[2024-01-24 15:10:23,134] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:23,138] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:23,138] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d3d9d10-3381-4a53-b960-f963a9067c99/dqc_reference
[2024-01-24 15:10:24,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,641] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg14bc2937-d134-4ab5-89d9-80466a5f72c6/GCF_014201675.1_ASM1420167v1_genomic.fna.gz | prodigal -d GCF_014201675.1_ASM1420167v1_genomic.fna/cds.fna -a GCF_014201675.1_ASM1420167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:31,063] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:31,064] [INFO] Task started: HMMsearch
[2024-01-24 15:10:31,064] [INFO] Running command: hmmsearch --tblout GCF_014201675.1_ASM1420167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d3d9d10-3381-4a53-b960-f963a9067c99/dqc_reference/reference_markers.hmm GCF_014201675.1_ASM1420167v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:31,304] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:31,305] [INFO] Found 6/6 markers.
[2024-01-24 15:10:31,336] [INFO] Query marker FASTA was written to GCF_014201675.1_ASM1420167v1_genomic.fna/markers.fasta
[2024-01-24 15:10:31,336] [INFO] Task started: Blastn
[2024-01-24 15:10:31,337] [INFO] Running command: blastn -query GCF_014201675.1_ASM1420167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d3d9d10-3381-4a53-b960-f963a9067c99/dqc_reference/reference_markers.fasta -out GCF_014201675.1_ASM1420167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:32,085] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:32,088] [INFO] Selected 11 target genomes.
[2024-01-24 15:10:32,089] [INFO] Target genome list was writen to GCF_014201675.1_ASM1420167v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:32,106] [INFO] Task started: fastANI
[2024-01-24 15:10:32,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg14bc2937-d134-4ab5-89d9-80466a5f72c6/GCF_014201675.1_ASM1420167v1_genomic.fna.gz --refList GCF_014201675.1_ASM1420167v1_genomic.fna/target_genomes.txt --output GCF_014201675.1_ASM1420167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:39,914] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:39,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d3d9d10-3381-4a53-b960-f963a9067c99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:39,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d3d9d10-3381-4a53-b960-f963a9067c99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:39,925] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:10:39,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:39,925] [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
Oceanithermus desulfurans	strain=DSM 15757	GCA_014201675.1	227924	227924	type	True	100.0	800	801	95	conclusive
Oceanithermus desulfurans	strain=NBRC 100063	GCA_007991015.1	227924	227924	type	True	99.9788	783	801	95	conclusive
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	92.5898	706	801	95	below_threshold
Marinithermus hydrothermalis	strain=DSM 14884	GCA_000195335.1	186192	186192	type	True	77.7095	214	801	95	below_threshold
Calidithermus terrae	strain=DSM 26712	GCA_003574345.1	1408545	1408545	type	True	77.4631	302	801	95	below_threshold
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	76.2318	104	801	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	75.9412	125	801	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	75.8681	121	801	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	75.645	109	801	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	74.9077	144	801	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	74.8656	124	801	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:39,927] [INFO] DFAST Taxonomy check result was written to GCF_014201675.1_ASM1420167v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:39,927] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:39,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:39,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d3d9d10-3381-4a53-b960-f963a9067c99/dqc_reference/checkm_data
[2024-01-24 15:10:39,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:39,954] [INFO] Task started: CheckM
[2024-01-24 15:10:39,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201675.1_ASM1420167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201675.1_ASM1420167v1_genomic.fna/checkm_input GCF_014201675.1_ASM1420167v1_genomic.fna/checkm_result
[2024-01-24 15:11:02,967] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:02,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:02,986] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:02,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:02,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201675.1_ASM1420167v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:02,986] [INFO] Task started: Blastn
[2024-01-24 15:11:02,987] [INFO] Running command: blastn -query GCF_014201675.1_ASM1420167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d3d9d10-3381-4a53-b960-f963a9067c99/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201675.1_ASM1420167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:04,102] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:04,105] [INFO] Selected 9 target genomes.
[2024-01-24 15:11:04,105] [INFO] Target genome list was writen to GCF_014201675.1_ASM1420167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:04,114] [INFO] Task started: fastANI
[2024-01-24 15:11:04,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg14bc2937-d134-4ab5-89d9-80466a5f72c6/GCF_014201675.1_ASM1420167v1_genomic.fna.gz --refList GCF_014201675.1_ASM1420167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201675.1_ASM1420167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:09,588] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:09,598] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:09,598] [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_014201675.1	s__Oceanithermus desulfurans	100.0	800	801	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	97.68	96.67	0.93	0.89	5	conclusive
GCF_000183745.1	s__Oceanithermus profundus	92.5898	706	801	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330655.1	s__Oceanithermus profundus_A	88.7942	498	801	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494055.1	s__Oceanithermus sp015494055	87.2386	493	801	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	99.03	99.03	0.84	0.84	2	-
GCA_015493285.1	s__Oceanithermus sp015493285	81.9086	284	801	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490435.1	s__WFXV01 sp015490435	78.8053	262	801	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__WFXV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195335.1	s__Marinithermus hydrothermalis	77.756	210	801	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Marinithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201885.1	s__Deinococcus budaensis	75.8807	120	801	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	74.9039	145	801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:09,600] [INFO] GTDB search result was written to GCF_014201675.1_ASM1420167v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:09,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:09,604] [INFO] DFAST_QC result json was written to GCF_014201675.1_ASM1420167v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:09,604] [INFO] DFAST_QC completed!
[2024-01-24 15:11:09,604] [INFO] Total running time: 0h0m46s