[2024-01-24 13:50:24,993] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:24,994] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:24,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg92f96505-999c-48ff-b044-8a981b24e131/dqc_reference
[2024-01-24 13:50:26,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:26,236] [INFO] Task started: Prodigal
[2024-01-24 13:50:26,236] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa4a3e2d-bff0-4525-b906-22ad3ca22690/GCF_003934285.1_ASM393428v1_genomic.fna.gz | prodigal -d GCF_003934285.1_ASM393428v1_genomic.fna/cds.fna -a GCF_003934285.1_ASM393428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:33,449] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:33,450] [INFO] Task started: HMMsearch
[2024-01-24 13:50:33,450] [INFO] Running command: hmmsearch --tblout GCF_003934285.1_ASM393428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92f96505-999c-48ff-b044-8a981b24e131/dqc_reference/reference_markers.hmm GCF_003934285.1_ASM393428v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:33,683] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:33,684] [INFO] Found 6/6 markers.
[2024-01-24 13:50:33,711] [INFO] Query marker FASTA was written to GCF_003934285.1_ASM393428v1_genomic.fna/markers.fasta
[2024-01-24 13:50:33,712] [INFO] Task started: Blastn
[2024-01-24 13:50:33,712] [INFO] Running command: blastn -query GCF_003934285.1_ASM393428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92f96505-999c-48ff-b044-8a981b24e131/dqc_reference/reference_markers.fasta -out GCF_003934285.1_ASM393428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:34,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:34,689] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:34,690] [INFO] Target genome list was writen to GCF_003934285.1_ASM393428v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:34,692] [INFO] Task started: fastANI
[2024-01-24 13:50:34,692] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa4a3e2d-bff0-4525-b906-22ad3ca22690/GCF_003934285.1_ASM393428v1_genomic.fna.gz --refList GCF_003934285.1_ASM393428v1_genomic.fna/target_genomes.txt --output GCF_003934285.1_ASM393428v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:43,095] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:43,096] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92f96505-999c-48ff-b044-8a981b24e131/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:43,096] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92f96505-999c-48ff-b044-8a981b24e131/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:43,110] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:43,111] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:43,111] [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 fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	100.0	874	876	95	conclusive
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	82.2893	584	876	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	81.9397	550	876	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	81.8518	630	876	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	81.6925	588	876	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	81.556	564	876	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	81.1946	525	876	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	81.1392	572	876	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	80.7117	538	876	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	78.3334	306	876	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.0954	354	876	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	77.9956	312	876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:43,113] [INFO] DFAST Taxonomy check result was written to GCF_003934285.1_ASM393428v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:43,113] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:43,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:43,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92f96505-999c-48ff-b044-8a981b24e131/dqc_reference/checkm_data
[2024-01-24 13:50:43,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:43,142] [INFO] Task started: CheckM
[2024-01-24 13:50:43,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003934285.1_ASM393428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003934285.1_ASM393428v1_genomic.fna/checkm_input GCF_003934285.1_ASM393428v1_genomic.fna/checkm_result
[2024-01-24 13:51:17,920] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:17,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:17,940] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:17,941] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:17,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003934285.1_ASM393428v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:17,941] [INFO] Task started: Blastn
[2024-01-24 13:51:17,942] [INFO] Running command: blastn -query GCF_003934285.1_ASM393428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92f96505-999c-48ff-b044-8a981b24e131/dqc_reference/reference_markers_gtdb.fasta -out GCF_003934285.1_ASM393428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:19,756] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:19,760] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:19,761] [INFO] Target genome list was writen to GCF_003934285.1_ASM393428v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:19,789] [INFO] Task started: fastANI
[2024-01-24 13:51:19,789] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa4a3e2d-bff0-4525-b906-22ad3ca22690/GCF_003934285.1_ASM393428v1_genomic.fna.gz --refList GCF_003934285.1_ASM393428v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003934285.1_ASM393428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:30,047] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:30,062] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:30,062] [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_003934285.1	s__Brevundimonas fluminis	100.0	874	876	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_018820275.1	s__Brevundimonas sp018820275	88.1552	727	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.93	99.85	0.97	0.95	5	-
GCA_013912005.1	s__Brevundimonas sp013912005	82.3871	576	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116065.1	s__Brevundimonas viscosa	82.2733	586	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001794825.1	s__Brevundimonas sp001794825	82.1505	598	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425945.1	s__Brevundimonas sp001425945	81.7945	623	876	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	81.6866	571	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183935.1	s__Brevundimonas sp016183935	81.6094	567	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742215.1	s__Brevundimonas sp016742215	81.5581	430	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296955.1	s__Brevundimonas sp004296955	81.5196	579	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
GCF_006547065.1	s__Brevundimonas sp006547065	81.4127	570	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424025.1	s__Brevundimonas sp001424025	81.4124	559	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308115.1	s__Brevundimonas sp017308115	81.3944	520	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295975.1	s__Brevundimonas sp001295975	81.1643	517	876	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701445.1	s__Brevundimonas bacteroides	81.1044	575	876	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 13:51:30,064] [INFO] GTDB search result was written to GCF_003934285.1_ASM393428v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:30,064] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:30,068] [INFO] DFAST_QC result json was written to GCF_003934285.1_ASM393428v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:30,068] [INFO] DFAST_QC completed!
[2024-01-24 13:51:30,068] [INFO] Total running time: 0h1m5s