[2024-01-24 14:03:03,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:03,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:03,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg51a45676-77f3-440e-b508-8166e87e1c8a/dqc_reference
[2024-01-24 14:03:04,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:04,571] [INFO] Task started: Prodigal
[2024-01-24 14:03:04,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg954ab479-4380-4d48-ae56-45911cdc303d/GCF_000153205.1_ASM15320v1_genomic.fna.gz | prodigal -d GCF_000153205.1_ASM15320v1_genomic.fna/cds.fna -a GCF_000153205.1_ASM15320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:15,801] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:15,802] [INFO] Task started: HMMsearch
[2024-01-24 14:03:15,802] [INFO] Running command: hmmsearch --tblout GCF_000153205.1_ASM15320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51a45676-77f3-440e-b508-8166e87e1c8a/dqc_reference/reference_markers.hmm GCF_000153205.1_ASM15320v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:16,106] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:16,108] [INFO] Found 6/6 markers.
[2024-01-24 14:03:16,151] [INFO] Query marker FASTA was written to GCF_000153205.1_ASM15320v1_genomic.fna/markers.fasta
[2024-01-24 14:03:16,152] [INFO] Task started: Blastn
[2024-01-24 14:03:16,152] [INFO] Running command: blastn -query GCF_000153205.1_ASM15320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51a45676-77f3-440e-b508-8166e87e1c8a/dqc_reference/reference_markers.fasta -out GCF_000153205.1_ASM15320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:16,854] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:16,859] [INFO] Selected 24 target genomes.
[2024-01-24 14:03:16,859] [INFO] Target genome list was writen to GCF_000153205.1_ASM15320v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:16,881] [INFO] Task started: fastANI
[2024-01-24 14:03:16,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg954ab479-4380-4d48-ae56-45911cdc303d/GCF_000153205.1_ASM15320v1_genomic.fna.gz --refList GCF_000153205.1_ASM15320v1_genomic.fna/target_genomes.txt --output GCF_000153205.1_ASM15320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:33,251] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:33,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51a45676-77f3-440e-b508-8166e87e1c8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:33,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51a45676-77f3-440e-b508-8166e87e1c8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:33,319] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:33,319] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:33,319] [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
Nitrococcus mobilis	strain=Nb-231	GCA_000153205.1	35797	35797	type	True	100.0	1204	1204	95	conclusive
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.4475	95	1204	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	76.3206	58	1204	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_007625165.1	531306	531306	type	True	76.1443	55	1204	95	below_threshold
Spiribacter vilamensis	strain=DSM 21056	GCA_004217415.1	531306	531306	type	True	75.8864	54	1204	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.5957	53	1204	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	75.3604	52	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:33,321] [INFO] DFAST Taxonomy check result was written to GCF_000153205.1_ASM15320v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:33,322] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:33,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:33,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51a45676-77f3-440e-b508-8166e87e1c8a/dqc_reference/checkm_data
[2024-01-24 14:03:33,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:33,383] [INFO] Task started: CheckM
[2024-01-24 14:03:33,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000153205.1_ASM15320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000153205.1_ASM15320v1_genomic.fna/checkm_input GCF_000153205.1_ASM15320v1_genomic.fna/checkm_result
[2024-01-24 14:04:09,233] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:09,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:09,258] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:09,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:09,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000153205.1_ASM15320v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:09,259] [INFO] Task started: Blastn
[2024-01-24 14:04:09,259] [INFO] Running command: blastn -query GCF_000153205.1_ASM15320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51a45676-77f3-440e-b508-8166e87e1c8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000153205.1_ASM15320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:10,445] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:10,449] [INFO] Selected 23 target genomes.
[2024-01-24 14:04:10,450] [INFO] Target genome list was writen to GCF_000153205.1_ASM15320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:10,471] [INFO] Task started: fastANI
[2024-01-24 14:04:10,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg954ab479-4380-4d48-ae56-45911cdc303d/GCF_000153205.1_ASM15320v1_genomic.fna.gz --refList GCF_000153205.1_ASM15320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000153205.1_ASM15320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:22,846] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:22,868] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:22,869] [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_000153205.1	s__Nitrococcus mobilis	100.0	1204	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Nitrococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003149435.1	s__E85 sp003149435	76.6958	106	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__E85	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374645.1	s__Arhodomonas aquaeolei	76.4475	95	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295635.1	s__S0819 sp009295635	76.3265	66	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018623495.1	s__JAAZVP01 sp018623495	76.0183	51	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217415.1	s__Spiribacter vilamensis	75.8864	54	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012523465.1	s__JAAYIK01 sp012523465	75.6322	50	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__JAAYIK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:22,871] [INFO] GTDB search result was written to GCF_000153205.1_ASM15320v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:22,871] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:22,874] [INFO] DFAST_QC result json was written to GCF_000153205.1_ASM15320v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:22,874] [INFO] DFAST_QC completed!
[2024-01-24 14:04:22,874] [INFO] Total running time: 0h1m20s