[2024-01-25 18:14:50,557] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:50,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:50,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d2cfc97-2215-460b-a6f8-0e617edf1d65/dqc_reference
[2024-01-25 18:14:51,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:51,743] [INFO] Task started: Prodigal
[2024-01-25 18:14:51,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg336a5897-6339-40dc-a673-8e083d2828ff/GCF_000373985.1_ASM37398v1_genomic.fna.gz | prodigal -d GCF_000373985.1_ASM37398v1_genomic.fna/cds.fna -a GCF_000373985.1_ASM37398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:05,005] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:05,005] [INFO] Task started: HMMsearch
[2024-01-25 18:15:05,005] [INFO] Running command: hmmsearch --tblout GCF_000373985.1_ASM37398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d2cfc97-2215-460b-a6f8-0e617edf1d65/dqc_reference/reference_markers.hmm GCF_000373985.1_ASM37398v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:05,327] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:05,330] [INFO] Found 6/6 markers.
[2024-01-25 18:15:05,375] [INFO] Query marker FASTA was written to GCF_000373985.1_ASM37398v1_genomic.fna/markers.fasta
[2024-01-25 18:15:05,375] [INFO] Task started: Blastn
[2024-01-25 18:15:05,375] [INFO] Running command: blastn -query GCF_000373985.1_ASM37398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d2cfc97-2215-460b-a6f8-0e617edf1d65/dqc_reference/reference_markers.fasta -out GCF_000373985.1_ASM37398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:05,936] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:05,939] [INFO] Selected 12 target genomes.
[2024-01-25 18:15:05,940] [INFO] Target genome list was writen to GCF_000373985.1_ASM37398v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:05,945] [INFO] Task started: fastANI
[2024-01-25 18:15:05,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg336a5897-6339-40dc-a673-8e083d2828ff/GCF_000373985.1_ASM37398v1_genomic.fna.gz --refList GCF_000373985.1_ASM37398v1_genomic.fna/target_genomes.txt --output GCF_000373985.1_ASM37398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:17,475] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:17,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d2cfc97-2215-460b-a6f8-0e617edf1d65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:17,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d2cfc97-2215-460b-a6f8-0e617edf1d65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:17,482] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:17,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:17,482] [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 curvatus	strain=DSM 3379	GCA_000373985.1	2290	2290	type	True	100.0	1746	1756	95	conclusive
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_003261095.1	2291	2291	type	True	86.9836	1030	1756	95	below_threshold
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_010499545.1	2291	2291	type	True	86.975	1027	1756	95	below_threshold
Desulfobacter hydrogenophilus	strain=AcRS1	GCA_004319545.1	2291	2291	type	True	86.8786	1053	1756	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	85.8635	942	1756	95	below_threshold
Desulfobacter postgatei	strain=2ac9	GCA_000233695.3	2293	2293	type	True	85.7427	894	1756	95	below_threshold
Desulfobacter latus	strain=AcRS2	GCA_013389365.1	2292	2292	type	True	85.2547	775	1756	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:17,483] [INFO] DFAST Taxonomy check result was written to GCF_000373985.1_ASM37398v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:17,484] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:17,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:17,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d2cfc97-2215-460b-a6f8-0e617edf1d65/dqc_reference/checkm_data
[2024-01-25 18:15:17,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:17,540] [INFO] Task started: CheckM
[2024-01-25 18:15:17,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000373985.1_ASM37398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000373985.1_ASM37398v1_genomic.fna/checkm_input GCF_000373985.1_ASM37398v1_genomic.fna/checkm_result
[2024-01-25 18:15:59,654] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:59,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:59,682] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:59,682] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:59,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000373985.1_ASM37398v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:59,683] [INFO] Task started: Blastn
[2024-01-25 18:15:59,683] [INFO] Running command: blastn -query GCF_000373985.1_ASM37398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d2cfc97-2215-460b-a6f8-0e617edf1d65/dqc_reference/reference_markers_gtdb.fasta -out GCF_000373985.1_ASM37398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:00,502] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:00,505] [INFO] Selected 6 target genomes.
[2024-01-25 18:16:00,505] [INFO] Target genome list was writen to GCF_000373985.1_ASM37398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:00,508] [INFO] Task started: fastANI
[2024-01-25 18:16:00,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg336a5897-6339-40dc-a673-8e083d2828ff/GCF_000373985.1_ASM37398v1_genomic.fna.gz --refList GCF_000373985.1_ASM37398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000373985.1_ASM37398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:08,207] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:08,212] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:08,212] [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_000373985.1	s__Desulfobacter curvatus	100.0	1746	1756	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004319545.1	s__Desulfobacter hydrogenophilus	86.8651	1054	1756	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	99.99	99.99	1.00	1.00	3	-
GCA_003252055.1	s__Desulfobacter postgatei_B	86.5968	584	1756	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	85.8458	945	1756	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	85.7605	892	1756	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	85.251	776	1756	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:08,214] [INFO] GTDB search result was written to GCF_000373985.1_ASM37398v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:08,214] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:08,216] [INFO] DFAST_QC result json was written to GCF_000373985.1_ASM37398v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:08,216] [INFO] DFAST_QC completed!
[2024-01-25 18:16:08,217] [INFO] Total running time: 0h1m18s