[2023-06-30 12:42:04,202] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:42:04,204] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:42:04,205] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9be30f9-ca7c-4877-a8b5-23d5f8a7948a/dqc_reference
[2023-06-30 12:42:05,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:42:05,708] [INFO] Task started: Prodigal
[2023-06-30 12:42:05,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e4ce764-38a5-4fe1-8753-300c4b5e426a/GCA_016779945.1_ASM1677994v1_genomic.fna.gz | prodigal -d GCA_016779945.1_ASM1677994v1_genomic.fna/cds.fna -a GCA_016779945.1_ASM1677994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:42:13,172] [INFO] Task succeeded: Prodigal
[2023-06-30 12:42:13,172] [INFO] Task started: HMMsearch
[2023-06-30 12:42:13,173] [INFO] Running command: hmmsearch --tblout GCA_016779945.1_ASM1677994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9be30f9-ca7c-4877-a8b5-23d5f8a7948a/dqc_reference/reference_markers.hmm GCA_016779945.1_ASM1677994v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:42:13,399] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:42:13,400] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1e4ce764-38a5-4fe1-8753-300c4b5e426a/GCA_016779945.1_ASM1677994v1_genomic.fna.gz]
[2023-06-30 12:42:13,425] [INFO] Query marker FASTA was written to GCA_016779945.1_ASM1677994v1_genomic.fna/markers.fasta
[2023-06-30 12:42:13,426] [INFO] Task started: Blastn
[2023-06-30 12:42:13,426] [INFO] Running command: blastn -query GCA_016779945.1_ASM1677994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9be30f9-ca7c-4877-a8b5-23d5f8a7948a/dqc_reference/reference_markers.fasta -out GCA_016779945.1_ASM1677994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:42:14,024] [INFO] Task succeeded: Blastn
[2023-06-30 12:42:14,028] [INFO] Selected 20 target genomes.
[2023-06-30 12:42:14,028] [INFO] Target genome list was writen to GCA_016779945.1_ASM1677994v1_genomic.fna/target_genomes.txt
[2023-06-30 12:42:14,033] [INFO] Task started: fastANI
[2023-06-30 12:42:14,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e4ce764-38a5-4fe1-8753-300c4b5e426a/GCA_016779945.1_ASM1677994v1_genomic.fna.gz --refList GCA_016779945.1_ASM1677994v1_genomic.fna/target_genomes.txt --output GCA_016779945.1_ASM1677994v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:42:26,202] [INFO] Task succeeded: fastANI
[2023-06-30 12:42:26,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9be30f9-ca7c-4877-a8b5-23d5f8a7948a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:42:26,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9be30f9-ca7c-4877-a8b5-23d5f8a7948a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:42:26,205] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:42:26,205] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 12:42:26,205] [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 12:42:26,208] [INFO] DFAST Taxonomy check result was written to GCA_016779945.1_ASM1677994v1_genomic.fna/tc_result.tsv
[2023-06-30 12:42:26,208] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:42:26,208] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:42:26,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9be30f9-ca7c-4877-a8b5-23d5f8a7948a/dqc_reference/checkm_data
[2023-06-30 12:42:26,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:42:26,241] [INFO] Task started: CheckM
[2023-06-30 12:42:26,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016779945.1_ASM1677994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016779945.1_ASM1677994v1_genomic.fna/checkm_input GCA_016779945.1_ASM1677994v1_genomic.fna/checkm_result
[2023-06-30 12:42:55,392] [INFO] Task succeeded: CheckM
[2023-06-30 12:42:55,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:42:55,420] [INFO] ===== Completeness check finished =====
[2023-06-30 12:42:55,420] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:42:55,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016779945.1_ASM1677994v1_genomic.fna/markers.fasta)
[2023-06-30 12:42:55,421] [INFO] Task started: Blastn
[2023-06-30 12:42:55,421] [INFO] Running command: blastn -query GCA_016779945.1_ASM1677994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9be30f9-ca7c-4877-a8b5-23d5f8a7948a/dqc_reference/reference_markers_gtdb.fasta -out GCA_016779945.1_ASM1677994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:42:56,314] [INFO] Task succeeded: Blastn
[2023-06-30 12:42:56,318] [INFO] Selected 19 target genomes.
[2023-06-30 12:42:56,318] [INFO] Target genome list was writen to GCA_016779945.1_ASM1677994v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:42:56,344] [INFO] Task started: fastANI
[2023-06-30 12:42:56,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e4ce764-38a5-4fe1-8753-300c4b5e426a/GCA_016779945.1_ASM1677994v1_genomic.fna.gz --refList GCA_016779945.1_ASM1677994v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016779945.1_ASM1677994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:43:06,204] [INFO] Task succeeded: fastANI
[2023-06-30 12:43:06,214] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:43:06,214] [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_016779945.1	s__UBA9320 sp016779945	100.0	659	670	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002746305.1	s__UBA9320 sp002746305	77.3684	74	670	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700895.1	s__UBA9320 sp018700895	76.6597	57	670	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042025.1	s__UBA9320 sp013042025	76.5707	59	670	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:43:06,216] [INFO] GTDB search result was written to GCA_016779945.1_ASM1677994v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:43:06,217] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:43:06,219] [INFO] DFAST_QC result json was written to GCA_016779945.1_ASM1677994v1_genomic.fna/dqc_result.json
[2023-06-30 12:43:06,220] [INFO] DFAST_QC completed!
[2023-06-30 12:43:06,220] [INFO] Total running time: 0h1m2s