[2023-06-30 21:01:16,239] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:01:16,242] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:01:16,242] [INFO] DQC Reference Directory: /var/lib/cwl/stg126e9f95-ae32-438c-997c-969c1e9c1b1b/dqc_reference
[2023-06-30 21:01:17,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:01:17,525] [INFO] Task started: Prodigal
[2023-06-30 21:01:17,525] [INFO] Running command: gunzip -c /var/lib/cwl/stgc360d2cd-029d-473c-a85e-1aba8f5af0c2/GCA_025360885.1_ASM2536088v1_genomic.fna.gz | prodigal -d GCA_025360885.1_ASM2536088v1_genomic.fna/cds.fna -a GCA_025360885.1_ASM2536088v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:01:26,666] [INFO] Task succeeded: Prodigal
[2023-06-30 21:01:26,666] [INFO] Task started: HMMsearch
[2023-06-30 21:01:26,666] [INFO] Running command: hmmsearch --tblout GCA_025360885.1_ASM2536088v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg126e9f95-ae32-438c-997c-969c1e9c1b1b/dqc_reference/reference_markers.hmm GCA_025360885.1_ASM2536088v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:01:26,925] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:01:26,926] [INFO] Found 6/6 markers.
[2023-06-30 21:01:26,964] [INFO] Query marker FASTA was written to GCA_025360885.1_ASM2536088v1_genomic.fna/markers.fasta
[2023-06-30 21:01:26,964] [INFO] Task started: Blastn
[2023-06-30 21:01:26,964] [INFO] Running command: blastn -query GCA_025360885.1_ASM2536088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg126e9f95-ae32-438c-997c-969c1e9c1b1b/dqc_reference/reference_markers.fasta -out GCA_025360885.1_ASM2536088v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:01:27,789] [INFO] Task succeeded: Blastn
[2023-06-30 21:01:27,796] [INFO] Selected 25 target genomes.
[2023-06-30 21:01:27,797] [INFO] Target genome list was writen to GCA_025360885.1_ASM2536088v1_genomic.fna/target_genomes.txt
[2023-06-30 21:01:27,801] [INFO] Task started: fastANI
[2023-06-30 21:01:27,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgc360d2cd-029d-473c-a85e-1aba8f5af0c2/GCA_025360885.1_ASM2536088v1_genomic.fna.gz --refList GCA_025360885.1_ASM2536088v1_genomic.fna/target_genomes.txt --output GCA_025360885.1_ASM2536088v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:01:46,934] [INFO] Task succeeded: fastANI
[2023-06-30 21:01:46,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg126e9f95-ae32-438c-997c-969c1e9c1b1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:01:46,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg126e9f95-ae32-438c-997c-969c1e9c1b1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:01:46,959] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:01:46,959] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 21:01:46,959] [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
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.7113	144	993	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	76.6804	146	993	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	76.6428	172	993	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.5963	156	993	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.4131	169	993	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.3753	209	993	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.368	148	993	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.3258	167	993	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	76.3166	164	993	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	76.3018	155	993	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	76.2825	187	993	95	below_threshold
Burkholderia oklahomensis	strain=C6786	GCA_000170375.1	342113	342113	type	True	76.2487	237	993	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	76.1602	131	993	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	76.1599	134	993	95	below_threshold
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	76.1131	262	993	95	below_threshold
Burkholderia pseudomallei	strain=WRAIR 286	GCA_006538545.1	28450	28450	type	True	76.0862	255	993	95	below_threshold
Burkholderia catarinensis	strain=89	GCA_001883705.2	1108140	1108140	type	True	76.083	253	993	95	below_threshold
Burkholderia pseudomallei	strain=ATCC 23343	GCA_001182285.1	28450	28450	type	True	76.0598	262	993	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.0295	269	993	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	76.0215	103	993	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	75.9575	235	993	95	below_threshold
