[2024-01-24 15:10:53,976] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:53,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:53,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg83217f23-5ef8-41e3-82f3-2e63e140ddcf/dqc_reference
[2024-01-24 15:10:56,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,634] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,634] [INFO] Running command: gunzip -c /var/lib/cwl/stg3912a8bf-cf07-4b75-b801-a6b1ed243e9a/GCF_030295385.1_ASM3029538v1_genomic.fna.gz | prodigal -d GCF_030295385.1_ASM3029538v1_genomic.fna/cds.fna -a GCF_030295385.1_ASM3029538v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:06,667] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:06,667] [INFO] Task started: HMMsearch
[2024-01-24 15:11:06,667] [INFO] Running command: hmmsearch --tblout GCF_030295385.1_ASM3029538v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83217f23-5ef8-41e3-82f3-2e63e140ddcf/dqc_reference/reference_markers.hmm GCF_030295385.1_ASM3029538v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:06,968] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:06,971] [INFO] Found 6/6 markers.
[2024-01-24 15:11:07,010] [INFO] Query marker FASTA was written to GCF_030295385.1_ASM3029538v1_genomic.fna/markers.fasta
[2024-01-24 15:11:07,011] [INFO] Task started: Blastn
[2024-01-24 15:11:07,011] [INFO] Running command: blastn -query GCF_030295385.1_ASM3029538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83217f23-5ef8-41e3-82f3-2e63e140ddcf/dqc_reference/reference_markers.fasta -out GCF_030295385.1_ASM3029538v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:07,764] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:07,768] [INFO] Selected 20 target genomes.
[2024-01-24 15:11:07,768] [INFO] Target genome list was writen to GCF_030295385.1_ASM3029538v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:07,810] [INFO] Task started: fastANI
[2024-01-24 15:11:07,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg3912a8bf-cf07-4b75-b801-a6b1ed243e9a/GCF_030295385.1_ASM3029538v1_genomic.fna.gz --refList GCF_030295385.1_ASM3029538v1_genomic.fna/target_genomes.txt --output GCF_030295385.1_ASM3029538v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:23,321] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:23,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83217f23-5ef8-41e3-82f3-2e63e140ddcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:23,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83217f23-5ef8-41e3-82f3-2e63e140ddcf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:23,336] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:11:23,336] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:11:23,336] [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
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	86.1047	799	1088	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.7943	261	1088	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	75.7285	92	1088	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	75.5578	70	1088	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	75.5169	50	1088	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	75.3945	142	1088	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.3898	98	1088	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	75.3796	92	1088	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.2585	130	1088	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.0142	131	1088	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	74.9476	69	1088	95	below_threshold
Streptomyces smyrnaeus	strain=DSM 42105	GCA_017676345.1	1387713	1387713	type	True	74.8163	76	1088	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	74.7705	67	1088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:23,338] [INFO] DFAST Taxonomy check result was written to GCF_030295385.1_ASM3029538v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:23,339] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:23,339] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:23,339] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83217f23-5ef8-41e3-82f3-2e63e140ddcf/dqc_reference/checkm_data
[2024-01-24 15:11:23,340] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:23,375] [INFO] Task started: CheckM
[2024-01-24 15:11:23,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030295385.1_ASM3029538v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030295385.1_ASM3029538v1_genomic.fna/checkm_input GCF_030295385.1_ASM3029538v1_genomic.fna/checkm_result
[2024-01-24 15:12:03,257] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:03,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:03,286] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:03,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:03,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030295385.1_ASM3029538v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:03,287] [INFO] Task started: Blastn
[2024-01-24 15:12:03,287] [INFO] Running command: blastn -query GCF_030295385.1_ASM3029538v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83217f23-5ef8-41e3-82f3-2e63e140ddcf/dqc_reference/reference_markers_gtdb.fasta -out GCF_030295385.1_ASM3029538v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:04,422] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:04,426] [INFO] Selected 12 target genomes.
[2024-01-24 15:12:04,426] [INFO] Target genome list was writen to GCF_030295385.1_ASM3029538v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:04,437] [INFO] Task started: fastANI
[2024-01-24 15:12:04,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg3912a8bf-cf07-4b75-b801-a6b1ed243e9a/GCF_030295385.1_ASM3029538v1_genomic.fna.gz --refList GCF_030295385.1_ASM3029538v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030295385.1_ASM3029538v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:13,979] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:13,990] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:12:13,990] [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_000428885.1	s__Geothrix fermentans	86.1179	798	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538615.1	s__Geothrix sp003538615	85.8853	613	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390615.1	s__Geothrix sp013390615	84.9038	830	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714685.1	s__Geothrix sp016714685	84.8624	789	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.39	97.91	0.89	0.88	4	-
GCA_017859995.1	s__Geothrix sp017859995	84.8023	718	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721195.1	s__Geothrix sp016721195	83.8202	798	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334395.1	s__Geothrix sp013334395	83.6932	599	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903863195.1	s__Geothrix sp903863195	83.2941	704	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.63	99.47	0.91	0.90	5	-
GCA_016195985.1	s__Geothrix sp016195985	83.2076	765	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.98	99.98	0.99	0.99	2	-
GCA_903839205.1	s__Geothrix sp903839205	83.0778	596	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884655.1	s__Geothrix sp903884655	82.6188	703	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.96	99.93	0.97	0.97	3	-
GCA_003158505.1	s__Geothrix sp003158505	82.4888	593	1088	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.60	99.60	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:13,992] [INFO] GTDB search result was written to GCF_030295385.1_ASM3029538v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:13,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:14,007] [INFO] DFAST_QC result json was written to GCF_030295385.1_ASM3029538v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:14,008] [INFO] DFAST_QC completed!
[2024-01-24 15:12:14,008] [INFO] Total running time: 0h1m20s