[2023-06-07 22:39:44,777] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:39:44,790] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:39:44,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a4a4ac1-3710-4cb3-a4e1-bb4fd02721a9/dqc_reference
[2023-06-07 22:39:48,385] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:39:48,386] [INFO] Task started: Prodigal
[2023-06-07 22:39:48,387] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7d5f93a-a731-4415-8681-cb562f095503/GCA_945902115.1_MoE-02may19-163_genomic.fna.gz | prodigal -d GCA_945902115.1_MoE-02may19-163_genomic.fna/cds.fna -a GCA_945902115.1_MoE-02may19-163_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:39:57,995] [INFO] Task succeeded: Prodigal
[2023-06-07 22:39:57,995] [INFO] Task started: HMMsearch
[2023-06-07 22:39:57,995] [INFO] Running command: hmmsearch --tblout GCA_945902115.1_MoE-02may19-163_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a4a4ac1-3710-4cb3-a4e1-bb4fd02721a9/dqc_reference/reference_markers.hmm GCA_945902115.1_MoE-02may19-163_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:39:58,231] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:39:58,232] [INFO] Found 6/6 markers.
[2023-06-07 22:39:58,259] [INFO] Query marker FASTA was written to GCA_945902115.1_MoE-02may19-163_genomic.fna/markers.fasta
[2023-06-07 22:39:58,259] [INFO] Task started: Blastn
[2023-06-07 22:39:58,260] [INFO] Running command: blastn -query GCA_945902115.1_MoE-02may19-163_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a4a4ac1-3710-4cb3-a4e1-bb4fd02721a9/dqc_reference/reference_markers.fasta -out GCA_945902115.1_MoE-02may19-163_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:39:58,834] [INFO] Task succeeded: Blastn
[2023-06-07 22:39:58,854] [INFO] Selected 26 target genomes.
[2023-06-07 22:39:58,854] [INFO] Target genome list was writen to GCA_945902115.1_MoE-02may19-163_genomic.fna/target_genomes.txt
[2023-06-07 22:39:58,857] [INFO] Task started: fastANI
[2023-06-07 22:39:58,857] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7d5f93a-a731-4415-8681-cb562f095503/GCA_945902115.1_MoE-02may19-163_genomic.fna.gz --refList GCA_945902115.1_MoE-02may19-163_genomic.fna/target_genomes.txt --output GCA_945902115.1_MoE-02may19-163_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:40:13,196] [INFO] Task succeeded: fastANI
[2023-06-07 22:40:13,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a4a4ac1-3710-4cb3-a4e1-bb4fd02721a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:40:13,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a4a4ac1-3710-4cb3-a4e1-bb4fd02721a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:40:13,200] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:40:13,200] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 22:40:13,200] [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
--------------------------------------------------------------------------------
[2023-06-07 22:40:13,202] [INFO] DFAST Taxonomy check result was written to GCA_945902115.1_MoE-02may19-163_genomic.fna/tc_result.tsv
[2023-06-07 22:40:13,202] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:40:13,202] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:40:13,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a4a4ac1-3710-4cb3-a4e1-bb4fd02721a9/dqc_reference/checkm_data
[2023-06-07 22:40:13,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:40:13,233] [INFO] Task started: CheckM
[2023-06-07 22:40:13,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945902115.1_MoE-02may19-163_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945902115.1_MoE-02may19-163_genomic.fna/checkm_input GCA_945902115.1_MoE-02may19-163_genomic.fna/checkm_result
[2023-06-07 22:40:45,932] [INFO] Task succeeded: CheckM
[2023-06-07 22:40:45,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:40:45,954] [INFO] ===== Completeness check finished =====
[2023-06-07 22:40:45,955] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:40:45,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945902115.1_MoE-02may19-163_genomic.fna/markers.fasta)
[2023-06-07 22:40:45,955] [INFO] Task started: Blastn
[2023-06-07 22:40:45,955] [INFO] Running command: blastn -query GCA_945902115.1_MoE-02may19-163_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a4a4ac1-3710-4cb3-a4e1-bb4fd02721a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_945902115.1_MoE-02may19-163_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:40:46,724] [INFO] Task succeeded: Blastn
[2023-06-07 22:40:46,737] [INFO] Selected 27 target genomes.
[2023-06-07 22:40:46,737] [INFO] Target genome list was writen to GCA_945902115.1_MoE-02may19-163_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:40:46,764] [INFO] Task started: fastANI
[2023-06-07 22:40:46,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7d5f93a-a731-4415-8681-cb562f095503/GCA_945902115.1_MoE-02may19-163_genomic.fna.gz --refList GCA_945902115.1_MoE-02may19-163_genomic.fna/target_genomes_gtdb.txt --output GCA_945902115.1_MoE-02may19-163_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:40:58,574] [INFO] Task succeeded: fastANI
[2023-06-07 22:40:58,583] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 22:40:58,583] [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_016866375.1	s__UBA952 sp016866375	77.2663	121	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003512365.1	s__UBA952 sp003512365	77.1777	149	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.55	99.55	0.81	0.81	2	-
GCA_016866415.1	s__UBA952 sp016866415	76.818	58	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926125.1	s__UBA952 sp009926125	76.7343	59	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883325.1	s__UBA952 sp018883325	75.9301	78	787	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 22:40:58,591] [INFO] GTDB search result was written to GCA_945902115.1_MoE-02may19-163_genomic.fna/result_gtdb.tsv
[2023-06-07 22:40:58,591] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:40:58,595] [INFO] DFAST_QC result json was written to GCA_945902115.1_MoE-02may19-163_genomic.fna/dqc_result.json
[2023-06-07 22:40:58,596] [INFO] DFAST_QC completed!
[2023-06-07 22:40:58,596] [INFO] Total running time: 0h1m14s