[2024-01-25 17:40:51,016] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:51,017] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:51,018] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a8a69be-13c2-4ff5-9df8-97e4c5b410b9/dqc_reference
[2024-01-25 17:40:52,189] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:52,190] [INFO] Task started: Prodigal
[2024-01-25 17:40:52,190] [INFO] Running command: gunzip -c /var/lib/cwl/stga5820458-0f5a-41a2-8c21-2e9bf562a237/GCF_000143845.1_ASM14384v1_genomic.fna.gz | prodigal -d GCF_000143845.1_ASM14384v1_genomic.fna/cds.fna -a GCF_000143845.1_ASM14384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:57,958] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:57,958] [INFO] Task started: HMMsearch
[2024-01-25 17:40:57,958] [INFO] Running command: hmmsearch --tblout GCF_000143845.1_ASM14384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a8a69be-13c2-4ff5-9df8-97e4c5b410b9/dqc_reference/reference_markers.hmm GCF_000143845.1_ASM14384v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:58,119] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:58,120] [INFO] Found 6/6 markers.
[2024-01-25 17:40:58,139] [INFO] Query marker FASTA was written to GCF_000143845.1_ASM14384v1_genomic.fna/markers.fasta
[2024-01-25 17:40:58,139] [INFO] Task started: Blastn
[2024-01-25 17:40:58,139] [INFO] Running command: blastn -query GCF_000143845.1_ASM14384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a8a69be-13c2-4ff5-9df8-97e4c5b410b9/dqc_reference/reference_markers.fasta -out GCF_000143845.1_ASM14384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:58,786] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:58,789] [INFO] Selected 9 target genomes.
[2024-01-25 17:40:58,789] [INFO] Target genome list was writen to GCF_000143845.1_ASM14384v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:58,793] [INFO] Task started: fastANI
[2024-01-25 17:40:58,794] [INFO] Running command: fastANI --query /var/lib/cwl/stga5820458-0f5a-41a2-8c21-2e9bf562a237/GCF_000143845.1_ASM14384v1_genomic.fna.gz --refList GCF_000143845.1_ASM14384v1_genomic.fna/target_genomes.txt --output GCF_000143845.1_ASM14384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:03,124] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:03,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a8a69be-13c2-4ff5-9df8-97e4c5b410b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:03,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a8a69be-13c2-4ff5-9df8-97e4c5b410b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:03,132] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:41:03,132] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:03,132] [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 uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	100.0	683	683	95	conclusive
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	99.984	676	683	95	conclusive
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	80.775	311	683	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.5593	307	683	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	80.1879	272	683	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.6316	247	683	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.537	255	683	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.9523	176	683	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	78.665	182	683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:03,134] [INFO] DFAST Taxonomy check result was written to GCF_000143845.1_ASM14384v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:03,134] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:03,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:03,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a8a69be-13c2-4ff5-9df8-97e4c5b410b9/dqc_reference/checkm_data
[2024-01-25 17:41:03,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:03,159] [INFO] Task started: CheckM
[2024-01-25 17:41:03,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000143845.1_ASM14384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000143845.1_ASM14384v1_genomic.fna/checkm_input GCF_000143845.1_ASM14384v1_genomic.fna/checkm_result
[2024-01-25 17:41:24,463] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:24,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:24,479] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:24,479] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:24,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000143845.1_ASM14384v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:24,480] [INFO] Task started: Blastn
[2024-01-25 17:41:24,480] [INFO] Running command: blastn -query GCF_000143845.1_ASM14384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a8a69be-13c2-4ff5-9df8-97e4c5b410b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000143845.1_ASM14384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:25,670] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:25,673] [INFO] Selected 16 target genomes.
[2024-01-25 17:41:25,674] [INFO] Target genome list was writen to GCF_000143845.1_ASM14384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:25,700] [INFO] Task started: fastANI
[2024-01-25 17:41:25,701] [INFO] Running command: fastANI --query /var/lib/cwl/stga5820458-0f5a-41a2-8c21-2e9bf562a237/GCF_000143845.1_ASM14384v1_genomic.fna.gz --refList GCF_000143845.1_ASM14384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000143845.1_ASM14384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:32,949] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:32,961] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:32,961] [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_000143845.1	s__Olsenella uli	100.0	683	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	conclusive
GCA_902780325.1	s__Parafannyhessea sp902787335	80.9526	234	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCF_900120385.1	s__Olsenella_I phocaeensis	80.7875	310	683	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_003862195.1	s__Parafannyhessea sp003862195	80.242	294	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCF_900155635.1	s__Olsenella_G urininfantis	80.1876	272	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214865.1	s__Olsenella_H sp905214865	80.0251	298	683	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	79.8951	306	683	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	79.8452	289	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	-
GCF_014982725.1	s__Thermophilibacter sp014982725	79.7626	249	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899935.1	s__Thermophilibacter uli_B	79.6551	245	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695875.1	s__Olsenella_H porci	79.6411	298	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	97.87	97.72	0.91	0.87	6	-
GCF_002159495.1	s__Thermophilibacter sp002159495	79.6068	257	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017941585.1	s__Parafannyhessea sp017941585	79.5787	206	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	79.537	255	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116265.1	s__Thermophilibacter stercoravium	79.3694	203	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795065.1	s__RUG721 sp900321745	78.7706	201	683	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	99.01	98.55	0.89	0.82	11	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:32,963] [INFO] GTDB search result was written to GCF_000143845.1_ASM14384v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:32,963] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:32,967] [INFO] DFAST_QC result json was written to GCF_000143845.1_ASM14384v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:32,967] [INFO] DFAST_QC completed!
[2024-01-25 17:41:32,967] [INFO] Total running time: 0h0m42s