[2024-01-24 12:36:21,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:21,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:21,183] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0149ed8-df62-4e25-b591-fdf86470de5b/dqc_reference
[2024-01-24 12:36:22,440] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:22,440] [INFO] Task started: Prodigal
[2024-01-24 12:36:22,441] [INFO] Running command: gunzip -c /var/lib/cwl/stg542cbe2a-58d5-431d-980d-48cb890d65db/GCF_014982725.1_ASM1498272v1_genomic.fna.gz | prodigal -d GCF_014982725.1_ASM1498272v1_genomic.fna/cds.fna -a GCF_014982725.1_ASM1498272v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:27,697] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:27,698] [INFO] Task started: HMMsearch
[2024-01-24 12:36:27,698] [INFO] Running command: hmmsearch --tblout GCF_014982725.1_ASM1498272v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0149ed8-df62-4e25-b591-fdf86470de5b/dqc_reference/reference_markers.hmm GCF_014982725.1_ASM1498272v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:27,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:27,901] [INFO] Found 6/6 markers.
[2024-01-24 12:36:27,921] [INFO] Query marker FASTA was written to GCF_014982725.1_ASM1498272v1_genomic.fna/markers.fasta
[2024-01-24 12:36:27,921] [INFO] Task started: Blastn
[2024-01-24 12:36:27,921] [INFO] Running command: blastn -query GCF_014982725.1_ASM1498272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0149ed8-df62-4e25-b591-fdf86470de5b/dqc_reference/reference_markers.fasta -out GCF_014982725.1_ASM1498272v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:28,744] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:28,747] [INFO] Selected 14 target genomes.
[2024-01-24 12:36:28,747] [INFO] Target genome list was writen to GCF_014982725.1_ASM1498272v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:28,806] [INFO] Task started: fastANI
[2024-01-24 12:36:28,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg542cbe2a-58d5-431d-980d-48cb890d65db/GCF_014982725.1_ASM1498272v1_genomic.fna.gz --refList GCF_014982725.1_ASM1498272v1_genomic.fna/target_genomes.txt --output GCF_014982725.1_ASM1498272v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:34,478] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:34,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0149ed8-df62-4e25-b591-fdf86470de5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:34,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0149ed8-df62-4e25-b591-fdf86470de5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:34,490] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:36:34,490] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:36:34,490] [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
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	86.5903	459	614	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	85.3717	445	614	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	82.2142	361	614	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	81.2485	291	614	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	80.4143	272	614	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	80.4075	272	614	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	80.0879	274	614	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.884	227	614	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.8766	237	614	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.8381	241	614	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.7697	253	614	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.6621	224	614	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.2707	207	614	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	78.9406	192	614	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:34,492] [INFO] DFAST Taxonomy check result was written to GCF_014982725.1_ASM1498272v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:34,493] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:34,493] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:34,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0149ed8-df62-4e25-b591-fdf86470de5b/dqc_reference/checkm_data
[2024-01-24 12:36:34,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:34,514] [INFO] Task started: CheckM
[2024-01-24 12:36:34,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014982725.1_ASM1498272v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014982725.1_ASM1498272v1_genomic.fna/checkm_input GCF_014982725.1_ASM1498272v1_genomic.fna/checkm_result
[2024-01-24 12:36:55,676] [INFO] Task succeeded: CheckM
[2024-01-24 12:36:55,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:36:55,698] [INFO] ===== Completeness check finished =====
[2024-01-24 12:36:55,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:36:55,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014982725.1_ASM1498272v1_genomic.fna/markers.fasta)
[2024-01-24 12:36:55,699] [INFO] Task started: Blastn
[2024-01-24 12:36:55,700] [INFO] Running command: blastn -query GCF_014982725.1_ASM1498272v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0149ed8-df62-4e25-b591-fdf86470de5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014982725.1_ASM1498272v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:57,209] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:57,214] [INFO] Selected 12 target genomes.
[2024-01-24 12:36:57,214] [INFO] Target genome list was writen to GCF_014982725.1_ASM1498272v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:36:57,234] [INFO] Task started: fastANI
[2024-01-24 12:36:57,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg542cbe2a-58d5-431d-980d-48cb890d65db/GCF_014982725.1_ASM1498272v1_genomic.fna.gz --refList GCF_014982725.1_ASM1498272v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014982725.1_ASM1498272v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:03,409] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:03,426] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:03,426] [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_014982725.1	s__Thermophilibacter sp014982725	100.0	614	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002159735.1	s__Thermophilibacter sp002159735	90.0082	496	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116265.1	s__Thermophilibacter stercoravium	88.9554	396	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305805.1	s__Thermophilibacter excrementavium	88.7454	457	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.86	97.86	0.86	0.86	2	-
GCF_016899935.1	s__Thermophilibacter uli_B	88.5273	485	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012027725.1	s__Thermophilibacter sp012027725	87.082	464	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159495.1	s__Thermophilibacter sp002159495	86.6251	458	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900775.1	s__Thermophilibacter uli_A	86.6198	468	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128445.1	s__Thermophilibacter provencensis	86.5432	459	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	96.98	96.17	0.87	0.80	3	-
GCF_002159625.1	s__Thermophilibacter avicola	86.228	447	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCF_002160255.1	s__Thermophilibacter avistercoris	85.9323	437	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.79	97.22	0.93	0.92	5	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	85.3524	446	614	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:03,428] [INFO] GTDB search result was written to GCF_014982725.1_ASM1498272v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:03,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:03,432] [INFO] DFAST_QC result json was written to GCF_014982725.1_ASM1498272v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:03,432] [INFO] DFAST_QC completed!
[2024-01-24 12:37:03,433] [INFO] Total running time: 0h0m42s