[2023-06-27 02:56:25,789] [INFO] DFAST_QC pipeline started.
[2023-06-27 02:56:25,791] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 02:56:25,791] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe823dad-866a-4532-b4bc-b1fbeacf507e/dqc_reference
[2023-06-27 02:56:27,020] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 02:56:27,021] [INFO] Task started: Prodigal
[2023-06-27 02:56:27,022] [INFO] Running command: gunzip -c /var/lib/cwl/stge400bbd4-59f7-49f2-9b3f-591a8ef46b79/GCA_002394825.1_ASM239482v1_genomic.fna.gz | prodigal -d GCA_002394825.1_ASM239482v1_genomic.fna/cds.fna -a GCA_002394825.1_ASM239482v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 02:56:33,330] [INFO] Task succeeded: Prodigal
[2023-06-27 02:56:33,331] [INFO] Task started: HMMsearch
[2023-06-27 02:56:33,331] [INFO] Running command: hmmsearch --tblout GCA_002394825.1_ASM239482v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe823dad-866a-4532-b4bc-b1fbeacf507e/dqc_reference/reference_markers.hmm GCA_002394825.1_ASM239482v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 02:56:33,563] [INFO] Task succeeded: HMMsearch
[2023-06-27 02:56:33,565] [INFO] Found 6/6 markers.
[2023-06-27 02:56:33,591] [INFO] Query marker FASTA was written to GCA_002394825.1_ASM239482v1_genomic.fna/markers.fasta
[2023-06-27 02:56:33,592] [INFO] Task started: Blastn
[2023-06-27 02:56:33,592] [INFO] Running command: blastn -query GCA_002394825.1_ASM239482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe823dad-866a-4532-b4bc-b1fbeacf507e/dqc_reference/reference_markers.fasta -out GCA_002394825.1_ASM239482v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:56:34,328] [INFO] Task succeeded: Blastn
[2023-06-27 02:56:34,333] [INFO] Selected 12 target genomes.
[2023-06-27 02:56:34,334] [INFO] Target genome list was writen to GCA_002394825.1_ASM239482v1_genomic.fna/target_genomes.txt
[2023-06-27 02:56:34,339] [INFO] Task started: fastANI
[2023-06-27 02:56:34,340] [INFO] Running command: fastANI --query /var/lib/cwl/stge400bbd4-59f7-49f2-9b3f-591a8ef46b79/GCA_002394825.1_ASM239482v1_genomic.fna.gz --refList GCA_002394825.1_ASM239482v1_genomic.fna/target_genomes.txt --output GCA_002394825.1_ASM239482v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 02:56:43,077] [INFO] Task succeeded: fastANI
[2023-06-27 02:56:43,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe823dad-866a-4532-b4bc-b1fbeacf507e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 02:56:43,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe823dad-866a-4532-b4bc-b1fbeacf507e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 02:56:43,094] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 02:56:43,095] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 02:56:43,095] [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 intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.723	313	654	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	80.137	264	654	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.8572	267	654	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.8093	214	654	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.7683	262	654	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.4636	249	654	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.2991	231	654	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	74.7868	69	654	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	74.7473	64	654	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	74.7442	65	654	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 02:56:43,130] [INFO] DFAST Taxonomy check result was written to GCA_002394825.1_ASM239482v1_genomic.fna/tc_result.tsv
[2023-06-27 02:56:43,131] [INFO] ===== Taxonomy check completed =====
[2023-06-27 02:56:43,131] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 02:56:43,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe823dad-866a-4532-b4bc-b1fbeacf507e/dqc_reference/checkm_data
[2023-06-27 02:56:43,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 02:56:43,321] [INFO] Task started: CheckM
[2023-06-27 02:56:43,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002394825.1_ASM239482v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002394825.1_ASM239482v1_genomic.fna/checkm_input GCA_002394825.1_ASM239482v1_genomic.fna/checkm_result
[2023-06-27 02:57:06,810] [INFO] Task succeeded: CheckM
[2023-06-27 02:57:06,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 02:57:06,860] [INFO] ===== Completeness check finished =====
[2023-06-27 02:57:06,861] [INFO] ===== Start GTDB Search =====
[2023-06-27 02:57:06,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002394825.1_ASM239482v1_genomic.fna/markers.fasta)
[2023-06-27 02:57:06,862] [INFO] Task started: Blastn
[2023-06-27 02:57:06,862] [INFO] Running command: blastn -query GCA_002394825.1_ASM239482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe823dad-866a-4532-b4bc-b1fbeacf507e/dqc_reference/reference_markers_gtdb.fasta -out GCA_002394825.1_ASM239482v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:57:07,956] [INFO] Task succeeded: Blastn
[2023-06-27 02:57:07,961] [INFO] Selected 12 target genomes.
[2023-06-27 02:57:07,961] [INFO] Target genome list was writen to GCA_002394825.1_ASM239482v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 02:57:07,975] [INFO] Task started: fastANI
[2023-06-27 02:57:07,976] [INFO] Running command: fastANI --query /var/lib/cwl/stge400bbd4-59f7-49f2-9b3f-591a8ef46b79/GCA_002394825.1_ASM239482v1_genomic.fna.gz --refList GCA_002394825.1_ASM239482v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002394825.1_ASM239482v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 02:57:13,871] [INFO] Task succeeded: fastANI
[2023-06-27 02:57:13,889] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 02:57:13,890] [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_900105025.1	s__Parafannyhessea umbonata	95.9362	595	654	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	conclusive
GCF_012844235.1	s__Parafannyhessea sp900538935	93.3579	594	654	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	96.97	96.59	0.88	0.86	4	-
GCA_003862195.1	s__Parafannyhessea sp003862195	85.4904	481	654	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCA_902780325.1	s__Parafannyhessea sp902787335	80.9827	246	654	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCA_905214865.1	s__Olsenella_H sp905214865	80.374	304	654	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_900111255.1	s__Parafannyhessea umbonata_A	80.189	288	654	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	99.32	99.30	0.95	0.94	4	-
GCF_900120385.1	s__Olsenella_I phocaeensis	80.1587	263	654	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_009695875.1	s__Olsenella_H porci	80.0823	291	654	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_000143845.1	s__Olsenella uli	79.7889	261	654	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	-
GCF_016899935.1	s__Thermophilibacter uli_B	79.4376	262	654	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777325.1	s__UBA1367 sp902777325	78.9904	239	654	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117265.1	s__Thermophilibacter pullicola	78.6505	198	654	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 02:57:13,913] [INFO] GTDB search result was written to GCA_002394825.1_ASM239482v1_genomic.fna/result_gtdb.tsv
[2023-06-27 02:57:13,914] [INFO] ===== GTDB Search completed =====
[2023-06-27 02:57:13,920] [INFO] DFAST_QC result json was written to GCA_002394825.1_ASM239482v1_genomic.fna/dqc_result.json
[2023-06-27 02:57:13,921] [INFO] DFAST_QC completed!
[2023-06-27 02:57:13,921] [INFO] Total running time: 0h0m48s