[2024-01-24 13:36:45,461] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,463] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ecc1a4c-3259-4aac-9a19-86c0aa7b1c13/dqc_reference
[2024-01-24 13:36:46,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,794] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg50b0a83b-dca3-45a6-a4dd-0070911281f2/GCF_000425385.1_ASM42538v1_genomic.fna.gz | prodigal -d GCF_000425385.1_ASM42538v1_genomic.fna/cds.fna -a GCF_000425385.1_ASM42538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:09,032] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:09,033] [INFO] Task started: HMMsearch
[2024-01-24 13:37:09,033] [INFO] Running command: hmmsearch --tblout GCF_000425385.1_ASM42538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ecc1a4c-3259-4aac-9a19-86c0aa7b1c13/dqc_reference/reference_markers.hmm GCF_000425385.1_ASM42538v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:09,418] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:09,419] [INFO] Found 6/6 markers.
[2024-01-24 13:37:09,475] [INFO] Query marker FASTA was written to GCF_000425385.1_ASM42538v1_genomic.fna/markers.fasta
[2024-01-24 13:37:09,476] [INFO] Task started: Blastn
[2024-01-24 13:37:09,476] [INFO] Running command: blastn -query GCF_000425385.1_ASM42538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ecc1a4c-3259-4aac-9a19-86c0aa7b1c13/dqc_reference/reference_markers.fasta -out GCF_000425385.1_ASM42538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:10,460] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:10,464] [INFO] Selected 23 target genomes.
[2024-01-24 13:37:10,464] [INFO] Target genome list was writen to GCF_000425385.1_ASM42538v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:10,477] [INFO] Task started: fastANI
[2024-01-24 13:37:10,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b0a83b-dca3-45a6-a4dd-0070911281f2/GCF_000425385.1_ASM42538v1_genomic.fna.gz --refList GCF_000425385.1_ASM42538v1_genomic.fna/target_genomes.txt --output GCF_000425385.1_ASM42538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:38,717] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:38,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ecc1a4c-3259-4aac-9a19-86c0aa7b1c13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:38,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ecc1a4c-3259-4aac-9a19-86c0aa7b1c13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:38,735] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:38,736] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:38,736] [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 guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	86.1225	1400	2017	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	82.2804	1115	2017	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	81.7229	1058	2017	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	81.4862	1083	2017	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	81.4003	971	2017	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	81.3131	971	2017	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	81.2227	985	2017	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	81.0822	986	2017	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	80.6011	905	2017	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.5095	822	2017	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	80.4931	741	2017	95	below_threshold
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	80.4694	952	2017	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	80.3754	824	2017	95	below_threshold
Massilia yuzhufengensis	strain=CGMCC 1.12041	GCA_900112225.1	1164594	1164594	type	True	80.2367	803	2017	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.2126	853	2017	95	below_threshold
Massilia arenosa	strain=MC02	GCA_004614185.1	2561931	2561931	type	True	80.0843	729	2017	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	80.0658	759	2017	95	below_threshold
Pseudoduganella ginsengisoli	strain=KCTC 42409	GCA_009720865.1	1462440	1462440	type	True	79.6734	872	2017	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	77.0179	441	2017	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	77.0131	431	2017	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	76.9935	441	2017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:38,745] [INFO] DFAST Taxonomy check result was written to GCF_000425385.1_ASM42538v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:38,746] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:38,746] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:38,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ecc1a4c-3259-4aac-9a19-86c0aa7b1c13/dqc_reference/checkm_data
[2024-01-24 13:37:38,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:38,808] [INFO] Task started: CheckM
[2024-01-24 13:37:38,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425385.1_ASM42538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425385.1_ASM42538v1_genomic.fna/checkm_input GCF_000425385.1_ASM42538v1_genomic.fna/checkm_result
[2024-01-24 13:38:38,642] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:38,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:38,668] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:38,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:38,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425385.1_ASM42538v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:38,670] [INFO] Task started: Blastn
[2024-01-24 13:38:38,670] [INFO] Running command: blastn -query GCF_000425385.1_ASM42538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ecc1a4c-3259-4aac-9a19-86c0aa7b1c13/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425385.1_ASM42538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:40,139] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:40,144] [INFO] Selected 11 target genomes.
[2024-01-24 13:38:40,144] [INFO] Target genome list was writen to GCF_000425385.1_ASM42538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:40,168] [INFO] Task started: fastANI
[2024-01-24 13:38:40,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg50b0a83b-dca3-45a6-a4dd-0070911281f2/GCF_000425385.1_ASM42538v1_genomic.fna.gz --refList GCF_000425385.1_ASM42538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425385.1_ASM42538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:53,459] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:53,467] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:53,467] [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_000425385.1	s__Pseudoduganella violaceinigra	100.0	2015	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004217275.1	s__Pseudoduganella sp004217275	86.8471	1549	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113115.1	s__Pseudoduganella sp900113115	86.825	1536	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720745.1	s__Pseudoduganella eburnea	86.7317	1460	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425005.1	s__Pseudoduganella sp001425005	86.6544	1544	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.68	99.68	0.97	0.97	2	-
GCF_001427305.1	s__Pseudoduganella sp001427305	86.6246	1539	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857475.1	s__Pseudoduganella guangdongensis	86.1038	1403	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218755.1	s__Acidovorax sp019218755	76.5508	349	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:53,470] [INFO] GTDB search result was written to GCF_000425385.1_ASM42538v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:53,471] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:53,476] [INFO] DFAST_QC result json was written to GCF_000425385.1_ASM42538v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:53,476] [INFO] DFAST_QC completed!
[2024-01-24 13:38:53,476] [INFO] Total running time: 0h2m8s