[2024-01-24 13:22:55,531] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg39a3eec2-c91c-40ba-a88c-839923cb0455/dqc_reference
[2024-01-24 13:22:56,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,833] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb94d463-c94e-4b8f-a499-f55a51563d36/GCF_010499545.1_ASM1049954v1_genomic.fna.gz | prodigal -d GCF_010499545.1_ASM1049954v1_genomic.fna/cds.fna -a GCF_010499545.1_ASM1049954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:11,014] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:11,015] [INFO] Task started: HMMsearch
[2024-01-24 13:23:11,015] [INFO] Running command: hmmsearch --tblout GCF_010499545.1_ASM1049954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39a3eec2-c91c-40ba-a88c-839923cb0455/dqc_reference/reference_markers.hmm GCF_010499545.1_ASM1049954v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:11,333] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:11,334] [INFO] Found 6/6 markers.
[2024-01-24 13:23:11,377] [INFO] Query marker FASTA was written to GCF_010499545.1_ASM1049954v1_genomic.fna/markers.fasta
[2024-01-24 13:23:11,377] [INFO] Task started: Blastn
[2024-01-24 13:23:11,377] [INFO] Running command: blastn -query GCF_010499545.1_ASM1049954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39a3eec2-c91c-40ba-a88c-839923cb0455/dqc_reference/reference_markers.fasta -out GCF_010499545.1_ASM1049954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:11,951] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:11,954] [INFO] Selected 11 target genomes.
[2024-01-24 13:23:11,954] [INFO] Target genome list was writen to GCF_010499545.1_ASM1049954v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:11,967] [INFO] Task started: fastANI
[2024-01-24 13:23:11,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb94d463-c94e-4b8f-a499-f55a51563d36/GCF_010499545.1_ASM1049954v1_genomic.fna.gz --refList GCF_010499545.1_ASM1049954v1_genomic.fna/target_genomes.txt --output GCF_010499545.1_ASM1049954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:23,633] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:23,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39a3eec2-c91c-40ba-a88c-839923cb0455/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:23,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39a3eec2-c91c-40ba-a88c-839923cb0455/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:23,645] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:23:23,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:23,646] [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
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_010499545.1	2291	2291	type	True	100.0	1588	1590	95	conclusive
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_003261095.1	2291	2291	type	True	99.9944	1583	1590	95	conclusive
Desulfobacter hydrogenophilus	strain=AcRS1	GCA_004319545.1	2291	2291	type	True	99.9928	1590	1590	95	conclusive
Desulfobacter curvatus	strain=DSM 3379	GCA_000373985.1	2290	2290	type	True	86.9863	1026	1590	95	below_threshold
Desulfobacter postgatei	strain=2ac9	GCA_000233695.3	2293	2293	type	True	86.1678	888	1590	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	86.0132	864	1590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:23,647] [INFO] DFAST Taxonomy check result was written to GCF_010499545.1_ASM1049954v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:23,648] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:23,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:23,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39a3eec2-c91c-40ba-a88c-839923cb0455/dqc_reference/checkm_data
[2024-01-24 13:23:23,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:23,708] [INFO] Task started: CheckM
[2024-01-24 13:23:23,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010499545.1_ASM1049954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010499545.1_ASM1049954v1_genomic.fna/checkm_input GCF_010499545.1_ASM1049954v1_genomic.fna/checkm_result
[2024-01-24 13:24:08,229] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:08,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:08,255] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:08,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:08,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010499545.1_ASM1049954v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:08,256] [INFO] Task started: Blastn
[2024-01-24 13:24:08,256] [INFO] Running command: blastn -query GCF_010499545.1_ASM1049954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39a3eec2-c91c-40ba-a88c-839923cb0455/dqc_reference/reference_markers_gtdb.fasta -out GCF_010499545.1_ASM1049954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:09,047] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:09,052] [INFO] Selected 7 target genomes.
[2024-01-24 13:24:09,052] [INFO] Target genome list was writen to GCF_010499545.1_ASM1049954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:09,066] [INFO] Task started: fastANI
[2024-01-24 13:24:09,066] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb94d463-c94e-4b8f-a499-f55a51563d36/GCF_010499545.1_ASM1049954v1_genomic.fna.gz --refList GCF_010499545.1_ASM1049954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010499545.1_ASM1049954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:17,351] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:17,364] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:17,364] [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_004319545.1	s__Desulfobacter hydrogenophilus	99.9928	1590	1590	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_000373985.1	s__Desulfobacter curvatus	86.9806	1027	1590	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252055.1	s__Desulfobacter postgatei_B	86.7639	589	1590	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000233695.2	s__Desulfobacter postgatei	86.1922	886	1590	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	96.23	96.02	0.82	0.77	7	-
GCF_013389365.1	s__Desulfobacter latus	86.0791	824	1590	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745975.1	s__Desulfobacter vibrioformis	86.0157	865	1590	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002747145.1	s__Desulfobacter postgatei_A	84.3945	386	1590	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:17,366] [INFO] GTDB search result was written to GCF_010499545.1_ASM1049954v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:17,367] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:17,369] [INFO] DFAST_QC result json was written to GCF_010499545.1_ASM1049954v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:17,369] [INFO] DFAST_QC completed!
[2024-01-24 13:24:17,369] [INFO] Total running time: 0h1m22s