[2023-06-29 14:51:12,552] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:51:12,554] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:51:12,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d88e988-fa86-490c-855e-144b3e815e47/dqc_reference
[2023-06-29 14:51:13,755] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:51:13,756] [INFO] Task started: Prodigal
[2023-06-29 14:51:13,757] [INFO] Running command: gunzip -c /var/lib/cwl/stg1377a0b0-9057-4679-87e0-b5d4f30929ae/GCA_021794285.1_ASM2179428v1_genomic.fna.gz | prodigal -d GCA_021794285.1_ASM2179428v1_genomic.fna/cds.fna -a GCA_021794285.1_ASM2179428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:51:20,278] [INFO] Task succeeded: Prodigal
[2023-06-29 14:51:20,278] [INFO] Task started: HMMsearch
[2023-06-29 14:51:20,279] [INFO] Running command: hmmsearch --tblout GCA_021794285.1_ASM2179428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d88e988-fa86-490c-855e-144b3e815e47/dqc_reference/reference_markers.hmm GCA_021794285.1_ASM2179428v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:51:20,532] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:51:20,534] [INFO] Found 6/6 markers.
[2023-06-29 14:51:20,558] [INFO] Query marker FASTA was written to GCA_021794285.1_ASM2179428v1_genomic.fna/markers.fasta
[2023-06-29 14:51:20,559] [INFO] Task started: Blastn
[2023-06-29 14:51:20,559] [INFO] Running command: blastn -query GCA_021794285.1_ASM2179428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d88e988-fa86-490c-855e-144b3e815e47/dqc_reference/reference_markers.fasta -out GCA_021794285.1_ASM2179428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:51:21,364] [INFO] Task succeeded: Blastn
[2023-06-29 14:51:21,370] [INFO] Selected 34 target genomes.
[2023-06-29 14:51:21,371] [INFO] Target genome list was writen to GCA_021794285.1_ASM2179428v1_genomic.fna/target_genomes.txt
[2023-06-29 14:51:21,378] [INFO] Task started: fastANI
[2023-06-29 14:51:21,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg1377a0b0-9057-4679-87e0-b5d4f30929ae/GCA_021794285.1_ASM2179428v1_genomic.fna.gz --refList GCA_021794285.1_ASM2179428v1_genomic.fna/target_genomes.txt --output GCA_021794285.1_ASM2179428v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:51:42,024] [INFO] Task succeeded: fastANI
[2023-06-29 14:51:42,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d88e988-fa86-490c-855e-144b3e815e47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:51:42,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d88e988-fa86-490c-855e-144b3e815e47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:51:42,041] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:51:42,041] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:51:42,042] [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
Thiobacillus denitrificans	strain=DSM 12475	GCA_000376425.1	36861	36861	type	True	76.5301	80	728	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.4931	113	728	95	below_threshold
Sulfuricella denitrificans	strain=skB26	GCA_000297055.2	649841	649841	type	True	76.4298	73	728	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	76.347	58	728	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	76.3252	87	728	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	76.1356	68	728	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	76.0302	53	728	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.0149	70	728	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	76.004	66	728	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	75.9704	65	728	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	75.9282	67	728	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	75.9206	72	728	95	below_threshold
Burkholderia plantarii	strain=LMG 9035	GCA_902832905.1	41899	41899	type	True	75.7398	67	728	95	below_threshold
Burkholderia plantarii	strain=ATCC 43733	GCA_001411805.1	41899	41899	type	True	75.6904	70	728	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	75.6561	63	728	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	75.6548	63	728	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:51:42,046] [INFO] DFAST Taxonomy check result was written to GCA_021794285.1_ASM2179428v1_genomic.fna/tc_result.tsv
[2023-06-29 14:51:42,047] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:51:42,047] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:51:42,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d88e988-fa86-490c-855e-144b3e815e47/dqc_reference/checkm_data
[2023-06-29 14:51:42,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:51:42,075] [INFO] Task started: CheckM
[2023-06-29 14:51:42,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021794285.1_ASM2179428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021794285.1_ASM2179428v1_genomic.fna/checkm_input GCA_021794285.1_ASM2179428v1_genomic.fna/checkm_result
[2023-06-29 14:52:06,877] [INFO] Task succeeded: CheckM
[2023-06-29 14:52:06,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:52:06,899] [INFO] ===== Completeness check finished =====
[2023-06-29 14:52:06,900] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:52:06,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021794285.1_ASM2179428v1_genomic.fna/markers.fasta)
[2023-06-29 14:52:06,901] [INFO] Task started: Blastn
[2023-06-29 14:52:06,901] [INFO] Running command: blastn -query GCA_021794285.1_ASM2179428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d88e988-fa86-490c-855e-144b3e815e47/dqc_reference/reference_markers_gtdb.fasta -out GCA_021794285.1_ASM2179428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:52:08,278] [INFO] Task succeeded: Blastn
[2023-06-29 14:52:08,284] [INFO] Selected 32 target genomes.
