[2024-01-24 12:21:44,675] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg19863489-95dd-48c1-a02c-81443f29014d/dqc_reference
[2024-01-24 12:21:46,062] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:46,062] [INFO] Task started: Prodigal
[2024-01-24 12:21:46,063] [INFO] Running command: gunzip -c /var/lib/cwl/stg90a987af-7071-4943-a0a2-1c277cf4b1c2/GCF_018476885.1_ASM1847688v1_genomic.fna.gz | prodigal -d GCF_018476885.1_ASM1847688v1_genomic.fna/cds.fna -a GCF_018476885.1_ASM1847688v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:59,182] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:59,182] [INFO] Task started: HMMsearch
[2024-01-24 12:21:59,182] [INFO] Running command: hmmsearch --tblout GCF_018476885.1_ASM1847688v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19863489-95dd-48c1-a02c-81443f29014d/dqc_reference/reference_markers.hmm GCF_018476885.1_ASM1847688v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:59,571] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:59,572] [INFO] Found 6/6 markers.
[2024-01-24 12:21:59,627] [INFO] Query marker FASTA was written to GCF_018476885.1_ASM1847688v1_genomic.fna/markers.fasta
[2024-01-24 12:21:59,628] [INFO] Task started: Blastn
[2024-01-24 12:21:59,628] [INFO] Running command: blastn -query GCF_018476885.1_ASM1847688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19863489-95dd-48c1-a02c-81443f29014d/dqc_reference/reference_markers.fasta -out GCF_018476885.1_ASM1847688v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:00,322] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:00,327] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:00,328] [INFO] Target genome list was writen to GCF_018476885.1_ASM1847688v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:00,334] [INFO] Task started: fastANI
[2024-01-24 12:22:00,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg90a987af-7071-4943-a0a2-1c277cf4b1c2/GCF_018476885.1_ASM1847688v1_genomic.fna.gz --refList GCF_018476885.1_ASM1847688v1_genomic.fna/target_genomes.txt --output GCF_018476885.1_ASM1847688v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:13,874] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:13,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19863489-95dd-48c1-a02c-81443f29014d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:13,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19863489-95dd-48c1-a02c-81443f29014d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:13,885] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:13,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:13,886] [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
Citrifermentans pelophilum	strain=DSM 12255	GCA_018476885.1	60036	60036	type	True	100.0	1464	1465	95	conclusive
Geobacter luticola	strain=JCM 17780	GCA_018476905.1	1114878	1114878	type	True	77.8401	187	1465	95	below_threshold
Geobacter argillaceus	strain=ATCC BAA-1139	GCA_007830735.1	345631	345631	type	True	77.647	237	1465	95	below_threshold
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	77.4659	119	1465	95	below_threshold
Geomonas limicola	strain=Red745	GCA_014193675.1	2740186	2740186	type	True	76.9559	146	1465	95	below_threshold
Geomonas silvestris	strain=Red330	GCA_014193515.1	2740184	2740184	type	True	76.9223	150	1465	95	below_threshold
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	76.9211	165	1465	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	76.8739	157	1465	95	below_threshold
Geomonas agri	strain=RG53	GCA_020179605.1	2873702	2873702	type	True	76.701	146	1465	95	below_threshold
Geotalea toluenoxydans	strain=JCM 15764	GCA_001311985.1	421624	421624	type	True	76.6929	117	1465	95	below_threshold
Geotalea daltonii	strain=FRC-32	GCA_000022265.1	1203471	1203471	type	True	76.4841	127	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:13,887] [INFO] DFAST Taxonomy check result was written to GCF_018476885.1_ASM1847688v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:13,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:13,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:13,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19863489-95dd-48c1-a02c-81443f29014d/dqc_reference/checkm_data
[2024-01-24 12:22:13,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:13,933] [INFO] Task started: CheckM
[2024-01-24 12:22:13,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018476885.1_ASM1847688v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018476885.1_ASM1847688v1_genomic.fna/checkm_input GCF_018476885.1_ASM1847688v1_genomic.fna/checkm_result
[2024-01-24 12:22:57,240] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:57,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:57,266] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:57,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:57,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018476885.1_ASM1847688v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:57,267] [INFO] Task started: Blastn
[2024-01-24 12:22:57,268] [INFO] Running command: blastn -query GCF_018476885.1_ASM1847688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19863489-95dd-48c1-a02c-81443f29014d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018476885.1_ASM1847688v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:58,198] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:58,201] [INFO] Selected 15 target genomes.
[2024-01-24 12:22:58,201] [INFO] Target genome list was writen to GCF_018476885.1_ASM1847688v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:58,241] [INFO] Task started: fastANI
[2024-01-24 12:22:58,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg90a987af-7071-4943-a0a2-1c277cf4b1c2/GCF_018476885.1_ASM1847688v1_genomic.fna.gz --refList GCF_018476885.1_ASM1847688v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018476885.1_ASM1847688v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:08,261] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:08,271] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:08,272] [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_018476885.1	s__Geoanaerobacter pelophilus	100.0	1464	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000813145.1	s__Geoanaerobacter sp000813145	80.9946	732	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223015.1	s__Geoanaerobacter sp016223015	78.8955	240	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018476905.1	s__Geomobilimonas luticola	77.8591	184	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomobilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009684525.1	s__Geoanaerobacter sp009684525	77.7907	323	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geoanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298925.1	s__Pelotalea sp002298925	77.7367	173	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712145.1	s__Geobacter sp003712145	77.5294	140	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339345.1	s__Geobacter sp905339345	76.9759	70	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380135.1	s__JACRCG01 sp014380135	76.8899	87	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574885.1	s__Geomobilimonas sp003574885	76.8771	149	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomobilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009668975.1	s__RPRC01 sp009668975	76.6243	75	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__RPRC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377095.1	s__Pseudopelobacter sp013377095	76.388	110	1465	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pseudopelobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:08,274] [INFO] GTDB search result was written to GCF_018476885.1_ASM1847688v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:08,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:08,278] [INFO] DFAST_QC result json was written to GCF_018476885.1_ASM1847688v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:08,278] [INFO] DFAST_QC completed!
[2024-01-24 12:23:08,278] [INFO] Total running time: 0h1m24s