[2024-01-24 11:51:22,754] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:22,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:22,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg383842df-b237-4464-a47c-d65126c06b45/dqc_reference
[2024-01-24 11:51:24,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:24,081] [INFO] Task started: Prodigal
[2024-01-24 11:51:24,082] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cd6e4fa-b087-4295-9875-9040a8c84015/GCF_013389365.1_ASM1338936v1_genomic.fna.gz | prodigal -d GCF_013389365.1_ASM1338936v1_genomic.fna/cds.fna -a GCF_013389365.1_ASM1338936v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:35,292] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:35,293] [INFO] Task started: HMMsearch
[2024-01-24 11:51:35,293] [INFO] Running command: hmmsearch --tblout GCF_013389365.1_ASM1338936v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg383842df-b237-4464-a47c-d65126c06b45/dqc_reference/reference_markers.hmm GCF_013389365.1_ASM1338936v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:35,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:35,607] [INFO] Found 6/6 markers.
[2024-01-24 11:51:35,656] [INFO] Query marker FASTA was written to GCF_013389365.1_ASM1338936v1_genomic.fna/markers.fasta
[2024-01-24 11:51:35,657] [INFO] Task started: Blastn
[2024-01-24 11:51:35,657] [INFO] Running command: blastn -query GCF_013389365.1_ASM1338936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg383842df-b237-4464-a47c-d65126c06b45/dqc_reference/reference_markers.fasta -out GCF_013389365.1_ASM1338936v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:36,234] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:36,238] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:36,238] [INFO] Target genome list was writen to GCF_013389365.1_ASM1338936v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:36,243] [INFO] Task started: fastANI
[2024-01-24 11:51:36,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cd6e4fa-b087-4295-9875-9040a8c84015/GCF_013389365.1_ASM1338936v1_genomic.fna.gz --refList GCF_013389365.1_ASM1338936v1_genomic.fna/target_genomes.txt --output GCF_013389365.1_ASM1338936v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:47,696] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:47,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg383842df-b237-4464-a47c-d65126c06b45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:47,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg383842df-b237-4464-a47c-d65126c06b45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:47,703] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:47,703] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:47,703] [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 latus	strain=AcRS2	GCA_013389365.1	2292	2292	type	True	100.0	1337	1343	95	conclusive
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_003261095.1	2291	2291	type	True	86.3068	802	1343	95	below_threshold
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_010499545.1	2291	2291	type	True	86.2364	803	1343	95	below_threshold
Desulfobacter hydrogenophilus	strain=AcRS1	GCA_004319545.1	2291	2291	type	True	86.1895	821	1343	95	below_threshold
Desulfobacter postgatei	strain=2ac9	GCA_000233695.3	2293	2293	type	True	85.5643	758	1343	95	below_threshold
Desulfobacter curvatus	strain=DSM 3379	GCA_000373985.1	2290	2290	type	True	85.1989	779	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:47,705] [INFO] DFAST Taxonomy check result was written to GCF_013389365.1_ASM1338936v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:47,706] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:47,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:47,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg383842df-b237-4464-a47c-d65126c06b45/dqc_reference/checkm_data
[2024-01-24 11:51:47,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:47,752] [INFO] Task started: CheckM
[2024-01-24 11:51:47,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013389365.1_ASM1338936v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013389365.1_ASM1338936v1_genomic.fna/checkm_input GCF_013389365.1_ASM1338936v1_genomic.fna/checkm_result
[2024-01-24 11:52:26,507] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:26,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:26,532] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:26,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:26,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013389365.1_ASM1338936v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:26,533] [INFO] Task started: Blastn
[2024-01-24 11:52:26,533] [INFO] Running command: blastn -query GCF_013389365.1_ASM1338936v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg383842df-b237-4464-a47c-d65126c06b45/dqc_reference/reference_markers_gtdb.fasta -out GCF_013389365.1_ASM1338936v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:27,391] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:27,396] [INFO] Selected 7 target genomes.
[2024-01-24 11:52:27,396] [INFO] Target genome list was writen to GCF_013389365.1_ASM1338936v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:27,402] [INFO] Task started: fastANI
[2024-01-24 11:52:27,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cd6e4fa-b087-4295-9875-9040a8c84015/GCF_013389365.1_ASM1338936v1_genomic.fna.gz --refList GCF_013389365.1_ASM1338936v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013389365.1_ASM1338936v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:35,344] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:35,358] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:35,358] [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_013389365.1	s__Desulfobacter latus	100.0	1337	1343	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003252055.1	s__Desulfobacter postgatei_B	86.3099	500	1343	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004319545.1	s__Desulfobacter hydrogenophilus	86.1818	822	1343	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000745975.1	s__Desulfobacter vibrioformis	85.698	700	1343	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	85.5375	759	1343	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	96.23	96.02	0.82	0.77	7	-
GCF_000373985.1	s__Desulfobacter curvatus	85.2266	776	1343	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	84.9974	350	1343	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 11:52:35,360] [INFO] GTDB search result was written to GCF_013389365.1_ASM1338936v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:35,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:35,364] [INFO] DFAST_QC result json was written to GCF_013389365.1_ASM1338936v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:35,364] [INFO] DFAST_QC completed!
[2024-01-24 11:52:35,364] [INFO] Total running time: 0h1m13s