[2023-06-29 03:34:24,189] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:34:24,191] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:34:24,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg84141ded-4e1b-416f-86c1-92625a9bc1a8/dqc_reference
[2023-06-29 03:34:25,520] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:34:25,521] [INFO] Task started: Prodigal
[2023-06-29 03:34:25,521] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8a39b17-6951-4190-9e3c-fbf306f33319/GCA_020355145.1_ASM2035514v1_genomic.fna.gz | prodigal -d GCA_020355145.1_ASM2035514v1_genomic.fna/cds.fna -a GCA_020355145.1_ASM2035514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:34:29,552] [INFO] Task succeeded: Prodigal
[2023-06-29 03:34:29,552] [INFO] Task started: HMMsearch
[2023-06-29 03:34:29,552] [INFO] Running command: hmmsearch --tblout GCA_020355145.1_ASM2035514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84141ded-4e1b-416f-86c1-92625a9bc1a8/dqc_reference/reference_markers.hmm GCA_020355145.1_ASM2035514v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:34:29,770] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:34:29,771] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd8a39b17-6951-4190-9e3c-fbf306f33319/GCA_020355145.1_ASM2035514v1_genomic.fna.gz]
[2023-06-29 03:34:29,796] [INFO] Query marker FASTA was written to GCA_020355145.1_ASM2035514v1_genomic.fna/markers.fasta
[2023-06-29 03:34:29,797] [INFO] Task started: Blastn
[2023-06-29 03:34:29,797] [INFO] Running command: blastn -query GCA_020355145.1_ASM2035514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84141ded-4e1b-416f-86c1-92625a9bc1a8/dqc_reference/reference_markers.fasta -out GCA_020355145.1_ASM2035514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:34:30,407] [INFO] Task succeeded: Blastn
[2023-06-29 03:34:30,411] [INFO] Selected 9 target genomes.
[2023-06-29 03:34:30,411] [INFO] Target genome list was writen to GCA_020355145.1_ASM2035514v1_genomic.fna/target_genomes.txt
[2023-06-29 03:34:30,414] [INFO] Task started: fastANI
[2023-06-29 03:34:30,414] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8a39b17-6951-4190-9e3c-fbf306f33319/GCA_020355145.1_ASM2035514v1_genomic.fna.gz --refList GCA_020355145.1_ASM2035514v1_genomic.fna/target_genomes.txt --output GCA_020355145.1_ASM2035514v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:34:35,973] [INFO] Task succeeded: fastANI
[2023-06-29 03:34:35,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84141ded-4e1b-416f-86c1-92625a9bc1a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:34:35,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84141ded-4e1b-416f-86c1-92625a9bc1a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:34:35,976] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:34:35,976] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 03:34:35,976] [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 03:34:35,981] [INFO] DFAST Taxonomy check result was written to GCA_020355145.1_ASM2035514v1_genomic.fna/tc_result.tsv
[2023-06-29 03:34:35,982] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:34:35,982] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:34:35,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84141ded-4e1b-416f-86c1-92625a9bc1a8/dqc_reference/checkm_data
[2023-06-29 03:34:35,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:34:36,017] [INFO] Task started: CheckM
[2023-06-29 03:34:36,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020355145.1_ASM2035514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020355145.1_ASM2035514v1_genomic.fna/checkm_input GCA_020355145.1_ASM2035514v1_genomic.fna/checkm_result
[2023-06-29 03:34:54,893] [INFO] Task succeeded: CheckM
[2023-06-29 03:34:54,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:34:54,923] [INFO] ===== Completeness check finished =====
[2023-06-29 03:34:54,923] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:34:54,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020355145.1_ASM2035514v1_genomic.fna/markers.fasta)
[2023-06-29 03:34:54,924] [INFO] Task started: Blastn
[2023-06-29 03:34:54,925] [INFO] Running command: blastn -query GCA_020355145.1_ASM2035514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84141ded-4e1b-416f-86c1-92625a9bc1a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_020355145.1_ASM2035514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:34:55,664] [INFO] Task succeeded: Blastn
[2023-06-29 03:34:55,670] [INFO] Selected 10 target genomes.
[2023-06-29 03:34:55,670] [INFO] Target genome list was writen to GCA_020355145.1_ASM2035514v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:34:55,677] [INFO] Task started: fastANI
[2023-06-29 03:34:55,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8a39b17-6951-4190-9e3c-fbf306f33319/GCA_020355145.1_ASM2035514v1_genomic.fna.gz --refList GCA_020355145.1_ASM2035514v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020355145.1_ASM2035514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:34:59,773] [INFO] Task succeeded: fastANI
[2023-06-29 03:34:59,783] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 03:34:59,783] [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_013375385.1	s__B33-G16 sp013375385	80.5547	249	559	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__B25-G16;g__B33-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013375335.1	s__B33-G16 sp013375335	80.4098	188	559	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__B25-G16;g__B33-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003646875.1	s__B33-G16 sp003646875	77.9204	169	559	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__B25-G16;g__B33-G16	95.0	98.46	98.46	0.69	0.69	2	-
GCA_015223015.1	s__B33-G16 sp015223015	77.4554	128	559	d__Bacteria;p__Desulfobacterota;c__DSM-4660;o__Desulfatiglandales;f__B25-G16;g__B33-G16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 03:34:59,786] [INFO] GTDB search result was written to GCA_020355145.1_ASM2035514v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:34:59,787] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:34:59,790] [INFO] DFAST_QC result json was written to GCA_020355145.1_ASM2035514v1_genomic.fna/dqc_result.json
[2023-06-29 03:34:59,791] [INFO] DFAST_QC completed!
[2023-06-29 03:34:59,791] [INFO] Total running time: 0h0m36s