[2023-06-04 17:30:22,984] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:30:22,997] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:30:22,998] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb398610-3ad7-4130-8801-aa68635c85a3/dqc_reference
[2023-06-04 17:30:24,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:30:24,309] [INFO] Task started: Prodigal
[2023-06-04 17:30:24,309] [INFO] Running command: gunzip -c /var/lib/cwl/stgb841679d-f7de-4037-9d4b-9710f4df739d/GCA_010026255.1_ASM1002625v1_genomic.fna.gz | prodigal -d GCA_010026255.1_ASM1002625v1_genomic.fna/cds.fna -a GCA_010026255.1_ASM1002625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:30:25,534] [INFO] Task succeeded: Prodigal
[2023-06-04 17:30:25,535] [INFO] Task started: HMMsearch
[2023-06-04 17:30:25,535] [INFO] Running command: hmmsearch --tblout GCA_010026255.1_ASM1002625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb398610-3ad7-4130-8801-aa68635c85a3/dqc_reference/reference_markers.hmm GCA_010026255.1_ASM1002625v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:30:25,725] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:30:25,727] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb841679d-f7de-4037-9d4b-9710f4df739d/GCA_010026255.1_ASM1002625v1_genomic.fna.gz]
[2023-06-04 17:30:25,748] [INFO] Query marker FASTA was written to GCA_010026255.1_ASM1002625v1_genomic.fna/markers.fasta
[2023-06-04 17:30:25,748] [INFO] Task started: Blastn
[2023-06-04 17:30:25,748] [INFO] Running command: blastn -query GCA_010026255.1_ASM1002625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb398610-3ad7-4130-8801-aa68635c85a3/dqc_reference/reference_markers.fasta -out GCA_010026255.1_ASM1002625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:30:30,283] [INFO] Task succeeded: Blastn
[2023-06-04 17:30:30,288] [INFO] Selected 8 target genomes.
[2023-06-04 17:30:30,289] [INFO] Target genome list was writen to GCA_010026255.1_ASM1002625v1_genomic.fna/target_genomes.txt
[2023-06-04 17:30:33,623] [INFO] Task started: fastANI
[2023-06-04 17:30:33,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgb841679d-f7de-4037-9d4b-9710f4df739d/GCA_010026255.1_ASM1002625v1_genomic.fna.gz --refList GCA_010026255.1_ASM1002625v1_genomic.fna/target_genomes.txt --output GCA_010026255.1_ASM1002625v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:30:36,732] [INFO] Task succeeded: fastANI
[2023-06-04 17:30:36,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb398610-3ad7-4130-8801-aa68635c85a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:30:36,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb398610-3ad7-4130-8801-aa68635c85a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:30:36,735] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:30:36,735] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 17:30:36,736] [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
--------------------------------------------------------------------------------
[2023-06-04 17:30:36,738] [INFO] DFAST Taxonomy check result was written to GCA_010026255.1_ASM1002625v1_genomic.fna/tc_result.tsv
[2023-06-04 17:30:36,739] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:30:36,739] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:30:36,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb398610-3ad7-4130-8801-aa68635c85a3/dqc_reference/checkm_data
[2023-06-04 17:30:36,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:30:36,754] [INFO] Task started: CheckM
[2023-06-04 17:30:36,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010026255.1_ASM1002625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010026255.1_ASM1002625v1_genomic.fna/checkm_input GCA_010026255.1_ASM1002625v1_genomic.fna/checkm_result
[2023-06-04 17:30:48,913] [INFO] Task succeeded: CheckM
[2023-06-04 17:30:48,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:30:48,933] [INFO] ===== Completeness check finished =====
[2023-06-04 17:30:48,933] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:30:48,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010026255.1_ASM1002625v1_genomic.fna/markers.fasta)
[2023-06-04 17:30:48,934] [INFO] Task started: Blastn
[2023-06-04 17:30:48,934] [INFO] Running command: blastn -query GCA_010026255.1_ASM1002625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb398610-3ad7-4130-8801-aa68635c85a3/dqc_reference/reference_markers_gtdb.fasta -out GCA_010026255.1_ASM1002625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:30:49,771] [INFO] Task succeeded: Blastn
[2023-06-04 17:30:49,776] [INFO] Selected 11 target genomes.
[2023-06-04 17:30:49,776] [INFO] Target genome list was writen to GCA_010026255.1_ASM1002625v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:30:50,265] [INFO] Task started: fastANI
[2023-06-04 17:30:50,265] [INFO] Running command: fastANI --query /var/lib/cwl/stgb841679d-f7de-4037-9d4b-9710f4df739d/GCA_010026255.1_ASM1002625v1_genomic.fna.gz --refList GCA_010026255.1_ASM1002625v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010026255.1_ASM1002625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:30:52,279] [INFO] Task succeeded: fastANI
[2023-06-04 17:30:52,286] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 17:30:52,286] [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_003569185.1	s__Nanopelagicus sp003569185	92.5946	73	89	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287885.2	s__Nanopelagicus limnes	89.8072	85	89	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000294575.1	s__Nanopelagicus sp000294575	81.0308	61	89	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	98.86	98.86	0.86	0.86	2	-
GCF_002288005.1	s__Nanopelagicus hibericus	80.881	60	89	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691185.1	s__Nanopelagicus sp009691185	79.7053	54	89	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000378865.1	s__Nanopelagicus sp000378865	79.4636	50	89	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__Nanopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 17:30:52,291] [INFO] GTDB search result was written to GCA_010026255.1_ASM1002625v1_genomic.fna/result_gtdb.tsv
[2023-06-04 17:30:52,292] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:30:52,295] [INFO] DFAST_QC result json was written to GCA_010026255.1_ASM1002625v1_genomic.fna/dqc_result.json
[2023-06-04 17:30:52,295] [INFO] DFAST_QC completed!
[2023-06-04 17:30:52,295] [INFO] Total running time: 0h0m29s