[2024-01-25 20:15:50,374] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:50,379] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:50,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg54defb26-bef6-4a39-b3ff-5b0f488b28dd/dqc_reference
[2024-01-25 20:15:51,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:51,540] [INFO] Task started: Prodigal
[2024-01-25 20:15:51,541] [INFO] Running command: gunzip -c /var/lib/cwl/stg8421c0b0-31b2-4904-92ac-14f698ca1427/GCF_009720835.1_ASM972083v1_genomic.fna.gz | prodigal -d GCF_009720835.1_ASM972083v1_genomic.fna/cds.fna -a GCF_009720835.1_ASM972083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:08,395] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:08,395] [INFO] Task started: HMMsearch
[2024-01-25 20:16:08,395] [INFO] Running command: hmmsearch --tblout GCF_009720835.1_ASM972083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54defb26-bef6-4a39-b3ff-5b0f488b28dd/dqc_reference/reference_markers.hmm GCF_009720835.1_ASM972083v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:08,807] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:08,808] [INFO] Found 6/6 markers.
[2024-01-25 20:16:08,863] [INFO] Query marker FASTA was written to GCF_009720835.1_ASM972083v1_genomic.fna/markers.fasta
[2024-01-25 20:16:08,863] [INFO] Task started: Blastn
[2024-01-25 20:16:08,863] [INFO] Running command: blastn -query GCF_009720835.1_ASM972083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54defb26-bef6-4a39-b3ff-5b0f488b28dd/dqc_reference/reference_markers.fasta -out GCF_009720835.1_ASM972083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:09,872] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:09,875] [INFO] Selected 16 target genomes.
[2024-01-25 20:16:09,875] [INFO] Target genome list was writen to GCF_009720835.1_ASM972083v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:09,880] [INFO] Task started: fastANI
[2024-01-25 20:16:09,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg8421c0b0-31b2-4904-92ac-14f698ca1427/GCF_009720835.1_ASM972083v1_genomic.fna.gz --refList GCF_009720835.1_ASM972083v1_genomic.fna/target_genomes.txt --output GCF_009720835.1_ASM972083v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:34,628] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:34,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54defb26-bef6-4a39-b3ff-5b0f488b28dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:34,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54defb26-bef6-4a39-b3ff-5b0f488b28dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:34,639] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:16:34,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:34,639] [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
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	100.0	1965	1983	95	conclusive
Pseudoduganella buxea	strain=CGMCC 1.15931	GCA_014644155.1	1949069	1949069	type	True	99.9924	1962	1983	95	conclusive
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	86.1883	1513	1983	95	below_threshold
Pseudoduganella plicata	strain=DSM 17505	GCA_004421005.1	321984	321984	type	True	85.5467	1473	1983	95	below_threshold
Pseudoduganella plicata	strain=KCTC 12344	GCA_014651435.1	321984	321984	type	True	85.519	1468	1983	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	84.037	1260	1983	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	83.4899	1377	1983	95	below_threshold
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	83.4551	1375	1983	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	83.0905	1342	1983	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	82.2618	1187	1983	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	81.9929	1143	1983	95	below_threshold
Pseudoduganella guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	81.2097	1010	1983	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	80.7521	791	1983	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.604	955	1983	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	80.5507	867	1983	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	80.3894	1006	1983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:34,640] [INFO] DFAST Taxonomy check result was written to GCF_009720835.1_ASM972083v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:34,641] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:34,641] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:34,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54defb26-bef6-4a39-b3ff-5b0f488b28dd/dqc_reference/checkm_data
[2024-01-25 20:16:34,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:34,700] [INFO] Task started: CheckM
[2024-01-25 20:16:34,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009720835.1_ASM972083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009720835.1_ASM972083v1_genomic.fna/checkm_input GCF_009720835.1_ASM972083v1_genomic.fna/checkm_result
[2024-01-25 20:17:29,307] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:29,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:29,328] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:29,328] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:29,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009720835.1_ASM972083v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:29,329] [INFO] Task started: Blastn
[2024-01-25 20:17:29,329] [INFO] Running command: blastn -query GCF_009720835.1_ASM972083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54defb26-bef6-4a39-b3ff-5b0f488b28dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_009720835.1_ASM972083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:31,547] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:31,550] [INFO] Selected 12 target genomes.
[2024-01-25 20:17:31,550] [INFO] Target genome list was writen to GCF_009720835.1_ASM972083v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:31,560] [INFO] Task started: fastANI
[2024-01-25 20:17:31,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg8421c0b0-31b2-4904-92ac-14f698ca1427/GCF_009720835.1_ASM972083v1_genomic.fna.gz --refList GCF_009720835.1_ASM972083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009720835.1_ASM972083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:52,093] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:52,101] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:52,101] [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_009720835.1	s__Pseudoduganella buxea	100.0	1965	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_008011715.1	s__Pseudoduganella haloabium	86.221	1502	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.13	98.13	0.91	0.91	2	-
GCF_003028855.1	s__Pseudoduganella armeniaca	86.2101	1509	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004421005.1	s__Pseudoduganella plicata	85.5581	1472	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002454505.1	s__Pseudoduganella sp002454505	84.2607	1200	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004322755.1	s__Pseudoduganella albidiflava	83.4979	1376	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009727155.1	s__Pseudoduganella dura	83.3159	1350	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004209755.1	s__Pseudoduganella lutea	83.1128	1339	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116645.1	s__Pseudoduganella namucuonensis	82.2354	1191	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053665.1	s__Pseudoduganella sp003053665	82.2271	1189	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.77	95.97	0.96	0.89	5	-
GCF_001191005.1	s__Pseudoduganella sp001191005	82.1196	1068	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013369485.1	s__Pseudoduganella sp013369485	81.9387	1040	1983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:52,103] [INFO] GTDB search result was written to GCF_009720835.1_ASM972083v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:52,104] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:52,107] [INFO] DFAST_QC result json was written to GCF_009720835.1_ASM972083v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:52,108] [INFO] DFAST_QC completed!
[2024-01-25 20:17:52,108] [INFO] Total running time: 0h2m2s