[2024-01-24 13:22:17,623] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:17,625] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:17,625] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbf6b8dc-aa40-4df9-9f23-55c4f939716a/dqc_reference
[2024-01-24 13:22:18,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:18,962] [INFO] Task started: Prodigal
[2024-01-24 13:22:18,962] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfca4e6f-5e65-4f41-a567-55b8100d7269/GCF_002937115.1_ASM293711v1_genomic.fna.gz | prodigal -d GCF_002937115.1_ASM293711v1_genomic.fna/cds.fna -a GCF_002937115.1_ASM293711v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:41,370] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:41,371] [INFO] Task started: HMMsearch
[2024-01-24 13:22:41,371] [INFO] Running command: hmmsearch --tblout GCF_002937115.1_ASM293711v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbf6b8dc-aa40-4df9-9f23-55c4f939716a/dqc_reference/reference_markers.hmm GCF_002937115.1_ASM293711v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:41,844] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:41,845] [INFO] Found 6/6 markers.
[2024-01-24 13:22:41,908] [INFO] Query marker FASTA was written to GCF_002937115.1_ASM293711v1_genomic.fna/markers.fasta
[2024-01-24 13:22:41,909] [INFO] Task started: Blastn
[2024-01-24 13:22:41,909] [INFO] Running command: blastn -query GCF_002937115.1_ASM293711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbf6b8dc-aa40-4df9-9f23-55c4f939716a/dqc_reference/reference_markers.fasta -out GCF_002937115.1_ASM293711v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:42,940] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:42,943] [INFO] Selected 18 target genomes.
[2024-01-24 13:22:42,944] [INFO] Target genome list was writen to GCF_002937115.1_ASM293711v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:42,954] [INFO] Task started: fastANI
[2024-01-24 13:22:42,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfca4e6f-5e65-4f41-a567-55b8100d7269/GCF_002937115.1_ASM293711v1_genomic.fna.gz --refList GCF_002937115.1_ASM293711v1_genomic.fna/target_genomes.txt --output GCF_002937115.1_ASM293711v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:07,887] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:07,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbf6b8dc-aa40-4df9-9f23-55c4f939716a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:07,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbf6b8dc-aa40-4df9-9f23-55c4f939716a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:07,903] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:07,904] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:07,904] [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
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	100.0	2257	2272	95	conclusive
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.3775	366	2272	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	78.2187	677	2272	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.4936	449	2272	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	77.3253	316	2272	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	77.2524	308	2272	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.2411	502	2272	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	77.2155	472	2272	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	77.203	447	2272	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	77.0841	439	2272	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	77.0502	533	2272	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	77.0137	346	2272	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.0047	357	2272	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	76.9365	398	2272	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	76.8807	492	2272	95	below_threshold
Roseomonas rosea	strain=DSM 14916	GCA_900141905.1	198092	198092	type	True	76.8339	367	2272	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.3166	312	2272	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.1921	512	2272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:07,906] [INFO] DFAST Taxonomy check result was written to GCF_002937115.1_ASM293711v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:07,906] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:07,906] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:07,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbf6b8dc-aa40-4df9-9f23-55c4f939716a/dqc_reference/checkm_data
[2024-01-24 13:23:07,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:07,978] [INFO] Task started: CheckM
[2024-01-24 13:23:07,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002937115.1_ASM293711v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002937115.1_ASM293711v1_genomic.fna/checkm_input GCF_002937115.1_ASM293711v1_genomic.fna/checkm_result
[2024-01-24 13:24:09,927] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:09,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:09,952] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:09,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:09,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002937115.1_ASM293711v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:09,953] [INFO] Task started: Blastn
[2024-01-24 13:24:09,953] [INFO] Running command: blastn -query GCF_002937115.1_ASM293711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbf6b8dc-aa40-4df9-9f23-55c4f939716a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002937115.1_ASM293711v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:11,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:11,767] [INFO] Selected 9 target genomes.
[2024-01-24 13:24:11,767] [INFO] Target genome list was writen to GCF_002937115.1_ASM293711v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:11,784] [INFO] Task started: fastANI
[2024-01-24 13:24:11,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfca4e6f-5e65-4f41-a567-55b8100d7269/GCF_002937115.1_ASM293711v1_genomic.fna.gz --refList GCF_002937115.1_ASM293711v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002937115.1_ASM293711v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:28,916] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:28,934] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:28,935] [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_002937115.1	s__Rhodopila globiformis	100.0	2257	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903944925.1	s__Rhodopila sp903944925	81.295	1068	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.96	99.95	0.97	0.97	3	-
GCA_903915725.1	s__Rhodopila sp903915725	81.2183	1069	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	100.00	100.00	0.99	0.99	3	-
GCA_903851415.1	s__Rhodopila sp903851415	81.1142	1075	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	99.89	99.89	0.92	0.92	2	-
GCF_009765975.1	s__Rhodopila sp009765975	79.5647	890	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	79.4921	726	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506895.1	s__Rhodopila sp003506895	79.1545	744	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898425.1	s__69-11 sp001898425	78.9476	795	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	99.84	99.84	0.96	0.96	2	-
GCA_001899585.1	s__70-18 sp001899585	78.3845	676	2272	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:28,937] [INFO] GTDB search result was written to GCF_002937115.1_ASM293711v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:28,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:28,943] [INFO] DFAST_QC result json was written to GCF_002937115.1_ASM293711v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:28,943] [INFO] DFAST_QC completed!
[2024-01-24 13:24:28,943] [INFO] Total running time: 0h2m11s