[2024-01-24 10:57:07,090] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,093] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,093] [INFO] DQC Reference Directory: /var/lib/cwl/stge4ca0325-d834-4e9c-b6f9-ecf55f39f1a3/dqc_reference
[2024-01-24 10:57:08,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,323] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,323] [INFO] Running command: gunzip -c /var/lib/cwl/stg364cff9b-2c99-4dfc-816d-d3dd2b4d29b9/GCF_022808775.1_ASM2280877v1_genomic.fna.gz | prodigal -d GCF_022808775.1_ASM2280877v1_genomic.fna/cds.fna -a GCF_022808775.1_ASM2280877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:18,457] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:18,458] [INFO] Task started: HMMsearch
[2024-01-24 10:57:18,458] [INFO] Running command: hmmsearch --tblout GCF_022808775.1_ASM2280877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4ca0325-d834-4e9c-b6f9-ecf55f39f1a3/dqc_reference/reference_markers.hmm GCF_022808775.1_ASM2280877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:18,707] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:18,708] [INFO] Found 6/6 markers.
[2024-01-24 10:57:18,739] [INFO] Query marker FASTA was written to GCF_022808775.1_ASM2280877v1_genomic.fna/markers.fasta
[2024-01-24 10:57:18,740] [INFO] Task started: Blastn
[2024-01-24 10:57:18,740] [INFO] Running command: blastn -query GCF_022808775.1_ASM2280877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4ca0325-d834-4e9c-b6f9-ecf55f39f1a3/dqc_reference/reference_markers.fasta -out GCF_022808775.1_ASM2280877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:19,455] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:19,461] [INFO] Selected 19 target genomes.
[2024-01-24 10:57:19,462] [INFO] Target genome list was writen to GCF_022808775.1_ASM2280877v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:19,481] [INFO] Task started: fastANI
[2024-01-24 10:57:19,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg364cff9b-2c99-4dfc-816d-d3dd2b4d29b9/GCF_022808775.1_ASM2280877v1_genomic.fna.gz --refList GCF_022808775.1_ASM2280877v1_genomic.fna/target_genomes.txt --output GCF_022808775.1_ASM2280877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:35,640] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:35,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4ca0325-d834-4e9c-b6f9-ecf55f39f1a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:35,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4ca0325-d834-4e9c-b6f9-ecf55f39f1a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:35,655] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:35,655] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:35,655] [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	88.9355	901	1136	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.6146	291	1136	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	75.6397	78	1136	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	75.5372	61	1136	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	75.4141	73	1136	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	75.3067	153	1136	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	75.3055	51	1136	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	75.2851	111	1136	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	75.2723	51	1136	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	75.2071	187	1136	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.1775	166	1136	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	74.8665	58	1136	95	below_threshold
Spongiactinospora rosea	strain=LHW63015	GCA_003315795.1	2248750	2248750	type	True	74.7753	122	1136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:35,657] [INFO] DFAST Taxonomy check result was written to GCF_022808775.1_ASM2280877v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:35,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:35,658] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:35,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4ca0325-d834-4e9c-b6f9-ecf55f39f1a3/dqc_reference/checkm_data
[2024-01-24 10:57:35,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:35,700] [INFO] Task started: CheckM
[2024-01-24 10:57:35,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022808775.1_ASM2280877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022808775.1_ASM2280877v1_genomic.fna/checkm_input GCF_022808775.1_ASM2280877v1_genomic.fna/checkm_result
[2024-01-24 10:58:11,594] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:11,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:11,617] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:11,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:11,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022808775.1_ASM2280877v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:11,619] [INFO] Task started: Blastn
[2024-01-24 10:58:11,619] [INFO] Running command: blastn -query GCF_022808775.1_ASM2280877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4ca0325-d834-4e9c-b6f9-ecf55f39f1a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_022808775.1_ASM2280877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:12,793] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:12,798] [INFO] Selected 11 target genomes.
[2024-01-24 10:58:12,798] [INFO] Target genome list was writen to GCF_022808775.1_ASM2280877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:12,808] [INFO] Task started: fastANI
[2024-01-24 10:58:12,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg364cff9b-2c99-4dfc-816d-d3dd2b4d29b9/GCF_022808775.1_ASM2280877v1_genomic.fna.gz --refList GCF_022808775.1_ASM2280877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022808775.1_ASM2280877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:22,022] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:22,034] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:58:22,035] [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	88.9355	901	1136	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	86.0694	589	1136	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	84.7588	804	1136	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	84.4285	765	1136	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.39	97.91	0.89	0.88	4	-
GCA_013334395.1	s__Geothrix sp013334395	83.777	578	1136	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	83.5273	781	1136	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195985.1	s__Geothrix sp016195985	83.0505	763	1136	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.98	99.98	0.99	0.99	2	-
GCA_903913215.1	s__Geothrix sp903913215	82.6763	690	1136	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.58	97.99	0.90	0.83	29	-
GCA_903884655.1	s__Geothrix sp903884655	82.3588	665	1136	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	82.0221	607	1136	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.60	99.60	0.90	0.90	2	-
GCA_903873655.1	s__Geothrix sp903873655	81.7596	560	1136	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.34	99.01	0.91	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:22,036] [INFO] GTDB search result was written to GCF_022808775.1_ASM2280877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:22,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:22,043] [INFO] DFAST_QC result json was written to GCF_022808775.1_ASM2280877v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:22,044] [INFO] DFAST_QC completed!
[2024-01-24 10:58:22,044] [INFO] Total running time: 0h1m15s