Burkholderia glumae	strain=ATCC 33617	GCA_000960995.1	337	337	type	True	75.9504	231	993	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	75.9263	164	993	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	75.9203	158	993	95	below_threshold
Verticiella sediminum	strain=DSM 27279	GCA_007558815.1	1247510	1247510	type	True	75.749	150	993	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 21:01:46,962] [INFO] DFAST Taxonomy check result was written to GCA_025360885.1_ASM2536088v1_genomic.fna/tc_result.tsv
[2023-06-30 21:01:46,962] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:01:46,962] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:01:46,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg126e9f95-ae32-438c-997c-969c1e9c1b1b/dqc_reference/checkm_data
[2023-06-30 21:01:46,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:01:47,008] [INFO] Task started: CheckM
[2023-06-30 21:01:47,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025360885.1_ASM2536088v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025360885.1_ASM2536088v1_genomic.fna/checkm_input GCA_025360885.1_ASM2536088v1_genomic.fna/checkm_result
[2023-06-30 21:02:18,080] [INFO] Task succeeded: CheckM
[2023-06-30 21:02:18,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.32%
Contamintation: 3.01%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 21:02:18,105] [INFO] ===== Completeness check finished =====
[2023-06-30 21:02:18,105] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:02:18,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025360885.1_ASM2536088v1_genomic.fna/markers.fasta)
[2023-06-30 21:02:18,106] [INFO] Task started: Blastn
[2023-06-30 21:02:18,106] [INFO] Running command: blastn -query GCA_025360885.1_ASM2536088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg126e9f95-ae32-438c-997c-969c1e9c1b1b/dqc_reference/reference_markers_gtdb.fasta -out GCA_025360885.1_ASM2536088v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:02:19,500] [INFO] Task succeeded: Blastn
[2023-06-30 21:02:19,505] [INFO] Selected 13 target genomes.
[2023-06-30 21:02:19,505] [INFO] Target genome list was writen to GCA_025360885.1_ASM2536088v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:02:19,510] [INFO] Task started: fastANI
[2023-06-30 21:02:19,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgc360d2cd-029d-473c-a85e-1aba8f5af0c2/GCA_025360885.1_ASM2536088v1_genomic.fna.gz --refList GCA_025360885.1_ASM2536088v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025360885.1_ASM2536088v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:02:29,979] [INFO] Task succeeded: fastANI
[2023-06-30 21:02:29,994] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:02:29,994] [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_010365205.1	s__CAIWHR01 sp010365205	96.8625	539	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016720425.1	s__CAIWHR01 sp016720425	80.0492	461	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	-
GCA_903912485.1	s__CAIWHR01 sp903912485	80.0386	419	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	99.88	99.81	0.92	0.91	3	-
GCA_016716425.1	s__VBCG01 sp016716425	79.4782	516	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704895.1	s__VBCG01 sp016704895	79.2351	470	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	96.62	96.45	0.90	0.90	3	-
GCA_905339295.1	s__VBCG01 sp905339295	78.901	466	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075645.1	s__VBCG01 sp015075645	78.7329	449	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241745.1	s__VBCG01 sp018241745	78.6849	360	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861105.1	s__VBCG01 sp016861105	78.6117	425	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971195.1	s__VBCG01 sp018971195	78.5155	324	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880805.1	s__PALSA-1003 sp017880805	77.9681	258	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__PALSA-1003	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888865.1	s__PALSA-1003 sp005888865	77.7436	265	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__PALSA-1003	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 21:02:29,996] [INFO] GTDB search result was written to GCA_025360885.1_ASM2536088v1_genomic.fna/result_gtdb.tsv
[2023-06-30 21:02:29,997] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:02:30,004] [INFO] DFAST_QC result json was written to GCA_025360885.1_ASM2536088v1_genomic.fna/dqc_result.json
[2023-06-30 21:02:30,004] [INFO] DFAST_QC completed!
[2023-06-30 21:02:30,004] [INFO] Total running time: 0h1m14s