[2024-01-24 14:38:49,867] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:49,870] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:49,870] [INFO] DQC Reference Directory: /var/lib/cwl/stg9200fe2b-1a26-4c97-81b6-d8592c27b1f9/dqc_reference
[2024-01-24 14:38:52,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:52,374] [INFO] Task started: Prodigal
[2024-01-24 14:38:52,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b062c4a-00a2-4972-9b8d-6e6519cb33fd/GCF_017086445.1_ASM1708644v1_genomic.fna.gz | prodigal -d GCF_017086445.1_ASM1708644v1_genomic.fna/cds.fna -a GCF_017086445.1_ASM1708644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:02,077] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:02,077] [INFO] Task started: HMMsearch
[2024-01-24 14:39:02,077] [INFO] Running command: hmmsearch --tblout GCF_017086445.1_ASM1708644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9200fe2b-1a26-4c97-81b6-d8592c27b1f9/dqc_reference/reference_markers.hmm GCF_017086445.1_ASM1708644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:02,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:02,338] [INFO] Found 6/6 markers.
[2024-01-24 14:39:02,376] [INFO] Query marker FASTA was written to GCF_017086445.1_ASM1708644v1_genomic.fna/markers.fasta
[2024-01-24 14:39:02,376] [INFO] Task started: Blastn
[2024-01-24 14:39:02,376] [INFO] Running command: blastn -query GCF_017086445.1_ASM1708644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9200fe2b-1a26-4c97-81b6-d8592c27b1f9/dqc_reference/reference_markers.fasta -out GCF_017086445.1_ASM1708644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:03,455] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:03,458] [INFO] Selected 11 target genomes.
[2024-01-24 14:39:03,459] [INFO] Target genome list was writen to GCF_017086445.1_ASM1708644v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:03,493] [INFO] Task started: fastANI
[2024-01-24 14:39:03,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b062c4a-00a2-4972-9b8d-6e6519cb33fd/GCF_017086445.1_ASM1708644v1_genomic.fna.gz --refList GCF_017086445.1_ASM1708644v1_genomic.fna/target_genomes.txt --output GCF_017086445.1_ASM1708644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:13,390] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:13,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9200fe2b-1a26-4c97-81b6-d8592c27b1f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:13,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9200fe2b-1a26-4c97-81b6-d8592c27b1f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:13,404] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:13,405] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:13,405] [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
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	94.3152	876	1100	95	below_threshold
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	93.6358	866	1100	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	86.2108	794	1100	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	85.4441	801	1100	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	85.1857	750	1100	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	84.8468	755	1100	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	82.0476	593	1100	95	below_threshold
Brevundimonas goettingensis	strain=LVF2	GCA_017487405.1	2774190	2774190	type	True	81.6552	687	1100	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	79.1875	392	1100	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.3	419	1100	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.9566	133	1100	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:13,408] [INFO] DFAST Taxonomy check result was written to GCF_017086445.1_ASM1708644v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:13,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:13,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:13,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9200fe2b-1a26-4c97-81b6-d8592c27b1f9/dqc_reference/checkm_data
[2024-01-24 14:39:13,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:13,461] [INFO] Task started: CheckM
[2024-01-24 14:39:13,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017086445.1_ASM1708644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017086445.1_ASM1708644v1_genomic.fna/checkm_input GCF_017086445.1_ASM1708644v1_genomic.fna/checkm_result
[2024-01-24 14:39:44,899] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:44,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:44,929] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:44,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:44,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017086445.1_ASM1708644v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:44,930] [INFO] Task started: Blastn
[2024-01-24 14:39:44,930] [INFO] Running command: blastn -query GCF_017086445.1_ASM1708644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9200fe2b-1a26-4c97-81b6-d8592c27b1f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017086445.1_ASM1708644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:46,793] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:46,796] [INFO] Selected 8 target genomes.
[2024-01-24 14:39:46,796] [INFO] Target genome list was writen to GCF_017086445.1_ASM1708644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:46,804] [INFO] Task started: fastANI
[2024-01-24 14:39:46,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b062c4a-00a2-4972-9b8d-6e6519cb33fd/GCF_017086445.1_ASM1708644v1_genomic.fna.gz --refList GCF_017086445.1_ASM1708644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017086445.1_ASM1708644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:54,565] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:54,580] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:54,581] [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_017086445.1	s__Brevundimonas vesicularis_A	100.0	1097	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.13	95.13	0.83	0.83	2	conclusive
GCA_000335735.1	s__Brevundimonas sp000335735	94.815	861	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592205.1	s__Brevundimonas vesicularis	94.3152	876	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.70	95.00	0.85	0.82	10	-
GCF_005484585.1	s__Brevundimonas sp005484585	93.9087	872	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.32	95.32	0.86	0.86	2	-
GCF_000813765.1	s__Brevundimonas nasdae_A	93.6665	835	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.42	95.42	0.82	0.82	2	-
GCF_014204545.1	s__Brevundimonas vesicularis_B	93.6147	872	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064825.1	s__Brevundimonas mediterranea_A	86.4366	792	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	98.11	97.23	0.89	0.83	17	-
GCF_014196125.1	s__Brevundimonas mediterranea	86.2201	793	1100	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0657	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:54,582] [INFO] GTDB search result was written to GCF_017086445.1_ASM1708644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:54,583] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:54,586] [INFO] DFAST_QC result json was written to GCF_017086445.1_ASM1708644v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:54,586] [INFO] DFAST_QC completed!
[2024-01-24 14:39:54,586] [INFO] Total running time: 0h1m5s