[2023-06-17 06:59:23,358] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:59:23,362] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:59:23,362] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a8588fe-184d-4798-a857-09e8f181132d/dqc_reference
[2023-06-17 06:59:25,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:59:25,158] [INFO] Task started: Prodigal
[2023-06-17 06:59:25,159] [INFO] Running command: gunzip -c /var/lib/cwl/stgec2c0988-01cb-4e90-81da-5bb81c77b8d6/GCA_028708845.1_ASM2870884v1_genomic.fna.gz | prodigal -d GCA_028708845.1_ASM2870884v1_genomic.fna/cds.fna -a GCA_028708845.1_ASM2870884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:59:32,684] [INFO] Task succeeded: Prodigal
[2023-06-17 06:59:32,685] [INFO] Task started: HMMsearch
[2023-06-17 06:59:32,685] [INFO] Running command: hmmsearch --tblout GCA_028708845.1_ASM2870884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a8588fe-184d-4798-a857-09e8f181132d/dqc_reference/reference_markers.hmm GCA_028708845.1_ASM2870884v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:59:32,952] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:59:32,953] [INFO] Found 6/6 markers.
[2023-06-17 06:59:32,981] [INFO] Query marker FASTA was written to GCA_028708845.1_ASM2870884v1_genomic.fna/markers.fasta
[2023-06-17 06:59:32,982] [INFO] Task started: Blastn
[2023-06-17 06:59:32,982] [INFO] Running command: blastn -query GCA_028708845.1_ASM2870884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a8588fe-184d-4798-a857-09e8f181132d/dqc_reference/reference_markers.fasta -out GCA_028708845.1_ASM2870884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:59:33,565] [INFO] Task succeeded: Blastn
[2023-06-17 06:59:33,570] [INFO] Selected 30 target genomes.
[2023-06-17 06:59:33,571] [INFO] Target genome list was writen to GCA_028708845.1_ASM2870884v1_genomic.fna/target_genomes.txt
[2023-06-17 06:59:33,579] [INFO] Task started: fastANI
[2023-06-17 06:59:33,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgec2c0988-01cb-4e90-81da-5bb81c77b8d6/GCA_028708845.1_ASM2870884v1_genomic.fna.gz --refList GCA_028708845.1_ASM2870884v1_genomic.fna/target_genomes.txt --output GCA_028708845.1_ASM2870884v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:59:50,876] [INFO] Task succeeded: fastANI
[2023-06-17 06:59:50,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a8588fe-184d-4798-a857-09e8f181132d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:59:50,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a8588fe-184d-4798-a857-09e8f181132d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:59:50,879] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:59:50,880] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 06:59:50,880] [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
--------------------------------------------------------------------------------
[2023-06-17 06:59:50,883] [INFO] DFAST Taxonomy check result was written to GCA_028708845.1_ASM2870884v1_genomic.fna/tc_result.tsv
[2023-06-17 06:59:50,883] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:59:50,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:59:50,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a8588fe-184d-4798-a857-09e8f181132d/dqc_reference/checkm_data
[2023-06-17 06:59:50,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:59:50,921] [INFO] Task started: CheckM
[2023-06-17 06:59:50,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708845.1_ASM2870884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708845.1_ASM2870884v1_genomic.fna/checkm_input GCA_028708845.1_ASM2870884v1_genomic.fna/checkm_result
[2023-06-17 07:00:18,828] [INFO] Task succeeded: CheckM
[2023-06-17 07:00:18,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 07:00:18,867] [INFO] ===== Completeness check finished =====
[2023-06-17 07:00:18,867] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:00:18,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708845.1_ASM2870884v1_genomic.fna/markers.fasta)
[2023-06-17 07:00:18,868] [INFO] Task started: Blastn
[2023-06-17 07:00:18,868] [INFO] Running command: blastn -query GCA_028708845.1_ASM2870884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a8588fe-184d-4798-a857-09e8f181132d/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708845.1_ASM2870884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:00:19,642] [INFO] Task succeeded: Blastn
[2023-06-17 07:00:19,647] [INFO] Selected 15 target genomes.
[2023-06-17 07:00:19,647] [INFO] Target genome list was writen to GCA_028708845.1_ASM2870884v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:00:19,649] [INFO] Task started: fastANI
[2023-06-17 07:00:19,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgec2c0988-01cb-4e90-81da-5bb81c77b8d6/GCA_028708845.1_ASM2870884v1_genomic.fna.gz --refList GCA_028708845.1_ASM2870884v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708845.1_ASM2870884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:00:27,315] [INFO] Task succeeded: fastANI
[2023-06-17 07:00:27,327] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 07:00:27,328] [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_012837565.1	s__UBA10566 sp012837565	91.9074	470	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA10566	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017988355.1	s__UBA10566 sp017988355	88.2054	327	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA10566	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399025.1	s__UBA10566 sp002399025	78.76	238	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA10566	95.0	98.49	98.49	0.85	0.85	2	-
GCA_002399565.1	s__UBA10566 sp002399565	78.4988	245	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA10566	95.0	97.15	97.15	0.77	0.77	2	-
GCA_002423895.1	s__UBA10566 sp002423895	78.4901	283	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA10566	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860255.1	s__UBA10566 sp017860255	78.2649	274	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA10566	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002407855.1	s__UBA10566 sp002407855	77.61	230	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA10566	95.0	99.29	99.05	0.94	0.92	7	-
GCA_017860275.1	s__UBA10566 sp017860275	77.3997	169	782	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA10566	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 07:00:27,331] [INFO] GTDB search result was written to GCA_028708845.1_ASM2870884v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:00:27,331] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:00:27,351] [INFO] DFAST_QC result json was written to GCA_028708845.1_ASM2870884v1_genomic.fna/dqc_result.json
[2023-06-17 07:00:27,351] [INFO] DFAST_QC completed!
[2023-06-17 07:00:27,351] [INFO] Total running time: 0h1m4s