[2023-06-08 14:28:14,988] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:28:14,991] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:28:14,991] [INFO] DQC Reference Directory: /var/lib/cwl/stg6202c92c-6757-498c-a60b-888b872c6930/dqc_reference
[2023-06-08 14:28:18,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:28:18,272] [INFO] Task started: Prodigal
[2023-06-08 14:28:18,273] [INFO] Running command: gunzip -c /var/lib/cwl/stgb246bcf7-375e-49ba-a0eb-bea06489a61f/GCA_947445165.1_CH-Jul18-79_genomic.fna.gz | prodigal -d GCA_947445165.1_CH-Jul18-79_genomic.fna/cds.fna -a GCA_947445165.1_CH-Jul18-79_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:28:23,893] [INFO] Task succeeded: Prodigal
[2023-06-08 14:28:23,894] [INFO] Task started: HMMsearch
[2023-06-08 14:28:23,894] [INFO] Running command: hmmsearch --tblout GCA_947445165.1_CH-Jul18-79_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6202c92c-6757-498c-a60b-888b872c6930/dqc_reference/reference_markers.hmm GCA_947445165.1_CH-Jul18-79_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:28:24,221] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:28:24,222] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb246bcf7-375e-49ba-a0eb-bea06489a61f/GCA_947445165.1_CH-Jul18-79_genomic.fna.gz]
[2023-06-08 14:28:24,250] [INFO] Query marker FASTA was written to GCA_947445165.1_CH-Jul18-79_genomic.fna/markers.fasta
[2023-06-08 14:28:24,251] [INFO] Task started: Blastn
[2023-06-08 14:28:24,251] [INFO] Running command: blastn -query GCA_947445165.1_CH-Jul18-79_genomic.fna/markers.fasta -db /var/lib/cwl/stg6202c92c-6757-498c-a60b-888b872c6930/dqc_reference/reference_markers.fasta -out GCA_947445165.1_CH-Jul18-79_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:28:25,141] [INFO] Task succeeded: Blastn
[2023-06-08 14:28:25,156] [INFO] Selected 25 target genomes.
[2023-06-08 14:28:25,157] [INFO] Target genome list was writen to GCA_947445165.1_CH-Jul18-79_genomic.fna/target_genomes.txt
[2023-06-08 14:28:25,165] [INFO] Task started: fastANI
[2023-06-08 14:28:25,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgb246bcf7-375e-49ba-a0eb-bea06489a61f/GCA_947445165.1_CH-Jul18-79_genomic.fna.gz --refList GCA_947445165.1_CH-Jul18-79_genomic.fna/target_genomes.txt --output GCA_947445165.1_CH-Jul18-79_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:28:44,036] [INFO] Task succeeded: fastANI
[2023-06-08 14:28:44,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6202c92c-6757-498c-a60b-888b872c6930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:28:44,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6202c92c-6757-498c-a60b-888b872c6930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:28:44,059] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:28:44,059] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 14:28:44,060] [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
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.0625	100	568	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.0138	102	568	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.7939	103	568	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.7616	104	568	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	77.7284	90	568	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	77.7282	85	568	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	77.728	92	568	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	77.6591	93	568	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	77.6288	109	568	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.5824	105	568	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	77.5744	88	568	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	77.4178	115	568	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	77.3077	90	568	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	77.252	123	568	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	77.2219	89	568	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	77.0094	123	568	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	76.945	93	568	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.933	124	568	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	76.6649	92	568	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	76.6354	98	568	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	76.5248	95	568	95	below_threshold
Massilia aurea	strain=JCM 13879	GCA_024753205.1	373040	373040	type	True	76.4883	72	568	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.3699	89	568	95	below_threshold
Pelomicrobium methylotrophicum	strain=SM250	GCA_008014345.1	2602750	2602750	type	True	76.2679	56	568	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:28:44,062] [INFO] DFAST Taxonomy check result was written to GCA_947445165.1_CH-Jul18-79_genomic.fna/tc_result.tsv
