[2023-06-30 16:40:13,335] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:40:13,338] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:40:13,338] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c608a88-8bed-45c8-a89e-f09555448589/dqc_reference
[2023-06-30 16:40:14,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:40:14,702] [INFO] Task started: Prodigal
[2023-06-30 16:40:14,703] [INFO] Running command: gunzip -c /var/lib/cwl/stg29fdc813-372f-44c6-9fc3-fe9ac5964bd8/GCA_025936775.1_ASM2593677v1_genomic.fna.gz | prodigal -d GCA_025936775.1_ASM2593677v1_genomic.fna/cds.fna -a GCA_025936775.1_ASM2593677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:40:30,626] [INFO] Task succeeded: Prodigal
[2023-06-30 16:40:30,627] [INFO] Task started: HMMsearch
[2023-06-30 16:40:30,627] [INFO] Running command: hmmsearch --tblout GCA_025936775.1_ASM2593677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c608a88-8bed-45c8-a89e-f09555448589/dqc_reference/reference_markers.hmm GCA_025936775.1_ASM2593677v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:40:30,863] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:40:30,865] [INFO] Found 6/6 markers.
[2023-06-30 16:40:30,905] [INFO] Query marker FASTA was written to GCA_025936775.1_ASM2593677v1_genomic.fna/markers.fasta
[2023-06-30 16:40:30,906] [INFO] Task started: Blastn
[2023-06-30 16:40:30,906] [INFO] Running command: blastn -query GCA_025936775.1_ASM2593677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c608a88-8bed-45c8-a89e-f09555448589/dqc_reference/reference_markers.fasta -out GCA_025936775.1_ASM2593677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:40:31,538] [INFO] Task succeeded: Blastn
[2023-06-30 16:40:31,543] [INFO] Selected 16 target genomes.
[2023-06-30 16:40:31,543] [INFO] Target genome list was writen to GCA_025936775.1_ASM2593677v1_genomic.fna/target_genomes.txt
[2023-06-30 16:40:31,548] [INFO] Task started: fastANI
[2023-06-30 16:40:31,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg29fdc813-372f-44c6-9fc3-fe9ac5964bd8/GCA_025936775.1_ASM2593677v1_genomic.fna.gz --refList GCA_025936775.1_ASM2593677v1_genomic.fna/target_genomes.txt --output GCA_025936775.1_ASM2593677v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:40:44,275] [INFO] Task succeeded: fastANI
[2023-06-30 16:40:44,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c608a88-8bed-45c8-a89e-f09555448589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:40:44,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c608a88-8bed-45c8-a89e-f09555448589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:40:44,284] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:40:44,285] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:40:44,285] [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
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	75.511	52	838	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	75.4895	52	838	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:40:44,287] [INFO] DFAST Taxonomy check result was written to GCA_025936775.1_ASM2593677v1_genomic.fna/tc_result.tsv
[2023-06-30 16:40:44,288] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:40:44,288] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:40:44,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c608a88-8bed-45c8-a89e-f09555448589/dqc_reference/checkm_data
[2023-06-30 16:40:44,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:40:44,320] [INFO] Task started: CheckM
[2023-06-30 16:40:44,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025936775.1_ASM2593677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025936775.1_ASM2593677v1_genomic.fna/checkm_input GCA_025936775.1_ASM2593677v1_genomic.fna/checkm_result
[2023-06-30 16:41:30,899] [INFO] Task succeeded: CheckM
[2023-06-30 16:41:30,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:41:30,922] [INFO] ===== Completeness check finished =====
[2023-06-30 16:41:30,922] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:41:30,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025936775.1_ASM2593677v1_genomic.fna/markers.fasta)
[2023-06-30 16:41:30,923] [INFO] Task started: Blastn
[2023-06-30 16:41:30,923] [INFO] Running command: blastn -query GCA_025936775.1_ASM2593677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c608a88-8bed-45c8-a89e-f09555448589/dqc_reference/reference_markers_gtdb.fasta -out GCA_025936775.1_ASM2593677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:41:31,873] [INFO] Task succeeded: Blastn
[2023-06-30 16:41:31,878] [INFO] Selected 16 target genomes.
[2023-06-30 16:41:31,878] [INFO] Target genome list was writen to GCA_025936775.1_ASM2593677v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:41:31,899] [INFO] Task started: fastANI
[2023-06-30 16:41:31,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg29fdc813-372f-44c6-9fc3-fe9ac5964bd8/GCA_025936775.1_ASM2593677v1_genomic.fna.gz --refList GCA_025936775.1_ASM2593677v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025936775.1_ASM2593677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:41:41,415] [INFO] Task succeeded: fastANI
[2023-06-30 16:41:41,433] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 16:41:41,433] [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
GCA_003169975.1	s__Palsa-1392 sp003169975	78.1296	345	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Palsa-1392	95.0	99.97	99.95	0.98	0.97	5	-
GCA_013815325.1	s__Palsa-1392 sp013815325	77.6634	274	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Palsa-1392	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695925.1	s__Palsa-1392 sp013695925	77.6271	247	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Palsa-1392	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821455.1	s__Palsa-1392 sp013821455	77.2652	246	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Palsa-1392	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167555.1	s__AV80 sp003167555	77.1137	165	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV80	95.0	97.13	95.66	0.86	0.82	7	-
GCA_003218375.1	s__AV80 sp003218375	76.8752	152	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV80	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003219225.1	s__AV17 sp003219225	76.71	71	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134765.1	s__AV80 sp003134765	76.7096	122	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV80	95.0	99.94	99.85	0.97	0.93	5	-
GCA_902810735.1	s__CADDYX01 sp902810735	76.5662	143	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__CADDYX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003219265.1	s__AV133 sp003219265	76.3939	78	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV133	95.0	97.95	97.38	0.79	0.78	3	-
GCA_003220055.1	s__AV40 sp003220055	76.3828	67	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV40	95.0	99.18	99.18	0.84	0.84	2	-
GCA_019244415.1	s__AV69 sp019244415	76.3284	90	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__AV69	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694595.1	s__JACCTI01 sp013694595	76.0744	113	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__JACCTI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003218475.1	s__Udaeobacter sp003218475	75.9449	65	838	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA10450;g__Udaeobacter	95.0	99.60	99.60	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-30 16:41:41,435] [INFO] GTDB search result was written to GCA_025936775.1_ASM2593677v1_genomic.fna/result_gtdb.tsv
[2023-06-30 16:41:41,436] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:41:41,439] [INFO] DFAST_QC result json was written to GCA_025936775.1_ASM2593677v1_genomic.fna/dqc_result.json
[2023-06-30 16:41:41,439] [INFO] DFAST_QC completed!
[2023-06-30 16:41:41,440] [INFO] Total running time: 0h1m28s