[2024-01-24 11:58:51,734] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:51,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:51,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg09abbb20-8c9b-488f-99af-9fd267b97078/dqc_reference
[2024-01-24 11:58:53,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:53,058] [INFO] Task started: Prodigal
[2024-01-24 11:58:53,058] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c16f8e1-8fba-4a53-9348-f30449bcf289/GCF_011761985.1_ASM1176198v1_genomic.fna.gz | prodigal -d GCF_011761985.1_ASM1176198v1_genomic.fna/cds.fna -a GCF_011761985.1_ASM1176198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:02,194] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:02,194] [INFO] Task started: HMMsearch
[2024-01-24 11:59:02,194] [INFO] Running command: hmmsearch --tblout GCF_011761985.1_ASM1176198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09abbb20-8c9b-488f-99af-9fd267b97078/dqc_reference/reference_markers.hmm GCF_011761985.1_ASM1176198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:02,466] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:02,467] [INFO] Found 6/6 markers.
[2024-01-24 11:59:02,500] [INFO] Query marker FASTA was written to GCF_011761985.1_ASM1176198v1_genomic.fna/markers.fasta
[2024-01-24 11:59:02,501] [INFO] Task started: Blastn
[2024-01-24 11:59:02,501] [INFO] Running command: blastn -query GCF_011761985.1_ASM1176198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09abbb20-8c9b-488f-99af-9fd267b97078/dqc_reference/reference_markers.fasta -out GCF_011761985.1_ASM1176198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:03,317] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:03,320] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:03,320] [INFO] Target genome list was writen to GCF_011761985.1_ASM1176198v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:03,353] [INFO] Task started: fastANI
[2024-01-24 11:59:03,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c16f8e1-8fba-4a53-9348-f30449bcf289/GCF_011761985.1_ASM1176198v1_genomic.fna.gz --refList GCF_011761985.1_ASM1176198v1_genomic.fna/target_genomes.txt --output GCF_011761985.1_ASM1176198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:11,318] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:11,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09abbb20-8c9b-488f-99af-9fd267b97078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:11,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09abbb20-8c9b-488f-99af-9fd267b97078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:11,330] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:11,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:11,330] [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 terrae	strain=DSM 17329	GCA_011761985.1	363631	363631	type	True	100.0	975	975	95	conclusive
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	82.9752	673	975	95	below_threshold
Brevundimonas pondensis	strain=LVF1	GCA_017487345.1	2774189	2774189	type	True	80.0886	527	975	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	80.0635	535	975	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	80.0276	514	975	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	79.9528	548	975	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	79.0487	379	975	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	78.8199	399	975	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	78.7122	354	975	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	78.6029	391	975	95	below_threshold
Brevundimonas halotolerans	strain=MCS24	GCA_003730275.1	69670	69670	type	True	78.5812	335	975	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	76.0993	64	975	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	75.9852	65	975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:11,332] [INFO] DFAST Taxonomy check result was written to GCF_011761985.1_ASM1176198v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:11,332] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:11,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:11,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09abbb20-8c9b-488f-99af-9fd267b97078/dqc_reference/checkm_data
[2024-01-24 11:59:11,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:11,362] [INFO] Task started: CheckM
[2024-01-24 11:59:11,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011761985.1_ASM1176198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011761985.1_ASM1176198v1_genomic.fna/checkm_input GCF_011761985.1_ASM1176198v1_genomic.fna/checkm_result
[2024-01-24 11:59:42,604] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:42,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:42,626] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:42,626] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:42,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011761985.1_ASM1176198v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:42,627] [INFO] Task started: Blastn
[2024-01-24 11:59:42,627] [INFO] Running command: blastn -query GCF_011761985.1_ASM1176198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09abbb20-8c9b-488f-99af-9fd267b97078/dqc_reference/reference_markers_gtdb.fasta -out GCF_011761985.1_ASM1176198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:44,061] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:44,064] [INFO] Selected 16 target genomes.
[2024-01-24 11:59:44,064] [INFO] Target genome list was writen to GCF_011761985.1_ASM1176198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:44,076] [INFO] Task started: fastANI
[2024-01-24 11:59:44,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c16f8e1-8fba-4a53-9348-f30449bcf289/GCF_011761985.1_ASM1176198v1_genomic.fna.gz --refList GCF_011761985.1_ASM1176198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011761985.1_ASM1176198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:53,744] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:53,757] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:53,757] [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_011761985.1	s__Brevundimonas terrae	100.0	975	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002432125.1	s__Brevundimonas sp002432125	83.4458	609	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002419815.1	s__Brevundimonas sp002419815	83.086	669	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013760785.1	s__Brevundimonas sp013760785	81.6748	564	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483865.1	s__Brevundimonas sp002483865	80.9384	352	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430835.1	s__Brevundimonas sp002430835	80.3016	474	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.55	99.55	0.86	0.86	2	-
GCF_003938605.1	s__Brevundimonas sp003938605	80.0931	542	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	96.78	96.68	0.85	0.83	3	-
GCF_900163625.1	s__Brevundimonas diminuta_A	80.0925	523	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627995.1	s__Brevundimonas naejangsanensis_B	80.0864	499	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017487345.1	s__Brevundimonas sp017487345	80.0856	527	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000635915.2	s__Brevundimonas naejangsanensis_A	80.0585	519	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.68	97.40	0.91	0.88	5	-
GCF_000204035.1	s__Brevundimonas diminuta	80.0532	536	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	97.62	95.74	0.88	0.81	19	-
GCF_014836405.1	s__Brevundimonas sp014836405	80.0325	514	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002484265.1	s__Brevundimonas sp002484265	78.9305	398	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.51	99.05	0.94	0.88	3	-
GCF_002157625.1	s__Brevundimonas sp002157625	78.8702	420	975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248925.1	s__Brevundimonas sp003248925	78.3569	310	975	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 11:59:53,759] [INFO] GTDB search result was written to GCF_011761985.1_ASM1176198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:53,760] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:53,764] [INFO] DFAST_QC result json was written to GCF_011761985.1_ASM1176198v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:53,764] [INFO] DFAST_QC completed!
[2024-01-24 11:59:53,764] [INFO] Total running time: 0h1m2s