[2024-01-24 11:05:49,402] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg6eb364e4-4dd7-439b-8283-d0df9d97bdda/dqc_reference
[2024-01-24 11:05:51,281] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,281] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg454492bb-b8eb-401f-ac80-223b8bd25389/GCF_014218725.1_ASM1421872v1_genomic.fna.gz | prodigal -d GCF_014218725.1_ASM1421872v1_genomic.fna/cds.fna -a GCF_014218725.1_ASM1421872v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:59,423] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:59,423] [INFO] Task started: HMMsearch
[2024-01-24 11:05:59,423] [INFO] Running command: hmmsearch --tblout GCF_014218725.1_ASM1421872v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6eb364e4-4dd7-439b-8283-d0df9d97bdda/dqc_reference/reference_markers.hmm GCF_014218725.1_ASM1421872v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:59,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:59,607] [INFO] Found 6/6 markers.
[2024-01-24 11:05:59,632] [INFO] Query marker FASTA was written to GCF_014218725.1_ASM1421872v1_genomic.fna/markers.fasta
[2024-01-24 11:05:59,633] [INFO] Task started: Blastn
[2024-01-24 11:05:59,633] [INFO] Running command: blastn -query GCF_014218725.1_ASM1421872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6eb364e4-4dd7-439b-8283-d0df9d97bdda/dqc_reference/reference_markers.fasta -out GCF_014218725.1_ASM1421872v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:00,554] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:00,557] [INFO] Selected 11 target genomes.
[2024-01-24 11:06:00,557] [INFO] Target genome list was writen to GCF_014218725.1_ASM1421872v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:00,563] [INFO] Task started: fastANI
[2024-01-24 11:06:00,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg454492bb-b8eb-401f-ac80-223b8bd25389/GCF_014218725.1_ASM1421872v1_genomic.fna.gz --refList GCF_014218725.1_ASM1421872v1_genomic.fna/target_genomes.txt --output GCF_014218725.1_ASM1421872v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:09,479] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:09,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6eb364e4-4dd7-439b-8283-d0df9d97bdda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:09,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6eb364e4-4dd7-439b-8283-d0df9d97bdda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:09,490] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:09,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:09,490] [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
Brevundimonas huaxiensis	strain=090558	GCA_014218725.1	2725493	2725493	type	True	100.0	1037	1040	95	conclusive
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	93.9731	854	1040	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	86.1727	767	1040	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	85.3658	778	1040	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	85.3648	738	1040	95	below_threshold
Brevundimonas nasdae	strain=JCM 11415	GCA_016654005.1	172043	172043	type	True	85.3499	736	1040	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	82.1156	598	1040	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.8139	600	1040	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	80.496	538	1040	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	79.3825	391	1040	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.189	351	1040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:09,492] [INFO] DFAST Taxonomy check result was written to GCF_014218725.1_ASM1421872v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:09,492] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:09,493] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:09,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6eb364e4-4dd7-439b-8283-d0df9d97bdda/dqc_reference/checkm_data
[2024-01-24 11:06:09,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:09,526] [INFO] Task started: CheckM
[2024-01-24 11:06:09,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014218725.1_ASM1421872v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014218725.1_ASM1421872v1_genomic.fna/checkm_input GCF_014218725.1_ASM1421872v1_genomic.fna/checkm_result
[2024-01-24 11:06:36,801] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:36,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:36,825] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:36,826] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:36,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014218725.1_ASM1421872v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:36,826] [INFO] Task started: Blastn
[2024-01-24 11:06:36,826] [INFO] Running command: blastn -query GCF_014218725.1_ASM1421872v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6eb364e4-4dd7-439b-8283-d0df9d97bdda/dqc_reference/reference_markers_gtdb.fasta -out GCF_014218725.1_ASM1421872v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:38,562] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:38,565] [INFO] Selected 7 target genomes.
[2024-01-24 11:06:38,565] [INFO] Target genome list was writen to GCF_014218725.1_ASM1421872v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:38,570] [INFO] Task started: fastANI
[2024-01-24 11:06:38,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg454492bb-b8eb-401f-ac80-223b8bd25389/GCF_014218725.1_ASM1421872v1_genomic.fna.gz --refList GCF_014218725.1_ASM1421872v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014218725.1_ASM1421872v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:44,196] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:44,203] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:06:44,204] [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_000813765.1	s__Brevundimonas nasdae_A	95.4155	854	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.42	95.42	0.82	0.82	2	inconclusive
GCF_005484585.1	s__Brevundimonas sp005484585	95.1979	885	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.32	95.32	0.86	0.86	2	inconclusive
GCF_001592205.1	s__Brevundimonas vesicularis	93.9568	855	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.70	95.00	0.85	0.82	10	-
GCF_014204545.1	s__Brevundimonas vesicularis_B	93.8828	863	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000335735.1	s__Brevundimonas sp000335735	93.7278	822	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086445.1	s__Brevundimonas vesicularis_A	93.5264	872	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.13	95.13	0.83	0.83	2	-
GCF_002157625.1	s__Brevundimonas sp002157625	87.9389	780	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:44,205] [INFO] GTDB search result was written to GCF_014218725.1_ASM1421872v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:44,206] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:44,208] [INFO] DFAST_QC result json was written to GCF_014218725.1_ASM1421872v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:44,209] [INFO] DFAST_QC completed!
[2024-01-24 11:06:44,209] [INFO] Total running time: 0h0m55s