[2024-01-24 12:13:37,497] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:37,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:37,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgb761534b-148e-40ae-a345-45c704a872ae/dqc_reference
[2024-01-24 12:13:38,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:38,747] [INFO] Task started: Prodigal
[2024-01-24 12:13:38,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f1f532b-1fa6-4cef-bc98-55f1246acec2/GCF_009695745.1_ASM969574v1_genomic.fna.gz | prodigal -d GCF_009695745.1_ASM969574v1_genomic.fna/cds.fna -a GCF_009695745.1_ASM969574v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:45,512] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:45,512] [INFO] Task started: HMMsearch
[2024-01-24 12:13:45,513] [INFO] Running command: hmmsearch --tblout GCF_009695745.1_ASM969574v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb761534b-148e-40ae-a345-45c704a872ae/dqc_reference/reference_markers.hmm GCF_009695745.1_ASM969574v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:45,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:45,763] [INFO] Found 6/6 markers.
[2024-01-24 12:13:45,785] [INFO] Query marker FASTA was written to GCF_009695745.1_ASM969574v1_genomic.fna/markers.fasta
[2024-01-24 12:13:45,785] [INFO] Task started: Blastn
[2024-01-24 12:13:45,785] [INFO] Running command: blastn -query GCF_009695745.1_ASM969574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb761534b-148e-40ae-a345-45c704a872ae/dqc_reference/reference_markers.fasta -out GCF_009695745.1_ASM969574v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:46,432] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:46,436] [INFO] Selected 12 target genomes.
[2024-01-24 12:13:46,436] [INFO] Target genome list was writen to GCF_009695745.1_ASM969574v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:46,484] [INFO] Task started: fastANI
[2024-01-24 12:13:46,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1f532b-1fa6-4cef-bc98-55f1246acec2/GCF_009695745.1_ASM969574v1_genomic.fna.gz --refList GCF_009695745.1_ASM969574v1_genomic.fna/target_genomes.txt --output GCF_009695745.1_ASM969574v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:53,102] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:53,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb761534b-148e-40ae-a345-45c704a872ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:53,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb761534b-148e-40ae-a345-45c704a872ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:53,109] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:53,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:53,109] [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
Pyramidobacter porci	strain=SM-530-WT-4B	GCA_009695745.1	2605789	2605789	type	True	100.0	833	833	95	conclusive
Pyramidobacter piscolens	strain=W5455	GCA_000177335.1	638849	638849	type	True	92.3939	659	833	95	below_threshold
Jonquetella anthropi	strain=DSM 22815	GCA_000237805.1	428712	428712	type	True	76.7615	61	833	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	74.8476	84	833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:53,111] [INFO] DFAST Taxonomy check result was written to GCF_009695745.1_ASM969574v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:53,111] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:53,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:53,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb761534b-148e-40ae-a345-45c704a872ae/dqc_reference/checkm_data
[2024-01-24 12:13:53,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:53,145] [INFO] Task started: CheckM
[2024-01-24 12:13:53,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695745.1_ASM969574v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695745.1_ASM969574v1_genomic.fna/checkm_input GCF_009695745.1_ASM969574v1_genomic.fna/checkm_result
[2024-01-24 12:14:19,014] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:19,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:19,038] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:19,039] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:19,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695745.1_ASM969574v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:19,039] [INFO] Task started: Blastn
[2024-01-24 12:14:19,040] [INFO] Running command: blastn -query GCF_009695745.1_ASM969574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb761534b-148e-40ae-a345-45c704a872ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695745.1_ASM969574v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:20,134] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:20,138] [INFO] Selected 8 target genomes.
[2024-01-24 12:14:20,138] [INFO] Target genome list was writen to GCF_009695745.1_ASM969574v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:20,217] [INFO] Task started: fastANI
[2024-01-24 12:14:20,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1f532b-1fa6-4cef-bc98-55f1246acec2/GCF_009695745.1_ASM969574v1_genomic.fna.gz --refList GCF_009695745.1_ASM969574v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695745.1_ASM969574v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:25,237] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:25,243] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:25,244] [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_009695745.1	s__Pyramidobacter porci	100.0	833	833	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002007215.1	s__Pyramidobacter sp002007215	92.9892	678	833	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	97.07	95.83	0.85	0.81	3	-
GCF_000177335.1	s__Pyramidobacter piscolens	92.4177	658	833	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	98.74	98.74	0.86	0.86	2	-
GCA_017940445.1	s__Pyramidobacter sp017940445	79.6243	228	833	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	96.84	96.36	0.70	0.63	5	-
GCA_016286835.1	s__Pyramidobacter sp016286835	79.5515	259	833	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Pyramidobacter	95.0	97.54	97.39	0.80	0.78	3	-
GCF_000237805.1	s__Jonquetella anthropi	76.7602	61	833	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Dethiosulfovibrionaceae;g__Jonquetella	95.0	99.63	99.55	0.98	0.97	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:25,245] [INFO] GTDB search result was written to GCF_009695745.1_ASM969574v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:25,246] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:25,250] [INFO] DFAST_QC result json was written to GCF_009695745.1_ASM969574v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:25,251] [INFO] DFAST_QC completed!
[2024-01-24 12:14:25,251] [INFO] Total running time: 0h0m48s