[2023-06-08 14:28:44,063] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:28:44,063] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:28:44,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6202c92c-6757-498c-a60b-888b872c6930/dqc_reference/checkm_data
[2023-06-08 14:28:44,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:28:44,103] [INFO] Task started: CheckM
[2023-06-08 14:28:44,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947445165.1_CH-Jul18-79_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947445165.1_CH-Jul18-79_genomic.fna/checkm_input GCA_947445165.1_CH-Jul18-79_genomic.fna/checkm_result
[2023-06-08 14:29:06,307] [INFO] Task succeeded: CheckM
[2023-06-08 14:29:06,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:29:06,329] [INFO] ===== Completeness check finished =====
[2023-06-08 14:29:06,329] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:29:06,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947445165.1_CH-Jul18-79_genomic.fna/markers.fasta)
[2023-06-08 14:29:06,330] [INFO] Task started: Blastn
[2023-06-08 14:29:06,330] [INFO] Running command: blastn -query GCA_947445165.1_CH-Jul18-79_genomic.fna/markers.fasta -db /var/lib/cwl/stg6202c92c-6757-498c-a60b-888b872c6930/dqc_reference/reference_markers_gtdb.fasta -out GCA_947445165.1_CH-Jul18-79_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:29:07,824] [INFO] Task succeeded: Blastn
[2023-06-08 14:29:07,828] [INFO] Selected 15 target genomes.
[2023-06-08 14:29:07,828] [INFO] Target genome list was writen to GCA_947445165.1_CH-Jul18-79_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:29:07,836] [INFO] Task started: fastANI
[2023-06-08 14:29:07,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgb246bcf7-375e-49ba-a0eb-bea06489a61f/GCA_947445165.1_CH-Jul18-79_genomic.fna.gz --refList GCA_947445165.1_CH-Jul18-79_genomic.fna/target_genomes_gtdb.txt --output GCA_947445165.1_CH-Jul18-79_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:29:15,878] [INFO] Task succeeded: fastANI
[2023-06-08 14:29:15,891] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:29:15,892] [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
GCA_018241645.1	s__SZAS-79 sp018241645	84.1998	363	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__SZAS-79	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713125.1	s__SZAS-79 sp016713125	80.1501	285	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__SZAS-79	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868105.1	s__RBG-16-66-20 sp016868105	79.1388	166	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__RBG-16-66-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005240145.1	s__RBG-16-66-20 sp005240145	78.5481	184	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__RBG-16-66-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770655.1	s__2-12-FULL-68-20 sp001770655	78.4817	171	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-68-20	95.0	99.77	99.77	0.95	0.95	2	-
GCA_001770285.1	s__RBG-16-66-20 sp001770285	78.4171	166	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__RBG-16-66-20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001303445.1	s__SG8-39 sp001303445	78.3253	140	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__SG8-39	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880775.1	s__JADGRQ01 sp017880775	78.186	195	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__JADGRQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298325.1	s__2-02-FULL-66-14 sp004298325	78.0941	151	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-02-FULL-66-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298295.1	s__2-02-FULL-66-14 sp004298295	78.0288	118	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-02-FULL-66-14	95.0	96.40	96.40	0.72	0.72	2	-
GCF_003865015.1	s__Sulfurisoma sediminicola	77.7616	104	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002347285.1	s__UBA2250 sp002347285	77.6212	92	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903834835.1	s__CAILKO01 sp903834835	77.3531	87	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__CAILKO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016210745.1	s__JACQTO01 sp016210745	77.16	76	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__JACQTO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016189945.1	s__JACQTO01 sp016189945	76.9147	88	568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__JACQTO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 14:29:15,894] [INFO] GTDB search result was written to GCA_947445165.1_CH-Jul18-79_genomic.fna/result_gtdb.tsv
[2023-06-08 14:29:15,894] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:29:15,899] [INFO] DFAST_QC result json was written to GCA_947445165.1_CH-Jul18-79_genomic.fna/dqc_result.json
[2023-06-08 14:29:15,899] [INFO] DFAST_QC completed!
[2023-06-08 14:29:15,899] [INFO] Total running time: 0h1m1s