[2024-01-24 13:36:46,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:46,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:46,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg8556cc06-5323-4372-b166-702f89262e3a/dqc_reference
[2024-01-24 13:36:47,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:47,523] [INFO] Task started: Prodigal
[2024-01-24 13:36:47,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e6407d8-daeb-455e-a272-5caa948661e0/GCF_009695875.1_ASM969587v1_genomic.fna.gz | prodigal -d GCF_009695875.1_ASM969587v1_genomic.fna/cds.fna -a GCF_009695875.1_ASM969587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:55,054] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:55,055] [INFO] Task started: HMMsearch
[2024-01-24 13:36:55,055] [INFO] Running command: hmmsearch --tblout GCF_009695875.1_ASM969587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8556cc06-5323-4372-b166-702f89262e3a/dqc_reference/reference_markers.hmm GCF_009695875.1_ASM969587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:55,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:55,317] [INFO] Found 6/6 markers.
[2024-01-24 13:36:55,344] [INFO] Query marker FASTA was written to GCF_009695875.1_ASM969587v1_genomic.fna/markers.fasta
[2024-01-24 13:36:55,345] [INFO] Task started: Blastn
[2024-01-24 13:36:55,345] [INFO] Running command: blastn -query GCF_009695875.1_ASM969587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8556cc06-5323-4372-b166-702f89262e3a/dqc_reference/reference_markers.fasta -out GCF_009695875.1_ASM969587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:56,095] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:56,097] [INFO] Selected 9 target genomes.
[2024-01-24 13:36:56,098] [INFO] Target genome list was writen to GCF_009695875.1_ASM969587v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:56,112] [INFO] Task started: fastANI
[2024-01-24 13:36:56,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e6407d8-daeb-455e-a272-5caa948661e0/GCF_009695875.1_ASM969587v1_genomic.fna.gz --refList GCF_009695875.1_ASM969587v1_genomic.fna/target_genomes.txt --output GCF_009695875.1_ASM969587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:59,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:59,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8556cc06-5323-4372-b166-702f89262e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:59,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8556cc06-5323-4372-b166-702f89262e3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:59,922] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:36:59,922] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:36:59,922] [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
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	80.5422	304	779	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.3119	283	779	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.8403	237	779	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.7943	278	779	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.7639	279	779	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.5821	256	779	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.4603	263	779	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.421	241	779	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.6355	202	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:59,924] [INFO] DFAST Taxonomy check result was written to GCF_009695875.1_ASM969587v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:59,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:59,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:59,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8556cc06-5323-4372-b166-702f89262e3a/dqc_reference/checkm_data
[2024-01-24 13:36:59,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:59,957] [INFO] Task started: CheckM
[2024-01-24 13:36:59,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695875.1_ASM969587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695875.1_ASM969587v1_genomic.fna/checkm_input GCF_009695875.1_ASM969587v1_genomic.fna/checkm_result
[2024-01-24 13:37:28,077] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:28,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:28,095] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:28,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:28,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695875.1_ASM969587v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:28,096] [INFO] Task started: Blastn
[2024-01-24 13:37:28,097] [INFO] Running command: blastn -query GCF_009695875.1_ASM969587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8556cc06-5323-4372-b166-702f89262e3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695875.1_ASM969587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:29,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:29,252] [INFO] Selected 13 target genomes.
[2024-01-24 13:37:29,253] [INFO] Target genome list was writen to GCF_009695875.1_ASM969587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:29,268] [INFO] Task started: fastANI
[2024-01-24 13:37:29,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e6407d8-daeb-455e-a272-5caa948661e0/GCF_009695875.1_ASM969587v1_genomic.fna.gz --refList GCF_009695875.1_ASM969587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695875.1_ASM969587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:35,942] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:35,953] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:35,953] [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_009695875.1	s__Olsenella_H porci	100.0	779	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	97.87	97.72	0.91	0.87	6	conclusive
GCA_905214865.1	s__Olsenella_H sp905214865	92.4913	658	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	99.90	99.90	0.96	0.96	2	-
GCF_012844235.1	s__Parafannyhessea sp900538935	81.1372	331	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	96.97	96.59	0.88	0.86	4	-
GCF_900105025.1	s__Parafannyhessea umbonata	80.9762	340	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	-
GCA_003862195.1	s__Parafannyhessea sp003862195	80.5592	335	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCF_900120385.1	s__Olsenella_I phocaeensis	80.5546	303	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_I	95.0	97.88	97.64	0.87	0.85	3	-
GCA_900314575.1	s__UBA7741 sp900314575	80.0684	273	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
GCF_016899935.1	s__Thermophilibacter uli_B	79.9459	244	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900775.1	s__Thermophilibacter uli_A	79.653	254	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000468755.1	s__Olsenella_F profusa_A	79.368	262	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779675.1	s__UBA1367 sp902779675	79.0331	236	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.95	97.30	0.86	0.82	4	-
GCA_017941585.1	s__Parafannyhessea sp017941585	78.8625	193	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795065.1	s__RUG721 sp900321745	78.6604	193	779	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	99.01	98.55	0.89	0.82	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:35,955] [INFO] GTDB search result was written to GCF_009695875.1_ASM969587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:35,955] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:35,959] [INFO] DFAST_QC result json was written to GCF_009695875.1_ASM969587v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:35,959] [INFO] DFAST_QC completed!
[2024-01-24 13:37:35,959] [INFO] Total running time: 0h0m50s