e427/dqc_reference/reference_markers.hmm GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:41:52,524] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:41:52,525] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5ea34f06-c0bc-48c1-ad17-20e7c73813f4/GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna.gz]
[2023-06-29 21:41:52,540] [INFO] Query marker FASTA was written to GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/markers.fasta
[2023-06-29 21:41:52,541] [INFO] Task started: Blastn
[2023-06-29 21:41:52,541] [INFO] Running command: blastn -query GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/markers.fasta -db /var/lib/cwl/stgc69062e1-03be-407e-9f32-e1569e47e427/dqc_reference/reference_markers.fasta -out GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:41:53,026] [INFO] Task succeeded: Blastn
[2023-06-29 21:41:53,030] [INFO] Selected 17 target genomes.
[2023-06-29 21:41:53,030] [INFO] Target genome list was writen to GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/target_genomes.txt
[2023-06-29 21:41:53,049] [INFO] Task started: fastANI
[2023-06-29 21:41:53,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea34f06-c0bc-48c1-ad17-20e7c73813f4/GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna.gz --refList GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/target_genomes.txt --output GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:42:00,352] [INFO] Task succeeded: fastANI
[2023-06-29 21:42:00,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc69062e1-03be-407e-9f32-e1569e47e427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:42:00,354] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc69062e1-03be-407e-9f32-e1569e47e427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:42:00,356] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:42:00,356] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 21:42:00,356] [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
--------------------------------------------------------------------------------
[2023-06-29 21:42:00,359] [INFO] DFAST Taxonomy check result was written to GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/tc_result.tsv
[2023-06-29 21:42:00,359] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:42:00,360] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:42:00,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc69062e1-03be-407e-9f32-e1569e47e427/dqc_reference/checkm_data
[2023-06-29 21:42:00,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:42:00,376] [INFO] Task started: CheckM
[2023-06-29 21:42:00,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/checkm_input GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/checkm_result
[2023-06-29 21:42:13,646] [INFO] Task succeeded: CheckM
[2023-06-29 21:42:13,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.45%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 21:42:13,668] [INFO] ===== Completeness check finished =====
[2023-06-29 21:42:13,668] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:42:13,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/markers.fasta)
[2023-06-29 21:42:13,669] [INFO] Task started: Blastn
[2023-06-29 21:42:13,669] [INFO] Running command: blastn -query GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/markers.fasta -db /var/lib/cwl/stgc69062e1-03be-407e-9f32-e1569e47e427/dqc_reference/reference_markers_gtdb.fasta -out GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:42:14,109] [INFO] Task succeeded: Blastn
[2023-06-29 21:42:14,113] [INFO] Selected 9 target genomes.
[2023-06-29 21:42:14,113] [INFO] Target genome list was writen to GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:42:14,118] [INFO] Task started: fastANI
[2023-06-29 21:42:14,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ea34f06-c0bc-48c1-ad17-20e7c73813f4/GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna.gz --refList GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/target_genomes_gtdb.txt --output GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:42:15,613] [INFO] Task succeeded: fastANI
[2023-06-29 21:42:15,619] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:42:15,619] [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_903899655.1	s__UBA1547 sp903899655	96.8681	185	205	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA1547;g__UBA1547	95.0	98.48	96.87	0.94	0.90	6	conclusive
GCA_903889015.1	s__UBA1547 sp903889015	84.9114	92	205	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA1547;g__UBA1547	95.0	98.64	98.64	0.83	0.83	2	-
GCA_903900345.1	s__UBA1547 sp903900345	81.1435	89	205	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA1547;g__UBA1547	95.0	100.00	100.00	0.99	0.99	2	-
GCA_001873625.1	s__UBA1547 sp001873625	78.9491	79	205	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA1547;g__UBA1547	95.0	99.93	99.83	0.98	0.97	7	-
GCA_002839415.1	s__UBA1547 sp002839415	78.5463	51	205	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA1547;g__UBA1547	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:42:15,621] [INFO] GTDB search result was written to GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/result_gtdb.tsv
[2023-06-29 21:42:15,622] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:42:15,625] [INFO] DFAST_QC result json was written to GCA_903848535.1_freshwater_MAG_---_Ki1-2-2m_bin-314_genomic.fna/dqc_result.json
[2023-06-29 21:42:15,625] [INFO] DFAST_QC completed!
[2023-06-29 21:42:15,625] [INFO] Total running time: 0h0m26s