[2024-01-25 20:12:05,880] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,882] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,882] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d5fc450-c477-457b-84b7-3e04c6107e9a/dqc_reference
[2024-01-25 20:12:07,153] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:07,154] [INFO] Task started: Prodigal
[2024-01-25 20:12:07,154] [INFO] Running command: gunzip -c /var/lib/cwl/stg684c766e-0c85-4f9b-9b7c-6f13dfca74ad/GCF_030811115.1_ASM3081111v1_genomic.fna.gz | prodigal -d GCF_030811115.1_ASM3081111v1_genomic.fna/cds.fna -a GCF_030811115.1_ASM3081111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:15,079] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:15,080] [INFO] Task started: HMMsearch
[2024-01-25 20:12:15,080] [INFO] Running command: hmmsearch --tblout GCF_030811115.1_ASM3081111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d5fc450-c477-457b-84b7-3e04c6107e9a/dqc_reference/reference_markers.hmm GCF_030811115.1_ASM3081111v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:15,253] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:15,254] [INFO] Found 6/6 markers.
[2024-01-25 20:12:15,276] [INFO] Query marker FASTA was written to GCF_030811115.1_ASM3081111v1_genomic.fna/markers.fasta
[2024-01-25 20:12:15,277] [INFO] Task started: Blastn
[2024-01-25 20:12:15,277] [INFO] Running command: blastn -query GCF_030811115.1_ASM3081111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5fc450-c477-457b-84b7-3e04c6107e9a/dqc_reference/reference_markers.fasta -out GCF_030811115.1_ASM3081111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:15,915] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:15,917] [INFO] Selected 9 target genomes.
[2024-01-25 20:12:15,917] [INFO] Target genome list was writen to GCF_030811115.1_ASM3081111v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:15,948] [INFO] Task started: fastANI
[2024-01-25 20:12:15,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg684c766e-0c85-4f9b-9b7c-6f13dfca74ad/GCF_030811115.1_ASM3081111v1_genomic.fna.gz --refList GCF_030811115.1_ASM3081111v1_genomic.fna/target_genomes.txt --output GCF_030811115.1_ASM3081111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:19,619] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:19,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d5fc450-c477-457b-84b7-3e04c6107e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:19,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d5fc450-c477-457b-84b7-3e04c6107e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:19,626] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:12:19,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:12:19,626] [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	80.2399	297	872	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	80.1297	280	872	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	80.1258	285	872	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	80.0193	285	872	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.5419	245	872	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	79.3309	266	872	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.1997	239	872	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.9192	251	872	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.7966	188	872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:19,627] [INFO] DFAST Taxonomy check result was written to GCF_030811115.1_ASM3081111v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:19,628] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:19,628] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:19,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d5fc450-c477-457b-84b7-3e04c6107e9a/dqc_reference/checkm_data
[2024-01-25 20:12:19,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:19,655] [INFO] Task started: CheckM
[2024-01-25 20:12:19,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030811115.1_ASM3081111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030811115.1_ASM3081111v1_genomic.fna/checkm_input GCF_030811115.1_ASM3081111v1_genomic.fna/checkm_result
[2024-01-25 20:12:46,690] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:46,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:46,706] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:46,706] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:46,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030811115.1_ASM3081111v1_genomic.fna/markers.fasta)
[2024-01-25 20:12:46,707] [INFO] Task started: Blastn
[2024-01-25 20:12:46,707] [INFO] Running command: blastn -query GCF_030811115.1_ASM3081111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5fc450-c477-457b-84b7-3e04c6107e9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030811115.1_ASM3081111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:47,799] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:47,802] [INFO] Selected 18 target genomes.
[2024-01-25 20:12:47,802] [INFO] Target genome list was writen to GCF_030811115.1_ASM3081111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:47,860] [INFO] Task started: fastANI
[2024-01-25 20:12:47,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg684c766e-0c85-4f9b-9b7c-6f13dfca74ad/GCF_030811115.1_ASM3081111v1_genomic.fna.gz --refList GCF_030811115.1_ASM3081111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030811115.1_ASM3081111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:56,214] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:56,225] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:56,225] [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_000468755.1	s__Olsenella_F profusa_A	98.6544	761	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000143845.1	s__Olsenella uli	80.2206	298	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	-
GCF_001457795.1	s__Olsenella_F massiliensis	80.1297	280	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	98.66	97.33	0.97	0.93	3	-
GCF_900120385.1	s__Olsenella_I phocaeensis	79.9976	287	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_I	95.0	97.88	97.64	0.87	0.85	3	-
GCF_012844235.1	s__Parafannyhessea sp900538935	79.5463	259	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	96.97	96.59	0.88	0.86	4	-
GCF_900155635.1	s__Olsenella_G urininfantis	79.5419	245	872	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_003862195.1	s__Parafannyhessea sp003862195	79.4895	280	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCF_009695875.1	s__Olsenella_H porci	79.3491	263	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	97.87	97.72	0.91	0.87	6	-
GCA_015062715.1	s__SIG37 sp015062715	79.3136	171	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__SIG37	95.0	96.94	96.94	0.73	0.73	2	-
GCF_900105025.1	s__Parafannyhessea umbonata	79.2974	268	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	-
GCA_902791035.1	s__CADAUA01 sp900315375	79.2199	266	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__CADAUA01	95.0	99.88	99.88	0.96	0.96	2	-
GCF_900128445.1	s__Thermophilibacter provencensis	79.1997	239	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	96.98	96.17	0.87	0.80	3	-
GCA_019116265.1	s__Thermophilibacter stercoravium	78.9126	197	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189515.2	s__Olsenella_F sp001189515	78.8511	264	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	97.18	97.18	0.92	0.92	2	-
GCA_900316105.1	s__Olsenella_F sp900316105	78.8281	222	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_F	95.0	99.68	99.68	0.95	0.93	3	-
GCA_902788705.1	s__UBA1367 sp902788705	78.7032	228	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.66	97.66	0.87	0.87	2	-
GCA_900314685.1	s__Olegusella sp900314685	78.5558	218	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olegusella	95.0	99.04	98.52	0.90	0.85	10	-
GCA_902772085.1	s__RUG440 sp902772085	77.0392	79	872	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	96.17	96.17	0.67	0.67	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:56,227] [INFO] GTDB search result was written to GCF_030811115.1_ASM3081111v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:56,227] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:56,230] [INFO] DFAST_QC result json was written to GCF_030811115.1_ASM3081111v1_genomic.fna/dqc_result.json
[2024-01-25 20:12:56,230] [INFO] DFAST_QC completed!
[2024-01-25 20:12:56,230] [INFO] Total running time: 0h0m50s