[2024-01-25 20:23:05,536] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:05,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:05,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e7a4dc5-2f1a-487c-b763-44cd1a877b76/dqc_reference
[2024-01-25 20:23:06,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:06,724] [INFO] Task started: Prodigal
[2024-01-25 20:23:06,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg6af204a6-3f6e-462f-8829-8e4e8f1d2b74/GCF_000007365.1_ASM736v1_genomic.fna.gz | prodigal -d GCF_000007365.1_ASM736v1_genomic.fna/cds.fna -a GCF_000007365.1_ASM736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:07,603] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:07,603] [INFO] Task started: HMMsearch
[2024-01-25 20:23:07,603] [INFO] Running command: hmmsearch --tblout GCF_000007365.1_ASM736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e7a4dc5-2f1a-487c-b763-44cd1a877b76/dqc_reference/reference_markers.hmm GCF_000007365.1_ASM736v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:07,739] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:07,740] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6af204a6-3f6e-462f-8829-8e4e8f1d2b74/GCF_000007365.1_ASM736v1_genomic.fna.gz]
[2024-01-25 20:23:07,749] [INFO] Query marker FASTA was written to GCF_000007365.1_ASM736v1_genomic.fna/markers.fasta
[2024-01-25 20:23:07,750] [INFO] Task started: Blastn
[2024-01-25 20:23:07,750] [INFO] Running command: blastn -query GCF_000007365.1_ASM736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e7a4dc5-2f1a-487c-b763-44cd1a877b76/dqc_reference/reference_markers.fasta -out GCF_000007365.1_ASM736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:08,279] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:08,282] [INFO] Selected 17 target genomes.
[2024-01-25 20:23:08,282] [INFO] Target genome list was writen to GCF_000007365.1_ASM736v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:08,290] [INFO] Task started: fastANI
[2024-01-25 20:23:08,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg6af204a6-3f6e-462f-8829-8e4e8f1d2b74/GCF_000007365.1_ASM736v1_genomic.fna.gz --refList GCF_000007365.1_ASM736v1_genomic.fna/target_genomes.txt --output GCF_000007365.1_ASM736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:14,747] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:14,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e7a4dc5-2f1a-487c-b763-44cd1a877b76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:14,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e7a4dc5-2f1a-487c-b763-44cd1a877b76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:14,752] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:14,752] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:14,752] [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
Buchnera aphidicola (Schizaphis graminum)	strain=Sg (ex Schizaphis graminum)	GCA_000007365.1	98794	9	suspected-type	True	100.0	212	213	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 20:23:14,753] [INFO] DFAST Taxonomy check result was written to GCF_000007365.1_ASM736v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:14,754] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:14,754] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:14,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e7a4dc5-2f1a-487c-b763-44cd1a877b76/dqc_reference/checkm_data
[2024-01-25 20:23:14,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:14,766] [INFO] Task started: CheckM
[2024-01-25 20:23:14,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000007365.1_ASM736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000007365.1_ASM736v1_genomic.fna/checkm_input GCF_000007365.1_ASM736v1_genomic.fna/checkm_result
[2024-01-25 20:23:24,793] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:24,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:24,808] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:24,808] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:24,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000007365.1_ASM736v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:24,808] [INFO] Task started: Blastn
[2024-01-25 20:23:24,809] [INFO] Running command: blastn -query GCF_000007365.1_ASM736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e7a4dc5-2f1a-487c-b763-44cd1a877b76/dqc_reference/reference_markers_gtdb.fasta -out GCF_000007365.1_ASM736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:25,563] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:25,566] [INFO] Selected 9 target genomes.
[2024-01-25 20:23:25,566] [INFO] Target genome list was writen to GCF_000007365.1_ASM736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:25,574] [INFO] Task started: fastANI
[2024-01-25 20:23:25,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg6af204a6-3f6e-462f-8829-8e4e8f1d2b74/GCF_000007365.1_ASM736v1_genomic.fna.gz --refList GCF_000007365.1_ASM736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000007365.1_ASM736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:27,242] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:27,249] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:27,249] [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
GCF_000007365.1	s__Buchnera aphidicola_O	100.0	212	213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_005080845.1	s__Buchnera aphidicola_AO	89.8677	211	213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671935.1	s__Buchnera aphidicola_AL	89.3896	206	213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009069125.1	s__Buchnera aphidicola_BB	82.2885	172	213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005083845.1	s__Buchnera aphidicola_AW	81.8368	183	213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005082145.1	s__Buchnera aphidicola_U	81.4682	185	213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	99.97	99.97	1.00	1.00	2	-
GCF_005083105.1	s__Buchnera aphidicola_AS	81.3731	183	213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005083345.1	s__Buchnera aphidicola_R	80.7784	178	213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	95.46	95.46	1.00	1.00	2	-
GCF_005081945.1	s__Buchnera aphidicola_AN	80.5538	175	213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:27,250] [INFO] GTDB search result was written to GCF_000007365.1_ASM736v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:27,251] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:27,253] [INFO] DFAST_QC result json was written to GCF_000007365.1_ASM736v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:27,253] [INFO] DFAST_QC completed!
[2024-01-25 20:23:27,253] [INFO] Total running time: 0h0m22s