[2024-01-25 19:59:05,585] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:05,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:05,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg84ad978e-1a1c-4fe8-80d2-3d0738a7dc25/dqc_reference
[2024-01-25 19:59:06,748] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:06,749] [INFO] Task started: Prodigal
[2024-01-25 19:59:06,749] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b5275e6-3904-4d9b-90d0-9d945481370c/GCF_900455935.1_50624_C01_genomic.fna.gz | prodigal -d GCF_900455935.1_50624_C01_genomic.fna/cds.fna -a GCF_900455935.1_50624_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:19,761] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:19,761] [INFO] Task started: HMMsearch
[2024-01-25 19:59:19,761] [INFO] Running command: hmmsearch --tblout GCF_900455935.1_50624_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84ad978e-1a1c-4fe8-80d2-3d0738a7dc25/dqc_reference/reference_markers.hmm GCF_900455935.1_50624_C01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:20,109] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:20,110] [INFO] Found 6/6 markers.
[2024-01-25 19:59:20,158] [INFO] Query marker FASTA was written to GCF_900455935.1_50624_C01_genomic.fna/markers.fasta
[2024-01-25 19:59:20,158] [INFO] Task started: Blastn
[2024-01-25 19:59:20,158] [INFO] Running command: blastn -query GCF_900455935.1_50624_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg84ad978e-1a1c-4fe8-80d2-3d0738a7dc25/dqc_reference/reference_markers.fasta -out GCF_900455935.1_50624_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:21,027] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:21,030] [INFO] Selected 13 target genomes.
[2024-01-25 19:59:21,031] [INFO] Target genome list was writen to GCF_900455935.1_50624_C01_genomic.fna/target_genomes.txt
[2024-01-25 19:59:21,037] [INFO] Task started: fastANI
[2024-01-25 19:59:21,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b5275e6-3904-4d9b-90d0-9d945481370c/GCF_900455935.1_50624_C01_genomic.fna.gz --refList GCF_900455935.1_50624_C01_genomic.fna/target_genomes.txt --output GCF_900455935.1_50624_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:37,163] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:37,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84ad978e-1a1c-4fe8-80d2-3d0738a7dc25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:37,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84ad978e-1a1c-4fe8-80d2-3d0738a7dc25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:37,174] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:59:37,174] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:37,175] [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
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	100.0	1662	1665	95	conclusive
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	99.9162	1576	1665	95	conclusive
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	93.2651	1228	1665	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	92.9743	1318	1665	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	80.5666	687	1665	95	below_threshold
Roseomonas pecuniae	strain=DSM 25622	GCA_014199205.1	693023	693023	type	True	79.8243	715	1665	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	79.7718	789	1665	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	79.6778	699	1665	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	79.4104	718	1665	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	79.0857	584	1665	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.8154	467	1665	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.4492	539	1665	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.332	544	1665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:37,178] [INFO] DFAST Taxonomy check result was written to GCF_900455935.1_50624_C01_genomic.fna/tc_result.tsv
[2024-01-25 19:59:37,180] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:37,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:37,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84ad978e-1a1c-4fe8-80d2-3d0738a7dc25/dqc_reference/checkm_data
[2024-01-25 19:59:37,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:37,244] [INFO] Task started: CheckM
[2024-01-25 19:59:37,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900455935.1_50624_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900455935.1_50624_C01_genomic.fna/checkm_input GCF_900455935.1_50624_C01_genomic.fna/checkm_result
[2024-01-25 20:01:08,139] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:08,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:08,162] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:08,162] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:08,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900455935.1_50624_C01_genomic.fna/markers.fasta)
[2024-01-25 20:01:08,163] [INFO] Task started: Blastn
[2024-01-25 20:01:08,163] [INFO] Running command: blastn -query GCF_900455935.1_50624_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg84ad978e-1a1c-4fe8-80d2-3d0738a7dc25/dqc_reference/reference_markers_gtdb.fasta -out GCF_900455935.1_50624_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:09,911] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:09,916] [INFO] Selected 18 target genomes.
[2024-01-25 20:01:09,916] [INFO] Target genome list was writen to GCF_900455935.1_50624_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:09,934] [INFO] Task started: fastANI
[2024-01-25 20:01:09,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b5275e6-3904-4d9b-90d0-9d945481370c/GCF_900455935.1_50624_C01_genomic.fna.gz --refList GCF_900455935.1_50624_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900455935.1_50624_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:32,426] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:32,438] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:32,438] [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_000622225.1	s__Roseomonas mucosa	99.9162	1576	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.41	98.67	0.95	0.89	8	conclusive
GCF_001941945.1	s__Roseomonas gilardii	93.0524	1415	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	96.77	95.72	0.89	0.83	6	-
GCF_000164635.1	s__Roseomonas cervicalis	80.541	690	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631185.1	s__Roseomonas rhizosphaerae	80.4477	755	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490445.1	s__Roseomonas ludipueritiae	80.0759	680	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696345.1	s__Roseomonas sp003696345	79.8431	780	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014199205.1	s__Roseomonas pecuniae	79.8148	717	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141905.1	s__Roseomonas rosea	79.7138	724	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813395.1	s__Roseomonas sp017813395	79.614	667	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706185.1	s__Roseomonas sp902706185	79.4972	772	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490485.1	s__Roseomonas aerophila	79.1261	676	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711725.1	s__Roseomonas aerilata	79.1196	664	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	79.1019	582	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCF_018129005.1	s__Roseomonas_B eburnea	79.0198	638	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425365.1	s__Roseococcus flocculans	78.761	529	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775475.1	s__Belnapia sp016775475	78.4911	694	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805645.1	s__CADCTG01 sp902805645	78.224	459	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CADCTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241695.1	s__Hansschlegelia sp003241695	76.4413	207	1665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:32,439] [INFO] GTDB search result was written to GCF_900455935.1_50624_C01_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:32,440] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:32,443] [INFO] DFAST_QC result json was written to GCF_900455935.1_50624_C01_genomic.fna/dqc_result.json
[2024-01-25 20:01:32,443] [INFO] DFAST_QC completed!
[2024-01-25 20:01:32,443] [INFO] Total running time: 0h2m27s