[2023-06-27 01:57:09,733] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:57:09,744] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:57:09,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg69087c37-e035-42d9-a6c2-ab841d004bf4/dqc_reference
[2023-06-27 01:57:12,944] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:57:12,945] [INFO] Task started: Prodigal
[2023-06-27 01:57:12,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg9489c1ae-ef2f-45c5-b704-054201fb9b5b/GCA_002169015.2_ASM216901v2_genomic.fna.gz | prodigal -d GCA_002169015.2_ASM216901v2_genomic.fna/cds.fna -a GCA_002169015.2_ASM216901v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:57:14,265] [INFO] Task succeeded: Prodigal
[2023-06-27 01:57:14,266] [INFO] Task started: HMMsearch
[2023-06-27 01:57:14,266] [INFO] Running command: hmmsearch --tblout GCA_002169015.2_ASM216901v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69087c37-e035-42d9-a6c2-ab841d004bf4/dqc_reference/reference_markers.hmm GCA_002169015.2_ASM216901v2_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:57:14,545] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:57:14,546] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9489c1ae-ef2f-45c5-b704-054201fb9b5b/GCA_002169015.2_ASM216901v2_genomic.fna.gz]
[2023-06-27 01:57:14,564] [INFO] Query marker FASTA was written to GCA_002169015.2_ASM216901v2_genomic.fna/markers.fasta
[2023-06-27 01:57:14,564] [INFO] Task started: Blastn
[2023-06-27 01:57:14,564] [INFO] Running command: blastn -query GCA_002169015.2_ASM216901v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg69087c37-e035-42d9-a6c2-ab841d004bf4/dqc_reference/reference_markers.fasta -out GCA_002169015.2_ASM216901v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:57:16,727] [INFO] Task succeeded: Blastn
[2023-06-27 01:57:16,748] [INFO] Selected 5 target genomes.
[2023-06-27 01:57:16,749] [INFO] Target genome list was writen to GCA_002169015.2_ASM216901v2_genomic.fna/target_genomes.txt
[2023-06-27 01:57:16,815] [INFO] Task started: fastANI
[2023-06-27 01:57:16,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg9489c1ae-ef2f-45c5-b704-054201fb9b5b/GCA_002169015.2_ASM216901v2_genomic.fna.gz --refList GCA_002169015.2_ASM216901v2_genomic.fna/target_genomes.txt --output GCA_002169015.2_ASM216901v2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 01:57:18,276] [INFO] Task succeeded: fastANI
[2023-06-27 01:57:18,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69087c37-e035-42d9-a6c2-ab841d004bf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 01:57:18,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69087c37-e035-42d9-a6c2-ab841d004bf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 01:57:18,283] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 01:57:18,283] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 01:57:18,284] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	77.1635	52	138	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 01:57:18,286] [INFO] DFAST Taxonomy check result was written to GCA_002169015.2_ASM216901v2_genomic.fna/tc_result.tsv
[2023-06-27 01:57:18,287] [INFO] ===== Taxonomy check completed =====
[2023-06-27 01:57:18,287] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:57:18,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69087c37-e035-42d9-a6c2-ab841d004bf4/dqc_reference/checkm_data
[2023-06-27 01:57:18,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:57:18,298] [INFO] Task started: CheckM
[2023-06-27 01:57:18,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002169015.2_ASM216901v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002169015.2_ASM216901v2_genomic.fna/checkm_input GCA_002169015.2_ASM216901v2_genomic.fna/checkm_result
[2023-06-27 01:57:32,331] [INFO] Task succeeded: CheckM
[2023-06-27 01:57:32,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:57:32,350] [INFO] ===== Completeness check finished =====
[2023-06-27 01:57:32,350] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:57:32,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002169015.2_ASM216901v2_genomic.fna/markers.fasta)
[2023-06-27 01:57:32,351] [INFO] Task started: Blastn
[2023-06-27 01:57:32,351] [INFO] Running command: blastn -query GCA_002169015.2_ASM216901v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg69087c37-e035-42d9-a6c2-ab841d004bf4/dqc_reference/reference_markers_gtdb.fasta -out GCA_002169015.2_ASM216901v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:57:32,884] [INFO] Task succeeded: Blastn
[2023-06-27 01:57:32,897] [INFO] Selected 8 target genomes.
[2023-06-27 01:57:32,897] [INFO] Target genome list was writen to GCA_002169015.2_ASM216901v2_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:57:32,924] [INFO] Task started: fastANI
[2023-06-27 01:57:32,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg9489c1ae-ef2f-45c5-b704-054201fb9b5b/GCA_002169015.2_ASM216901v2_genomic.fna.gz --refList GCA_002169015.2_ASM216901v2_genomic.fna/target_genomes_gtdb.txt --output GCA_002169015.2_ASM216901v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:57:34,313] [INFO] Task succeeded: fastANI
[2023-06-27 01:57:34,324] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 01:57:34,325] [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_902514605.1	s__Pelagibacter sp902514605	92.4003	55	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557215.1	s__Pelagibacter sp902557215	84.5376	84	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.87	99.87	0.88	0.88	2	-
GCA_902615445.1	s__Pelagibacter sp902615445	84.4315	75	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594255.1	s__Pelagibacter sp902594255	83.8475	60	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.66	95.66	0.78	0.78	2	-
GCA_902524535.1	s__Pelagibacter sp902524535	83.5811	85	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635685.1	s__Pelagibacter sp902635685	83.5704	64	138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.82	99.78	0.83	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-27 01:57:34,336] [INFO] GTDB search result was written to GCA_002169015.2_ASM216901v2_genomic.fna/result_gtdb.tsv
[2023-06-27 01:57:34,337] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:57:34,344] [INFO] DFAST_QC result json was written to GCA_002169015.2_ASM216901v2_genomic.fna/dqc_result.json
[2023-06-27 01:57:34,344] [INFO] DFAST_QC completed!
[2023-06-27 01:57:34,345] [INFO] Total running time: 0h0m25s