[2023-06-14 00:12:47,659] [INFO] DFAST_QC pipeline started.
[2023-06-14 00:12:47,661] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 00:12:47,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c330445-965d-47bd-863f-fcfcbae29f6e/dqc_reference
[2023-06-14 00:12:49,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 00:12:49,413] [INFO] Task started: Prodigal
[2023-06-14 00:12:49,413] [INFO] Running command: gunzip -c /var/lib/cwl/stge9dafd43-cb6d-4c24-90a1-04db0e886c3a/GCA_947626855.1_Lapin-008_bin40_genomic.fna.gz | prodigal -d GCA_947626855.1_Lapin-008_bin40_genomic.fna/cds.fna -a GCA_947626855.1_Lapin-008_bin40_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 00:12:51,250] [INFO] Task succeeded: Prodigal
[2023-06-14 00:12:51,250] [INFO] Task started: HMMsearch
[2023-06-14 00:12:51,250] [INFO] Running command: hmmsearch --tblout GCA_947626855.1_Lapin-008_bin40_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c330445-965d-47bd-863f-fcfcbae29f6e/dqc_reference/reference_markers.hmm GCA_947626855.1_Lapin-008_bin40_genomic.fna/protein.faa > /dev/null
[2023-06-14 00:12:51,549] [INFO] Task succeeded: HMMsearch
[2023-06-14 00:12:51,550] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge9dafd43-cb6d-4c24-90a1-04db0e886c3a/GCA_947626855.1_Lapin-008_bin40_genomic.fna.gz]
[2023-06-14 00:12:51,572] [INFO] Query marker FASTA was written to GCA_947626855.1_Lapin-008_bin40_genomic.fna/markers.fasta
[2023-06-14 00:12:51,572] [INFO] Task started: Blastn
[2023-06-14 00:12:51,572] [INFO] Running command: blastn -query GCA_947626855.1_Lapin-008_bin40_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c330445-965d-47bd-863f-fcfcbae29f6e/dqc_reference/reference_markers.fasta -out GCA_947626855.1_Lapin-008_bin40_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:12:52,948] [INFO] Task succeeded: Blastn
[2023-06-14 00:12:52,952] [INFO] Selected 23 target genomes.
[2023-06-14 00:12:52,952] [INFO] Target genome list was writen to GCA_947626855.1_Lapin-008_bin40_genomic.fna/target_genomes.txt
[2023-06-14 00:12:52,977] [INFO] Task started: fastANI
[2023-06-14 00:12:52,977] [INFO] Running command: fastANI --query /var/lib/cwl/stge9dafd43-cb6d-4c24-90a1-04db0e886c3a/GCA_947626855.1_Lapin-008_bin40_genomic.fna.gz --refList GCA_947626855.1_Lapin-008_bin40_genomic.fna/target_genomes.txt --output GCA_947626855.1_Lapin-008_bin40_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 00:13:00,379] [INFO] Task succeeded: fastANI
[2023-06-14 00:13:00,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c330445-965d-47bd-863f-fcfcbae29f6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 00:13:00,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c330445-965d-47bd-863f-fcfcbae29f6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 00:13:00,381] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 00:13:00,381] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 00:13:00,381] [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
--------------------------------------------------------------------------------
[2023-06-14 00:13:00,383] [INFO] DFAST Taxonomy check result was written to GCA_947626855.1_Lapin-008_bin40_genomic.fna/tc_result.tsv
[2023-06-14 00:13:00,383] [INFO] ===== Taxonomy check completed =====
[2023-06-14 00:13:00,383] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 00:13:00,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c330445-965d-47bd-863f-fcfcbae29f6e/dqc_reference/checkm_data
[2023-06-14 00:13:00,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 00:13:00,404] [INFO] Task started: CheckM
[2023-06-14 00:13:00,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947626855.1_Lapin-008_bin40_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947626855.1_Lapin-008_bin40_genomic.fna/checkm_input GCA_947626855.1_Lapin-008_bin40_genomic.fna/checkm_result
[2023-06-14 00:13:13,284] [INFO] Task succeeded: CheckM
[2023-06-14 00:13:13,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 00:13:13,307] [INFO] ===== Completeness check finished =====
[2023-06-14 00:13:13,308] [INFO] ===== Start GTDB Search =====
[2023-06-14 00:13:13,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947626855.1_Lapin-008_bin40_genomic.fna/markers.fasta)
[2023-06-14 00:13:13,308] [INFO] Task started: Blastn
[2023-06-14 00:13:13,308] [INFO] Running command: blastn -query GCA_947626855.1_Lapin-008_bin40_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c330445-965d-47bd-863f-fcfcbae29f6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_947626855.1_Lapin-008_bin40_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:13:14,079] [INFO] Task succeeded: Blastn
[2023-06-14 00:13:14,083] [INFO] Selected 24 target genomes.
[2023-06-14 00:13:14,083] [INFO] Target genome list was writen to GCA_947626855.1_Lapin-008_bin40_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 00:13:14,087] [INFO] Task started: fastANI
[2023-06-14 00:13:14,087] [INFO] Running command: fastANI --query /var/lib/cwl/stge9dafd43-cb6d-4c24-90a1-04db0e886c3a/GCA_947626855.1_Lapin-008_bin40_genomic.fna.gz --refList GCA_947626855.1_Lapin-008_bin40_genomic.fna/target_genomes_gtdb.txt --output GCA_947626855.1_Lapin-008_bin40_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 00:13:19,666] [INFO] Task succeeded: fastANI
[2023-06-14 00:13:19,672] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 00:13:19,673] [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_910589375.1	s__UBA5578 sp910589375	78.9511	148	413	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584165.1	s__UBA5578 sp910584165	78.8575	156	413	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017527675.1	s__RGIG6635 sp017527675	77.7269	50	413	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG6635	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425325.1	s__UBA5578 sp002425325	77.6609	62	413	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 00:13:19,674] [INFO] GTDB search result was written to GCA_947626855.1_Lapin-008_bin40_genomic.fna/result_gtdb.tsv
[2023-06-14 00:13:19,675] [INFO] ===== GTDB Search completed =====
[2023-06-14 00:13:19,677] [INFO] DFAST_QC result json was written to GCA_947626855.1_Lapin-008_bin40_genomic.fna/dqc_result.json
[2023-06-14 00:13:19,677] [INFO] DFAST_QC completed!
[2023-06-14 00:13:19,677] [INFO] Total running time: 0h0m32s