[2024-01-24 11:59:12,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:12,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:12,804] [INFO] DQC Reference Directory: /var/lib/cwl/stga4bd84b9-fcbd-4e64-bc45-338c43503a33/dqc_reference
[2024-01-24 11:59:14,201] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,202] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,203] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c689824-220f-4604-9608-e7327762ad98/GCF_030268085.1_ASM3026808v1_genomic.fna.gz | prodigal -d GCF_030268085.1_ASM3026808v1_genomic.fna/cds.fna -a GCF_030268085.1_ASM3026808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:27,352] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:27,353] [INFO] Task started: HMMsearch
[2024-01-24 11:59:27,353] [INFO] Running command: hmmsearch --tblout GCF_030268085.1_ASM3026808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4bd84b9-fcbd-4e64-bc45-338c43503a33/dqc_reference/reference_markers.hmm GCF_030268085.1_ASM3026808v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:27,680] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:27,682] [INFO] Found 6/6 markers.
[2024-01-24 11:59:27,724] [INFO] Query marker FASTA was written to GCF_030268085.1_ASM3026808v1_genomic.fna/markers.fasta
[2024-01-24 11:59:27,725] [INFO] Task started: Blastn
[2024-01-24 11:59:27,725] [INFO] Running command: blastn -query GCF_030268085.1_ASM3026808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4bd84b9-fcbd-4e64-bc45-338c43503a33/dqc_reference/reference_markers.fasta -out GCF_030268085.1_ASM3026808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:28,539] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:28,544] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:28,545] [INFO] Target genome list was writen to GCF_030268085.1_ASM3026808v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:28,554] [INFO] Task started: fastANI
[2024-01-24 11:59:28,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c689824-220f-4604-9608-e7327762ad98/GCF_030268085.1_ASM3026808v1_genomic.fna.gz --refList GCF_030268085.1_ASM3026808v1_genomic.fna/target_genomes.txt --output GCF_030268085.1_ASM3026808v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:44,951] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:44,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4bd84b9-fcbd-4e64-bc45-338c43503a33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:44,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4bd84b9-fcbd-4e64-bc45-338c43503a33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:44,968] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:44,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:44,969] [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	83.9633	787	1400	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.2918	280	1400	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	75.9377	59	1400	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	75.3807	56	1400	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	75.3406	134	1400	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	75.2008	157	1400	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	75.1913	88	1400	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	75.1173	111	1400	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.0999	98	1400	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	75.0446	179	1400	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.0116	101	1400	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	74.9738	90	1400	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	74.945	93	1400	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	74.9255	81	1400	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:44,971] [INFO] DFAST Taxonomy check result was written to GCF_030268085.1_ASM3026808v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:44,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:44,972] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:44,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4bd84b9-fcbd-4e64-bc45-338c43503a33/dqc_reference/checkm_data
[2024-01-24 11:59:44,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:45,019] [INFO] Task started: CheckM
[2024-01-24 11:59:45,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030268085.1_ASM3026808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030268085.1_ASM3026808v1_genomic.fna/checkm_input GCF_030268085.1_ASM3026808v1_genomic.fna/checkm_result
[2024-01-24 12:00:27,084] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:27,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:27,107] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:27,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:27,108] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030268085.1_ASM3026808v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:27,108] [INFO] Task started: Blastn
[2024-01-24 12:00:27,108] [INFO] Running command: blastn -query GCF_030268085.1_ASM3026808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4bd84b9-fcbd-4e64-bc45-338c43503a33/dqc_reference/reference_markers_gtdb.fasta -out GCF_030268085.1_ASM3026808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:28,219] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:28,223] [INFO] Selected 10 target genomes.
[2024-01-24 12:00:28,224] [INFO] Target genome list was writen to GCF_030268085.1_ASM3026808v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:28,238] [INFO] Task started: fastANI
[2024-01-24 12:00:28,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c689824-220f-4604-9608-e7327762ad98/GCF_030268085.1_ASM3026808v1_genomic.fna.gz --refList GCF_030268085.1_ASM3026808v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030268085.1_ASM3026808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:36,590] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:36,599] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:36,599] [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_013390615.1	s__Geothrix sp013390615	84.8498	882	1400	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	84.4452	810	1400	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.39	97.91	0.89	0.88	4	-
GCA_003538615.1	s__Geothrix sp003538615	84.138	583	1400	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428885.1	s__Geothrix fermentans	83.9638	787	1400	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859995.1	s__Geothrix sp017859995	83.9532	724	1400	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	83.9064	925	1400	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.98	99.98	0.99	0.99	2	-
GCA_016721195.1	s__Geothrix sp016721195	83.6372	815	1400	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	82.9591	603	1400	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839205.1	s__Geothrix sp903839205	82.7028	632	1400	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913215.1	s__Geothrix sp903913215	82.0732	740	1400	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	98.58	97.99	0.90	0.83	29	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:36,601] [INFO] GTDB search result was written to GCF_030268085.1_ASM3026808v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:36,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:36,604] [INFO] DFAST_QC result json was written to GCF_030268085.1_ASM3026808v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:36,604] [INFO] DFAST_QC completed!
[2024-01-24 12:00:36,605] [INFO] Total running time: 0h1m24s