[2024-01-24 13:49:15,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:15,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:15,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg7969f59f-2897-4706-b3c4-c3ac7111d184/dqc_reference
[2024-01-24 13:49:16,799] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:16,800] [INFO] Task started: Prodigal
[2024-01-24 13:49:16,800] [INFO] Running command: gunzip -c /var/lib/cwl/stge00bca79-0a94-4f64-911b-13339f2b0955/GCF_026230195.1_ASM2623019v1_genomic.fna.gz | prodigal -d GCF_026230195.1_ASM2623019v1_genomic.fna/cds.fna -a GCF_026230195.1_ASM2623019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:24,470] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:24,471] [INFO] Task started: HMMsearch
[2024-01-24 13:49:24,471] [INFO] Running command: hmmsearch --tblout GCF_026230195.1_ASM2623019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7969f59f-2897-4706-b3c4-c3ac7111d184/dqc_reference/reference_markers.hmm GCF_026230195.1_ASM2623019v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:24,740] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:24,741] [INFO] Found 6/6 markers.
[2024-01-24 13:49:24,766] [INFO] Query marker FASTA was written to GCF_026230195.1_ASM2623019v1_genomic.fna/markers.fasta
[2024-01-24 13:49:24,766] [INFO] Task started: Blastn
[2024-01-24 13:49:24,766] [INFO] Running command: blastn -query GCF_026230195.1_ASM2623019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7969f59f-2897-4706-b3c4-c3ac7111d184/dqc_reference/reference_markers.fasta -out GCF_026230195.1_ASM2623019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:25,486] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:25,490] [INFO] Selected 28 target genomes.
[2024-01-24 13:49:25,491] [INFO] Target genome list was writen to GCF_026230195.1_ASM2623019v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:25,520] [INFO] Task started: fastANI
[2024-01-24 13:49:25,521] [INFO] Running command: fastANI --query /var/lib/cwl/stge00bca79-0a94-4f64-911b-13339f2b0955/GCF_026230195.1_ASM2623019v1_genomic.fna.gz --refList GCF_026230195.1_ASM2623019v1_genomic.fna/target_genomes.txt --output GCF_026230195.1_ASM2623019v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:44,712] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:44,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7969f59f-2897-4706-b3c4-c3ac7111d184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:44,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7969f59f-2897-4706-b3c4-c3ac7111d184/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:44,715] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:44,715] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:49:44,715] [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
--------------------------------------------------------------------------------
[2024-01-24 13:49:44,717] [INFO] DFAST Taxonomy check result was written to GCF_026230195.1_ASM2623019v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:44,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:44,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:44,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7969f59f-2897-4706-b3c4-c3ac7111d184/dqc_reference/checkm_data
[2024-01-24 13:49:44,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:44,750] [INFO] Task started: CheckM
[2024-01-24 13:49:44,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026230195.1_ASM2623019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026230195.1_ASM2623019v1_genomic.fna/checkm_input GCF_026230195.1_ASM2623019v1_genomic.fna/checkm_result
[2024-01-24 13:50:14,727] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:14,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:14,747] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:14,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:14,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026230195.1_ASM2623019v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:14,748] [INFO] Task started: Blastn
[2024-01-24 13:50:14,748] [INFO] Running command: blastn -query GCF_026230195.1_ASM2623019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7969f59f-2897-4706-b3c4-c3ac7111d184/dqc_reference/reference_markers_gtdb.fasta -out GCF_026230195.1_ASM2623019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:15,989] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:15,993] [INFO] Selected 25 target genomes.
[2024-01-24 13:50:15,993] [INFO] Target genome list was writen to GCF_026230195.1_ASM2623019v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:16,032] [INFO] Task started: fastANI
[2024-01-24 13:50:16,032] [INFO] Running command: fastANI --query /var/lib/cwl/stge00bca79-0a94-4f64-911b-13339f2b0955/GCF_026230195.1_ASM2623019v1_genomic.fna.gz --refList GCF_026230195.1_ASM2623019v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026230195.1_ASM2623019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:30,318] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:30,325] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:30,325] [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_002689915.1	s__Luminiphilus sp002689915	97.2092	604	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	conclusive
GCA_000227505.4	s__Luminiphilus sp000227505	79.2303	372	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523185.1	s__Luminiphilus sp003523185	79.133	181	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937065.1	s__Luminiphilus sp009937065	78.9369	152	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691565.1	s__Luminiphilus sp002691565	78.4365	106	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.50	98.99	0.85	0.71	3	-
GCA_002390485.1	s__Luminiphilus sp002390485	77.9877	125	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.01	96.90	0.92	0.88	5	-
GCA_902547755.1	s__Luminiphilus sp902547755	77.8851	149	908	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:30,327] [INFO] GTDB search result was written to GCF_026230195.1_ASM2623019v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:30,327] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:30,329] [INFO] DFAST_QC result json was written to GCF_026230195.1_ASM2623019v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:30,330] [INFO] DFAST_QC completed!
[2024-01-24 13:50:30,330] [INFO] Total running time: 0h1m15s