[2023-06-29 14:52:08,284] [INFO] Target genome list was writen to GCA_021794285.1_ASM2179428v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:52:08,295] [INFO] Task started: fastANI
[2023-06-29 14:52:08,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg1377a0b0-9057-4679-87e0-b5d4f30929ae/GCA_021794285.1_ASM2179428v1_genomic.fna.gz --refList GCA_021794285.1_ASM2179428v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021794285.1_ASM2179428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:52:26,486] [INFO] Task succeeded: fastANI
[2023-06-29 14:52:26,517] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:52:26,518] [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_013044025.1	s__JABEVD01 sp013044025	78.2619	281	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JABEVD01;g__JABEVD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899765.1	s__Thiobacillus sp001899765	76.5851	67	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.02	98.01	0.93	0.89	5	-
GCA_016235045.1	s__Sideroxydans sp016235045	76.5135	74	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764585.1	s__Sulfurimicrobium lacus	76.4931	113	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfurimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784065.1	s__Sulfuricella sp002784065	76.4846	84	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__Sulfuricella	95.0	99.65	99.21	0.84	0.80	4	-
GCA_016183615.1	s__JACPEG01 sp016183615	76.4729	93	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA6910;g__JACPEG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124745.1	s__Thiobacillus sp016124745	76.4293	70	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526165.1	s__Desulfobacillus sp011526165	76.3447	75	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.84	98.84	0.79	0.79	2	-
GCA_008923285.1	s__UBA6918 sp008923285	76.3274	73	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__UBA6918	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217225.1	s__Azospira oryzae	76.2666	67	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira	95.0	98.24	98.03	0.94	0.90	6	-
GCA_016868295.1	s__Desulfobacillus sp016868295	76.2442	84	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008923315.1	s__Thiobacillus sp001897705	76.122	63	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	98.92	98.92	0.91	0.90	4	-
GCA_018262095.1	s__Propionivibrio sp018262095	76.0838	55	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880745.1	s__2-12-FULL-64-23 sp017880745	76.0714	51	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336195.1	s__JAGXQV01 sp018336195	76.041	82	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__JAGXQV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112695.1	s__Azospira sp003112695	76.0045	62	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347285.1	s__UBA2250 sp002347285	75.948	63	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801175.1	s__Gallionella sp001801175	75.945	73	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Gallionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	75.9408	71	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_008933825.1	s__Desulfobacillus sp008933825	75.9334	70	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	99.14	98.51	0.86	0.84	3	-
GCA_003105015.1	s__Desulfobacillus sp003105015	75.8875	74	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.07	97.07	0.88	0.88	2	-
GCF_001544975.2	s__Caballeronia arationis	75.718	51	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia	95.0	99.46	99.46	0.88	0.88	2	-
GCA_000471925.1	s__Cupriavidus pickettii_A	75.4452	60	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379565.1	s__Cupriavidus sp000379565	75.3173	55	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:52:26,520] [INFO] GTDB search result was written to GCA_021794285.1_ASM2179428v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:52:26,520] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:52:26,525] [INFO] DFAST_QC result json was written to GCA_021794285.1_ASM2179428v1_genomic.fna/dqc_result.json
[2023-06-29 14:52:26,525] [INFO] DFAST_QC completed!
[2023-06-29 14:52:26,525] [INFO] Total running time: 0h1m14s