[2023-06-29 16:46:47,167] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:46:47,169] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:46:47,169] [INFO] DQC Reference Directory: /var/lib/cwl/stgc85625e0-8fe8-42e6-b193-f12715eb8b73/dqc_reference
[2023-06-29 16:46:48,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:46:48,388] [INFO] Task started: Prodigal
[2023-06-29 16:46:48,388] [INFO] Running command: gunzip -c /var/lib/cwl/stgc12a43a5-b0af-4f2d-9f5b-bc8d629cfb75/GCA_021617455.1_ASM2161745v1_genomic.fna.gz | prodigal -d GCA_021617455.1_ASM2161745v1_genomic.fna/cds.fna -a GCA_021617455.1_ASM2161745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:47:07,450] [INFO] Task succeeded: Prodigal
[2023-06-29 16:47:07,450] [INFO] Task started: HMMsearch
[2023-06-29 16:47:07,451] [INFO] Running command: hmmsearch --tblout GCA_021617455.1_ASM2161745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc85625e0-8fe8-42e6-b193-f12715eb8b73/dqc_reference/reference_markers.hmm GCA_021617455.1_ASM2161745v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:47:07,729] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:47:07,731] [INFO] Found 6/6 markers.
[2023-06-29 16:47:07,763] [INFO] Query marker FASTA was written to GCA_021617455.1_ASM2161745v1_genomic.fna/markers.fasta
[2023-06-29 16:47:07,764] [INFO] Task started: Blastn
[2023-06-29 16:47:07,764] [INFO] Running command: blastn -query GCA_021617455.1_ASM2161745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc85625e0-8fe8-42e6-b193-f12715eb8b73/dqc_reference/reference_markers.fasta -out GCA_021617455.1_ASM2161745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:08,369] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:08,374] [INFO] Selected 30 target genomes.
[2023-06-29 16:47:08,375] [INFO] Target genome list was writen to GCA_021617455.1_ASM2161745v1_genomic.fna/target_genomes.txt
[2023-06-29 16:47:08,383] [INFO] Task started: fastANI
[2023-06-29 16:47:08,384] [INFO] Running command: fastANI --query /var/lib/cwl/stgc12a43a5-b0af-4f2d-9f5b-bc8d629cfb75/GCA_021617455.1_ASM2161745v1_genomic.fna.gz --refList GCA_021617455.1_ASM2161745v1_genomic.fna/target_genomes.txt --output GCA_021617455.1_ASM2161745v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:47:27,211] [INFO] Task succeeded: fastANI
[2023-06-29 16:47:27,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc85625e0-8fe8-42e6-b193-f12715eb8b73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:47:27,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc85625e0-8fe8-42e6-b193-f12715eb8b73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:47:27,214] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:47:27,214] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 16:47:27,215] [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 16:47:27,217] [INFO] DFAST Taxonomy check result was written to GCA_021617455.1_ASM2161745v1_genomic.fna/tc_result.tsv
[2023-06-29 16:47:27,218] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:47:27,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:47:27,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc85625e0-8fe8-42e6-b193-f12715eb8b73/dqc_reference/checkm_data
[2023-06-29 16:47:27,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:47:27,267] [INFO] Task started: CheckM
[2023-06-29 16:47:27,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021617455.1_ASM2161745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021617455.1_ASM2161745v1_genomic.fna/checkm_input GCA_021617455.1_ASM2161745v1_genomic.fna/checkm_result
[2023-06-29 16:48:22,677] [INFO] Task succeeded: CheckM
[2023-06-29 16:48:22,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:48:22,700] [INFO] ===== Completeness check finished =====
[2023-06-29 16:48:22,701] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:48:22,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021617455.1_ASM2161745v1_genomic.fna/markers.fasta)
[2023-06-29 16:48:22,701] [INFO] Task started: Blastn
[2023-06-29 16:48:22,701] [INFO] Running command: blastn -query GCA_021617455.1_ASM2161745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc85625e0-8fe8-42e6-b193-f12715eb8b73/dqc_reference/reference_markers_gtdb.fasta -out GCA_021617455.1_ASM2161745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:48:23,593] [INFO] Task succeeded: Blastn
[2023-06-29 16:48:23,598] [INFO] Selected 9 target genomes.
[2023-06-29 16:48:23,599] [INFO] Target genome list was writen to GCA_021617455.1_ASM2161745v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:48:23,604] [INFO] Task started: fastANI
[2023-06-29 16:48:23,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgc12a43a5-b0af-4f2d-9f5b-bc8d629cfb75/GCA_021617455.1_ASM2161745v1_genomic.fna.gz --refList GCA_021617455.1_ASM2161745v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021617455.1_ASM2161745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:48:29,546] [INFO] Task succeeded: fastANI
[2023-06-29 16:48:29,557] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:48:29,557] [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_000433355.1	s__Cryptobacteroides sp000433355	97.8758	816	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	97.93	0.86	0.80	6	conclusive
GCA_900544195.1	s__Cryptobacteroides sp900544195	92.6105	696	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.99	97.97	0.92	0.84	3	-
GCA_000431015.1	s__Cryptobacteroides sp000431015	88.4667	594	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.39	98.13	0.87	0.74	9	-
GCA_002314195.1	s__Cryptobacteroides sp002314195	84.5557	560	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.70	98.15	0.81	0.75	7	-
GCA_002321335.1	s__Cryptobacteroides sp002321335	84.5231	607	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.53	99.38	0.88	0.86	3	-
GCA_002438845.1	s__Cryptobacteroides sp002438845	84.3694	551	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.65	99.58	0.89	0.89	3	-
GCA_002439875.1	s__Cryptobacteroides sp002439875	83.8937	569	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297815.1	s__Cryptobacteroides sp002297815	82.5023	546	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.51	97.81	0.90	0.86	6	-
GCA_002438905.1	s__Cryptobacteroides sp002438905	77.2842	64	1139	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:48:29,559] [INFO] GTDB search result was written to GCA_021617455.1_ASM2161745v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:48:29,560] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:48:29,562] [INFO] DFAST_QC result json was written to GCA_021617455.1_ASM2161745v1_genomic.fna/dqc_result.json
[2023-06-29 16:48:29,562] [INFO] DFAST_QC completed!
[2023-06-29 16:48:29,562] [INFO] Total running time: 0h1m42s