[2024-01-24 11:51:24,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,220] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,220] [INFO] DQC Reference Directory: /var/lib/cwl/stge870af16-8356-4450-8636-c988bde76f2a/dqc_reference
[2024-01-24 11:51:25,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,615] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,615] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5c5f47f-9d83-44ce-9905-90a278e05191/GCF_007990505.1_ASM799050v1_genomic.fna.gz | prodigal -d GCF_007990505.1_ASM799050v1_genomic.fna/cds.fna -a GCF_007990505.1_ASM799050v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:29,994] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:29,995] [INFO] Task started: HMMsearch
[2024-01-24 11:51:29,995] [INFO] Running command: hmmsearch --tblout GCF_007990505.1_ASM799050v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge870af16-8356-4450-8636-c988bde76f2a/dqc_reference/reference_markers.hmm GCF_007990505.1_ASM799050v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:30,217] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:30,218] [INFO] Found 6/6 markers.
[2024-01-24 11:51:30,245] [INFO] Query marker FASTA was written to GCF_007990505.1_ASM799050v1_genomic.fna/markers.fasta
[2024-01-24 11:51:30,245] [INFO] Task started: Blastn
[2024-01-24 11:51:30,245] [INFO] Running command: blastn -query GCF_007990505.1_ASM799050v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge870af16-8356-4450-8636-c988bde76f2a/dqc_reference/reference_markers.fasta -out GCF_007990505.1_ASM799050v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:30,827] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:30,831] [INFO] Selected 13 target genomes.
[2024-01-24 11:51:30,832] [INFO] Target genome list was writen to GCF_007990505.1_ASM799050v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:30,859] [INFO] Task started: fastANI
[2024-01-24 11:51:30,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5c5f47f-9d83-44ce-9905-90a278e05191/GCF_007990505.1_ASM799050v1_genomic.fna.gz --refList GCF_007990505.1_ASM799050v1_genomic.fna/target_genomes.txt --output GCF_007990505.1_ASM799050v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:38,474] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:38,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge870af16-8356-4450-8636-c988bde76f2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:38,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge870af16-8356-4450-8636-c988bde76f2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:38,483] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:38,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:38,484] [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
Pseudoleptotrichia goodfellowii	strain=JCM16774	GCA_007990505.1	157692	157692	type	True	100.0	762	763	95	conclusive
Pseudoleptotrichia goodfellowii	strain=DSM 19756	GCA_000516535.1	157692	157692	type	True	99.9894	756	763	95	conclusive
Leptotrichia wadei	strain=JCM16777	GCA_007990545.2	157687	157687	type	True	77.4019	148	763	95	below_threshold
Leptotrichia massiliensis	strain=Marseille-P3007	GCA_900104625.1	1852388	1852388	type	True	77.2928	159	763	95	below_threshold
Leptotrichia trevisanii	strain=DSM 22070	GCA_000482505.1	109328	109328	type	True	77.2079	166	763	95	below_threshold
Sebaldella termitidis	strain=NCTC11300	GCA_900456835.1	826	826	type	True	76.9271	122	763	95	below_threshold
Leptotrichia wadei	strain=DSM 19758	GCA_000373345.1	157687	157687	type	True	76.9254	144	763	95	below_threshold
Leptotrichia shahii	strain=DSM 19757	GCA_000373045.1	157691	157691	type	True	76.864	143	763	95	below_threshold
Sebaldella termitidis	strain=ATCC 33386	GCA_000024405.1	826	826	type	True	76.8633	119	763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:38,485] [INFO] DFAST Taxonomy check result was written to GCF_007990505.1_ASM799050v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:38,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:38,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:38,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge870af16-8356-4450-8636-c988bde76f2a/dqc_reference/checkm_data
[2024-01-24 11:51:38,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:38,514] [INFO] Task started: CheckM
[2024-01-24 11:51:38,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990505.1_ASM799050v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990505.1_ASM799050v1_genomic.fna/checkm_input GCF_007990505.1_ASM799050v1_genomic.fna/checkm_result
[2024-01-24 11:52:00,099] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:00,100] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:00,122] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:00,122] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:00,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990505.1_ASM799050v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:00,123] [INFO] Task started: Blastn
[2024-01-24 11:52:00,124] [INFO] Running command: blastn -query GCF_007990505.1_ASM799050v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge870af16-8356-4450-8636-c988bde76f2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990505.1_ASM799050v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:00,923] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:00,928] [INFO] Selected 16 target genomes.
[2024-01-24 11:52:00,928] [INFO] Target genome list was writen to GCF_007990505.1_ASM799050v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:00,943] [INFO] Task started: fastANI
[2024-01-24 11:52:00,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5c5f47f-9d83-44ce-9905-90a278e05191/GCF_007990505.1_ASM799050v1_genomic.fna.gz --refList GCF_007990505.1_ASM799050v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990505.1_ASM799050v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:08,799] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:08,814] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:08,814] [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_007990505.1	s__Pseudoleptotrichia goodfellowii	100.0	762	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Pseudoleptotrichia	95.0	98.75	97.51	0.96	0.93	3	conclusive
GCF_003932895.1	s__Pseudoleptotrichia sp003932895	79.7791	424	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Pseudoleptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000469505.1	s__Leptotrichia_A sp000469505	78.8058	264	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274535.1	s__Leptotrichia_A sp001274535	78.5239	311	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia_A	95.0	97.10	97.10	0.94	0.94	2	-
GCA_905371725.1	s__Leptotrichia_A sp905371725	78.1913	161	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018128225.1	s__Leptotrichia sp018128225	77.4118	136	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104625.1	s__Leptotrichia massiliensis	77.3414	159	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	96.80	96.21	0.92	0.89	3	-
GCA_018060185.1	s__JAGOWQ01 sp018060185	77.2263	168	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__JAGOWQ01	95.0	99.67	99.60	0.85	0.80	4	-
GCF_007990445.1	s__Leptotrichia wadei_A	77.2177	179	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	97.03	96.85	0.85	0.83	4	-
GCF_000482505.1	s__Leptotrichia trevisanii	77.2043	167	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Leptotrichia	95.0	97.98	97.58	0.90	0.88	4	-
GCF_000024405.1	s__Sebaldella termitidis	77.0221	123	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__Sebaldella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018059165.1	s__JAGOYM01 sp018059165	76.5904	65	763	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Leptotrichiaceae;g__JAGOYM01	95.0	99.63	99.53	0.85	0.81	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:08,816] [INFO] GTDB search result was written to GCF_007990505.1_ASM799050v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:08,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:08,819] [INFO] DFAST_QC result json was written to GCF_007990505.1_ASM799050v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:08,820] [INFO] DFAST_QC completed!
[2024-01-24 11:52:08,820] [INFO] Total running time: 0h0m45s