[2024-01-25 20:19:50,498] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:50,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:50,500] [INFO] DQC Reference Directory: /var/lib/cwl/stg24b95beb-f85b-42b8-b26b-90f06228443a/dqc_reference
[2024-01-25 20:19:51,669] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:51,670] [INFO] Task started: Prodigal
[2024-01-25 20:19:51,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg03dac9d2-be4f-4d46-8915-eda6d29efd67/GCF_030814835.1_ASM3081483v1_genomic.fna.gz | prodigal -d GCF_030814835.1_ASM3081483v1_genomic.fna/cds.fna -a GCF_030814835.1_ASM3081483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:03,067] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:03,068] [INFO] Task started: HMMsearch
[2024-01-25 20:20:03,068] [INFO] Running command: hmmsearch --tblout GCF_030814835.1_ASM3081483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24b95beb-f85b-42b8-b26b-90f06228443a/dqc_reference/reference_markers.hmm GCF_030814835.1_ASM3081483v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:03,336] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:03,337] [INFO] Found 6/6 markers.
[2024-01-25 20:20:03,381] [INFO] Query marker FASTA was written to GCF_030814835.1_ASM3081483v1_genomic.fna/markers.fasta
[2024-01-25 20:20:03,381] [INFO] Task started: Blastn
[2024-01-25 20:20:03,381] [INFO] Running command: blastn -query GCF_030814835.1_ASM3081483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b95beb-f85b-42b8-b26b-90f06228443a/dqc_reference/reference_markers.fasta -out GCF_030814835.1_ASM3081483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:04,301] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:04,303] [INFO] Selected 18 target genomes.
[2024-01-25 20:20:04,303] [INFO] Target genome list was writen to GCF_030814835.1_ASM3081483v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:04,316] [INFO] Task started: fastANI
[2024-01-25 20:20:04,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg03dac9d2-be4f-4d46-8915-eda6d29efd67/GCF_030814835.1_ASM3081483v1_genomic.fna.gz --refList GCF_030814835.1_ASM3081483v1_genomic.fna/target_genomes.txt --output GCF_030814835.1_ASM3081483v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:22,722] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:22,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24b95beb-f85b-42b8-b26b-90f06228443a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:22,723] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24b95beb-f85b-42b8-b26b-90f06228443a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:22,734] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:20:22,734] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:20:22,734] [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
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	80.2324	821	1593	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	80.0255	768	1593	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	79.967	784	1593	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	79.8108	748	1593	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	79.7587	782	1593	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	79.733	771	1593	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.6819	732	1593	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	79.6692	778	1593	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.6541	690	1593	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	79.4955	674	1593	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	79.4669	626	1593	95	below_threshold
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	79.4534	681	1593	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	79.4028	662	1593	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.3816	656	1593	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.5297	460	1593	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	78.5167	370	1593	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	78.0361	472	1593	95	below_threshold
Brevundimonas aveniformis	strain=DSM 17977	GCA_000428765.1	370977	370977	type	True	77.7149	266	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:22,737] [INFO] DFAST Taxonomy check result was written to GCF_030814835.1_ASM3081483v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:22,738] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:22,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:22,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24b95beb-f85b-42b8-b26b-90f06228443a/dqc_reference/checkm_data
[2024-01-25 20:20:22,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:22,784] [INFO] Task started: CheckM
[2024-01-25 20:20:22,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814835.1_ASM3081483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814835.1_ASM3081483v1_genomic.fna/checkm_input GCF_030814835.1_ASM3081483v1_genomic.fna/checkm_result
[2024-01-25 20:20:56,960] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:56,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:56,980] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:56,980] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:56,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814835.1_ASM3081483v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:56,981] [INFO] Task started: Blastn
[2024-01-25 20:20:56,981] [INFO] Running command: blastn -query GCF_030814835.1_ASM3081483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b95beb-f85b-42b8-b26b-90f06228443a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814835.1_ASM3081483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:58,869] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:58,872] [INFO] Selected 21 target genomes.
[2024-01-25 20:20:58,873] [INFO] Target genome list was writen to GCF_030814835.1_ASM3081483v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:58,902] [INFO] Task started: fastANI
[2024-01-25 20:20:58,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg03dac9d2-be4f-4d46-8915-eda6d29efd67/GCF_030814835.1_ASM3081483v1_genomic.fna.gz --refList GCF_030814835.1_ASM3081483v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814835.1_ASM3081483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:20,734] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:20,748] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:21:20,749] [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_016234625.1	s__Caulobacter sp016234625	81.3506	688	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144935.1	s__Caulobacter sp004144935	81.0236	628	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125585.1	s__Caulobacter sp016125585	80.7658	802	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905535.1	s__Caulobacter sp009905535	80.7385	791	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858185.1	s__Caulobacter sp903858185	80.3767	689	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.71	99.71	0.95	0.95	2	-
GCF_900114015.1	s__Caulobacter sp900114015	80.3564	772	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712075.1	s__Caulobacter sp000712075	80.2961	797	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467375.1	s__Caulobacter sp016467375	80.2472	605	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002749615.1	s__Caulobacter mirabilis	80.2369	824	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418605.1	s__CAISGS01 sp017418605	80.2258	678	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745545.1	s__Caulobacter henricii_C	80.2062	802	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.38	99.38	0.95	0.95	2	-
GCF_000019145.1	s__Caulobacter sp000019145	80.1621	767	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045195.1	s__Caulobacter soli	79.9238	792	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003094615.1	s__Caulobacter radicis	79.7538	756	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0713	96.08	96.08	0.90	0.90	2	-
GCF_016135805.1	s__Caulobacter hibisci	79.7396	786	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241335.1	s__Palsa-881 sp018241335	79.6785	657	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858865.1	s__Caulobacter vibrioides	79.4699	628	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.80	98.06	0.96	0.95	6	-
GCF_018135625.1	s__BOG-935 sp018135625	79.4694	686	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240795.1	s__Phenylobacterium sp018240795	79.3962	591	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	79.3817	656	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_017991675.1	s__Phenylobacterium sp017991675	79.328	494	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:20,750] [INFO] GTDB search result was written to GCF_030814835.1_ASM3081483v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:20,751] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:20,754] [INFO] DFAST_QC result json was written to GCF_030814835.1_ASM3081483v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:20,754] [INFO] DFAST_QC completed!
[2024-01-25 20:21:20,755] [INFO] Total running time: 0h1m30s