[2024-01-24 14:54:54,860] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:54,862] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:54,862] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1465dd9-734f-499c-9957-567d1a9fed36/dqc_reference
[2024-01-24 14:54:56,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:56,204] [INFO] Task started: Prodigal
[2024-01-24 14:54:56,205] [INFO] Running command: gunzip -c /var/lib/cwl/stg4009e33c-fb8f-4276-a272-f33335242647/GCF_030296935.1_ASM3029693v1_genomic.fna.gz | prodigal -d GCF_030296935.1_ASM3029693v1_genomic.fna/cds.fna -a GCF_030296935.1_ASM3029693v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:10,523] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:10,523] [INFO] Task started: HMMsearch
[2024-01-24 14:55:10,523] [INFO] Running command: hmmsearch --tblout GCF_030296935.1_ASM3029693v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1465dd9-734f-499c-9957-567d1a9fed36/dqc_reference/reference_markers.hmm GCF_030296935.1_ASM3029693v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:10,824] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:10,825] [INFO] Found 6/6 markers.
[2024-01-24 14:55:10,857] [INFO] Query marker FASTA was written to GCF_030296935.1_ASM3029693v1_genomic.fna/markers.fasta
[2024-01-24 14:55:10,857] [INFO] Task started: Blastn
[2024-01-24 14:55:10,857] [INFO] Running command: blastn -query GCF_030296935.1_ASM3029693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1465dd9-734f-499c-9957-567d1a9fed36/dqc_reference/reference_markers.fasta -out GCF_030296935.1_ASM3029693v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:11,475] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:11,478] [INFO] Selected 21 target genomes.
[2024-01-24 14:55:11,479] [INFO] Target genome list was writen to GCF_030296935.1_ASM3029693v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:11,487] [INFO] Task started: fastANI
[2024-01-24 14:55:11,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg4009e33c-fb8f-4276-a272-f33335242647/GCF_030296935.1_ASM3029693v1_genomic.fna.gz --refList GCF_030296935.1_ASM3029693v1_genomic.fna/target_genomes.txt --output GCF_030296935.1_ASM3029693v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:27,018] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:27,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1465dd9-734f-499c-9957-567d1a9fed36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:27,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1465dd9-734f-499c-9957-567d1a9fed36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:27,029] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:55:27,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:27,029] [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
Coprobacter fastidiosus	strain=NSB1	GCA_003634345.1	1099853	1099853	type	True	99.9824	1127	1148	95	conclusive
Coprobacter fastidiosus	strain=NSB1	GCA_000473955.1	1099853	1099853	type	True	99.9628	1109	1148	95	conclusive
Coprobacter secundus subsp. similis	strain=2CBH44	GCA_015097275.1	2751153	1501392	type	True	78.713	161	1148	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	78.6803	54	1148	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	77.6729	58	1148	95	below_threshold
Barnesiella intestinihominis	strain=YIT 11860	GCA_000296465.1	487174	487174	type	True	77.6569	82	1148	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	77.6217	63	1148	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	77.5638	59	1148	95	below_threshold
Parabacteroides pacaensis	strain=Marseille-P4001	GCA_900292045.1	2086575	2086575	type	True	77.2755	55	1148	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	76.909	50	1148	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	76.909	50	1148	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:27,031] [INFO] DFAST Taxonomy check result was written to GCF_030296935.1_ASM3029693v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:27,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:27,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:27,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1465dd9-734f-499c-9957-567d1a9fed36/dqc_reference/checkm_data
[2024-01-24 14:55:27,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:27,068] [INFO] Task started: CheckM
[2024-01-24 14:55:27,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296935.1_ASM3029693v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296935.1_ASM3029693v1_genomic.fna/checkm_input GCF_030296935.1_ASM3029693v1_genomic.fna/checkm_result
[2024-01-24 14:56:11,223] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:11,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:11,244] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:11,244] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:11,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296935.1_ASM3029693v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:11,245] [INFO] Task started: Blastn
[2024-01-24 14:56:11,246] [INFO] Running command: blastn -query GCF_030296935.1_ASM3029693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1465dd9-734f-499c-9957-567d1a9fed36/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296935.1_ASM3029693v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:12,083] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:12,087] [INFO] Selected 19 target genomes.
[2024-01-24 14:56:12,088] [INFO] Target genome list was writen to GCF_030296935.1_ASM3029693v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:12,102] [INFO] Task started: fastANI
[2024-01-24 14:56:12,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg4009e33c-fb8f-4276-a272-f33335242647/GCF_030296935.1_ASM3029693v1_genomic.fna.gz --refList GCF_030296935.1_ASM3029693v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296935.1_ASM3029693v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:23,978] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:23,990] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:23,991] [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_003634345.1	s__Coprobacter fastidiosus	99.9824	1127	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	98.46	97.98	0.89	0.59	13	conclusive
GCA_900545915.1	s__Coprobacter sp900545915	93.4547	941	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.49	96.20	0.84	0.83	3	-
GCA_000803105.1	s__Coprobacter secundus	77.9109	158	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.96	96.86	0.90	0.85	6	-
GCF_000296465.1	s__Barnesiella intestinihominis	77.6562	80	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	98.49	98.18	0.93	0.86	27	-
GCA_019114445.1	s__Barnesiella excrementigallinarum	77.5338	76	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__Barnesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434215.1	s__UBA11471 sp000434215	77.1023	64	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	99.32	98.64	0.92	0.84	6	-
GCA_017467745.1	s__Gallibacteroides sp017467745	76.8966	62	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__CHK158-818;g__Gallibacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015550595.1	s__Parabacteroides sp900540715	76.3747	53	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:23,998] [INFO] GTDB search result was written to GCF_030296935.1_ASM3029693v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:23,999] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:24,003] [INFO] DFAST_QC result json was written to GCF_030296935.1_ASM3029693v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:24,003] [INFO] DFAST_QC completed!
[2024-01-24 14:56:24,003] [INFO] Total running time: 0h1m29s