[2024-01-24 13:58:25,510] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg1849dc8c-9c55-4e19-99de-7943dfe7862f/dqc_reference
[2024-01-24 13:58:26,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,819] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg151d7bd3-75be-4b08-90df-9d0d296b90c9/GCF_004366815.1_ASM436681v1_genomic.fna.gz | prodigal -d GCF_004366815.1_ASM436681v1_genomic.fna/cds.fna -a GCF_004366815.1_ASM436681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:36,437] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:36,437] [INFO] Task started: HMMsearch
[2024-01-24 13:58:36,438] [INFO] Running command: hmmsearch --tblout GCF_004366815.1_ASM436681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1849dc8c-9c55-4e19-99de-7943dfe7862f/dqc_reference/reference_markers.hmm GCF_004366815.1_ASM436681v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:36,699] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:36,701] [INFO] Found 6/6 markers.
[2024-01-24 13:58:36,734] [INFO] Query marker FASTA was written to GCF_004366815.1_ASM436681v1_genomic.fna/markers.fasta
[2024-01-24 13:58:36,734] [INFO] Task started: Blastn
[2024-01-24 13:58:36,735] [INFO] Running command: blastn -query GCF_004366815.1_ASM436681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1849dc8c-9c55-4e19-99de-7943dfe7862f/dqc_reference/reference_markers.fasta -out GCF_004366815.1_ASM436681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:37,335] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:37,339] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:37,340] [INFO] Target genome list was writen to GCF_004366815.1_ASM436681v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:37,357] [INFO] Task started: fastANI
[2024-01-24 13:58:37,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg151d7bd3-75be-4b08-90df-9d0d296b90c9/GCF_004366815.1_ASM436681v1_genomic.fna.gz --refList GCF_004366815.1_ASM436681v1_genomic.fna/target_genomes.txt --output GCF_004366815.1_ASM436681v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:52,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:52,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1849dc8c-9c55-4e19-99de-7943dfe7862f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:52,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1849dc8c-9c55-4e19-99de-7943dfe7862f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:52,200] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:52,200] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:52,201] [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
Aminivibrio pyruvatiphilus	strain=DSM 25964	GCA_004366815.1	1005740	1005740	type	True	100.0	1081	1085	95	conclusive
Aminomonas paucivorans	strain=DSM 12260	GCA_000165795.1	81412	81412	type	True	76.9268	85	1085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:52,202] [INFO] DFAST Taxonomy check result was written to GCF_004366815.1_ASM436681v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:52,203] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:52,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:52,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1849dc8c-9c55-4e19-99de-7943dfe7862f/dqc_reference/checkm_data
[2024-01-24 13:58:52,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:52,245] [INFO] Task started: CheckM
[2024-01-24 13:58:52,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004366815.1_ASM436681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004366815.1_ASM436681v1_genomic.fna/checkm_input GCF_004366815.1_ASM436681v1_genomic.fna/checkm_result
[2024-01-24 13:59:23,628] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:23,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:23,654] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:23,655] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:23,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004366815.1_ASM436681v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:23,656] [INFO] Task started: Blastn
[2024-01-24 13:59:23,656] [INFO] Running command: blastn -query GCF_004366815.1_ASM436681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1849dc8c-9c55-4e19-99de-7943dfe7862f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004366815.1_ASM436681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:24,453] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:24,457] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:24,457] [INFO] Target genome list was writen to GCF_004366815.1_ASM436681v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:24,467] [INFO] Task started: fastANI
[2024-01-24 13:59:24,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg151d7bd3-75be-4b08-90df-9d0d296b90c9/GCF_004366815.1_ASM436681v1_genomic.fna.gz --refList GCF_004366815.1_ASM436681v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004366815.1_ASM436681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:29,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:29,974] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:29,974] [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_004366815.1	s__Aminivibrio pyruvatiphilus	100.0	1081	1085	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio	95.0	97.66	97.66	0.93	0.93	2	conclusive
GCA_018436595.1	s__Aminivibrio sp009929115	89.4313	884	1085	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio	95.0	98.41	98.25	0.85	0.80	3	-
GCA_016756745.1	s__Aminivibrio sp016756745	88.6999	767	1085	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057035.1	s__Aminivibrio sp018057035	86.5661	143	1085	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012523155.1	s__Aminivibrio sp012523155	80.2094	212	1085	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018436725.1	s__JAAYLU01 sp018436725	78.8737	343	1085	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__JAAYLU01	95.0	98.42	97.96	0.92	0.90	4	-
GCA_012519165.1	s__Aminivibrio sp012519165	77.9977	215	1085	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__Aminivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:29,976] [INFO] GTDB search result was written to GCF_004366815.1_ASM436681v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:29,977] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:29,980] [INFO] DFAST_QC result json was written to GCF_004366815.1_ASM436681v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:29,980] [INFO] DFAST_QC completed!
[2024-01-24 13:59:29,980] [INFO] Total running time: 0h1m4s