[2023-06-19 04:28:50,576] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:28:50,578] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:28:50,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg110c4866-40e4-4f35-9b2c-f999f6ca1109/dqc_reference
[2023-06-19 04:28:52,025] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:28:52,026] [INFO] Task started: Prodigal
[2023-06-19 04:28:52,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ac5f9d2-43df-4ecb-9419-5d8c73fe287d/GCA_018647415.1_ASM1864741v1_genomic.fna.gz | prodigal -d GCA_018647415.1_ASM1864741v1_genomic.fna/cds.fna -a GCA_018647415.1_ASM1864741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:28:53,800] [INFO] Task succeeded: Prodigal
[2023-06-19 04:28:53,801] [INFO] Task started: HMMsearch
[2023-06-19 04:28:53,801] [INFO] Running command: hmmsearch --tblout GCA_018647415.1_ASM1864741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg110c4866-40e4-4f35-9b2c-f999f6ca1109/dqc_reference/reference_markers.hmm GCA_018647415.1_ASM1864741v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:28:53,996] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:28:53,998] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6ac5f9d2-43df-4ecb-9419-5d8c73fe287d/GCA_018647415.1_ASM1864741v1_genomic.fna.gz]
[2023-06-19 04:28:54,017] [INFO] Query marker FASTA was written to GCA_018647415.1_ASM1864741v1_genomic.fna/markers.fasta
[2023-06-19 04:28:54,017] [INFO] Task started: Blastn
[2023-06-19 04:28:54,017] [INFO] Running command: blastn -query GCA_018647415.1_ASM1864741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg110c4866-40e4-4f35-9b2c-f999f6ca1109/dqc_reference/reference_markers.fasta -out GCA_018647415.1_ASM1864741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:28:56,573] [INFO] Task succeeded: Blastn
[2023-06-19 04:28:56,577] [INFO] Selected 8 target genomes.
[2023-06-19 04:28:56,578] [INFO] Target genome list was writen to GCA_018647415.1_ASM1864741v1_genomic.fna/target_genomes.txt
[2023-06-19 04:28:56,609] [INFO] Task started: fastANI
[2023-06-19 04:28:56,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ac5f9d2-43df-4ecb-9419-5d8c73fe287d/GCA_018647415.1_ASM1864741v1_genomic.fna.gz --refList GCA_018647415.1_ASM1864741v1_genomic.fna/target_genomes.txt --output GCA_018647415.1_ASM1864741v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:28:59,794] [INFO] Task succeeded: fastANI
[2023-06-19 04:28:59,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg110c4866-40e4-4f35-9b2c-f999f6ca1109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:28:59,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg110c4866-40e4-4f35-9b2c-f999f6ca1109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:28:59,797] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:28:59,798] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:28:59,798] [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
--------------------------------------------------------------------------------
[2023-06-19 04:28:59,800] [INFO] DFAST Taxonomy check result was written to GCA_018647415.1_ASM1864741v1_genomic.fna/tc_result.tsv
[2023-06-19 04:28:59,801] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:28:59,801] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:28:59,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg110c4866-40e4-4f35-9b2c-f999f6ca1109/dqc_reference/checkm_data
[2023-06-19 04:28:59,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:28:59,824] [INFO] Task started: CheckM
[2023-06-19 04:28:59,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018647415.1_ASM1864741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018647415.1_ASM1864741v1_genomic.fna/checkm_input GCA_018647415.1_ASM1864741v1_genomic.fna/checkm_result
[2023-06-19 04:29:13,574] [INFO] Task succeeded: CheckM
[2023-06-19 04:29:13,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:29:13,623] [INFO] ===== Completeness check finished =====
[2023-06-19 04:29:13,623] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:29:13,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018647415.1_ASM1864741v1_genomic.fna/markers.fasta)
[2023-06-19 04:29:13,624] [INFO] Task started: Blastn
[2023-06-19 04:29:13,624] [INFO] Running command: blastn -query GCA_018647415.1_ASM1864741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg110c4866-40e4-4f35-9b2c-f999f6ca1109/dqc_reference/reference_markers_gtdb.fasta -out GCA_018647415.1_ASM1864741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:29:14,061] [INFO] Task succeeded: Blastn
[2023-06-19 04:29:14,069] [INFO] Selected 12 target genomes.
[2023-06-19 04:29:14,069] [INFO] Target genome list was writen to GCA_018647415.1_ASM1864741v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:29:14,080] [INFO] Task started: fastANI
[2023-06-19 04:29:14,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ac5f9d2-43df-4ecb-9419-5d8c73fe287d/GCA_018647415.1_ASM1864741v1_genomic.fna.gz --refList GCA_018647415.1_ASM1864741v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018647415.1_ASM1864741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:29:16,604] [INFO] Task succeeded: fastANI
[2023-06-19 04:29:16,609] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:29:16,609] [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_002701925.2	s__GCA-2701925 sp002701925	97.4227	306	335	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-2701925	95.0	97.33	97.15	0.95	0.94	4	conclusive
GCA_905181755.1	s__TMED58 sp905181755	77.0252	74	335	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED58	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:29:16,611] [INFO] GTDB search result was written to GCA_018647415.1_ASM1864741v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:29:16,611] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:29:16,614] [INFO] DFAST_QC result json was written to GCA_018647415.1_ASM1864741v1_genomic.fna/dqc_result.json
[2023-06-19 04:29:16,614] [INFO] DFAST_QC completed!
[2023-06-19 04:29:16,614] [INFO] Total running time: 0h0m26s