[2023-06-30 09:30:19,547] [INFO] DFAST_QC pipeline started.
[2023-06-30 09:30:19,550] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 09:30:19,550] [INFO] DQC Reference Directory: /var/lib/cwl/stgba93037d-cdbb-4a7b-944f-1e64d1cbef85/dqc_reference
[2023-06-30 09:30:20,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 09:30:20,897] [INFO] Task started: Prodigal
[2023-06-30 09:30:20,897] [INFO] Running command: gunzip -c /var/lib/cwl/stgc98253a7-8144-4867-be76-d82087b750ae/GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna.gz | prodigal -d GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/cds.fna -a GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 09:30:29,823] [INFO] Task succeeded: Prodigal
[2023-06-30 09:30:29,824] [INFO] Task started: HMMsearch
[2023-06-30 09:30:29,824] [INFO] Running command: hmmsearch --tblout GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba93037d-cdbb-4a7b-944f-1e64d1cbef85/dqc_reference/reference_markers.hmm GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/protein.faa > /dev/null
[2023-06-30 09:30:30,106] [INFO] Task succeeded: HMMsearch
[2023-06-30 09:30:30,108] [INFO] Found 6/6 markers.
[2023-06-30 09:30:30,142] [INFO] Query marker FASTA was written to GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/markers.fasta
[2023-06-30 09:30:30,143] [INFO] Task started: Blastn
[2023-06-30 09:30:30,143] [INFO] Running command: blastn -query GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/markers.fasta -db /var/lib/cwl/stgba93037d-cdbb-4a7b-944f-1e64d1cbef85/dqc_reference/reference_markers.fasta -out GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:30:30,731] [INFO] Task succeeded: Blastn
[2023-06-30 09:30:30,737] [INFO] Selected 15 target genomes.
[2023-06-30 09:30:30,737] [INFO] Target genome list was writen to GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/target_genomes.txt
[2023-06-30 09:30:30,739] [INFO] Task started: fastANI
[2023-06-30 09:30:30,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgc98253a7-8144-4867-be76-d82087b750ae/GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna.gz --refList GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/target_genomes.txt --output GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 09:30:38,635] [INFO] Task succeeded: fastANI
[2023-06-30 09:30:38,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba93037d-cdbb-4a7b-944f-1e64d1cbef85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 09:30:38,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba93037d-cdbb-4a7b-944f-1e64d1cbef85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 09:30:38,638] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 09:30:38,639] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 09:30:38,639] [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 09:30:38,641] [INFO] DFAST Taxonomy check result was written to GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/tc_result.tsv
[2023-06-30 09:30:38,642] [INFO] ===== Taxonomy check completed =====
[2023-06-30 09:30:38,642] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 09:30:38,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba93037d-cdbb-4a7b-944f-1e64d1cbef85/dqc_reference/checkm_data
[2023-06-30 09:30:38,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 09:30:38,681] [INFO] Task started: CheckM
[2023-06-30 09:30:38,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/checkm_input GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/checkm_result
[2023-06-30 09:31:11,375] [INFO] Task succeeded: CheckM
[2023-06-30 09:31:11,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 09:31:11,396] [INFO] ===== Completeness check finished =====
[2023-06-30 09:31:11,397] [INFO] ===== Start GTDB Search =====
[2023-06-30 09:31:11,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/markers.fasta)
[2023-06-30 09:31:11,398] [INFO] Task started: Blastn
[2023-06-30 09:31:11,398] [INFO] Running command: blastn -query GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/markers.fasta -db /var/lib/cwl/stgba93037d-cdbb-4a7b-944f-1e64d1cbef85/dqc_reference/reference_markers_gtdb.fasta -out GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 09:31:12,129] [INFO] Task succeeded: Blastn
[2023-06-30 09:31:12,135] [INFO] Selected 16 target genomes.
[2023-06-30 09:31:12,135] [INFO] Target genome list was writen to GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 09:31:12,143] [INFO] Task started: fastANI
[2023-06-30 09:31:12,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgc98253a7-8144-4867-be76-d82087b750ae/GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna.gz --refList GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/target_genomes_gtdb.txt --output GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 09:31:20,143] [INFO] Task succeeded: fastANI
[2023-06-30 09:31:20,153] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 09:31:20,153] [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_903933385.1	s__RFOM01 sp903933385	99.3752	811	924	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__RFOM01	95.0	99.40	99.40	0.89	0.88	3	conclusive
GCA_009918675.1	s__RFOM01 sp009918675	77.7486	182	924	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__RFOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868315.1	s__RFOM01 sp016868315	77.727	221	924	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__RFOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926615.1	s__RFOM01 sp009926615	77.012	116	924	d__Bacteria;p__Bdellovibrionota;c__Oligoflexia;o__Silvanigrellales;f__Silvanigrellaceae;g__RFOM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 09:31:20,155] [INFO] GTDB search result was written to GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/result_gtdb.tsv
[2023-06-30 09:31:20,156] [INFO] ===== GTDB Search completed =====
[2023-06-30 09:31:20,158] [INFO] DFAST_QC result json was written to GCA_903945285.1_freshwater_MAG_---_Loc090721-5m_bin-720_genomic.fna/dqc_result.json
[2023-06-30 09:31:20,159] [INFO] DFAST_QC completed!
[2023-06-30 09:31:20,159] [INFO] Total running time: 0h1m1s