[2023-06-28 20:07:08,030] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:07:08,034] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:07:08,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg85d25cb3-b631-41ce-a8b8-d30e58be10ae/dqc_reference
[2023-06-28 20:07:09,446] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:07:09,447] [INFO] Task started: Prodigal
[2023-06-28 20:07:09,448] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6c728c8-b606-42e8-9c69-89a863a710bf/GCA_020402265.1_ASM2040226v1_genomic.fna.gz | prodigal -d GCA_020402265.1_ASM2040226v1_genomic.fna/cds.fna -a GCA_020402265.1_ASM2040226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:07:15,251] [INFO] Task succeeded: Prodigal
[2023-06-28 20:07:15,251] [INFO] Task started: HMMsearch
[2023-06-28 20:07:15,251] [INFO] Running command: hmmsearch --tblout GCA_020402265.1_ASM2040226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85d25cb3-b631-41ce-a8b8-d30e58be10ae/dqc_reference/reference_markers.hmm GCA_020402265.1_ASM2040226v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:07:15,512] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:07:15,514] [INFO] Found 6/6 markers.
[2023-06-28 20:07:15,562] [INFO] Query marker FASTA was written to GCA_020402265.1_ASM2040226v1_genomic.fna/markers.fasta
[2023-06-28 20:07:15,563] [INFO] Task started: Blastn
[2023-06-28 20:07:15,563] [INFO] Running command: blastn -query GCA_020402265.1_ASM2040226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85d25cb3-b631-41ce-a8b8-d30e58be10ae/dqc_reference/reference_markers.fasta -out GCA_020402265.1_ASM2040226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:07:16,333] [INFO] Task succeeded: Blastn
[2023-06-28 20:07:16,338] [INFO] Selected 13 target genomes.
[2023-06-28 20:07:16,339] [INFO] Target genome list was writen to GCA_020402265.1_ASM2040226v1_genomic.fna/target_genomes.txt
[2023-06-28 20:07:16,345] [INFO] Task started: fastANI
[2023-06-28 20:07:16,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6c728c8-b606-42e8-9c69-89a863a710bf/GCA_020402265.1_ASM2040226v1_genomic.fna.gz --refList GCA_020402265.1_ASM2040226v1_genomic.fna/target_genomes.txt --output GCA_020402265.1_ASM2040226v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:07:26,043] [INFO] Task succeeded: fastANI
[2023-06-28 20:07:26,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85d25cb3-b631-41ce-a8b8-d30e58be10ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:07:26,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85d25cb3-b631-41ce-a8b8-d30e58be10ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:07:26,059] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:07:26,059] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:07:26,059] [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
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	85.8172	612	740	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.7795	407	740	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	79.3759	361	740	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.3461	382	740	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.2543	354	740	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	79.0662	334	740	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	79.0037	362	740	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	78.8744	324	740	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	78.5779	263	740	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	78.4818	302	740	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	78.2075	250	740	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	78.1867	285	740	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	77.0943	151	740	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:07:26,062] [INFO] DFAST Taxonomy check result was written to GCA_020402265.1_ASM2040226v1_genomic.fna/tc_result.tsv
[2023-06-28 20:07:26,063] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:07:26,063] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:07:26,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85d25cb3-b631-41ce-a8b8-d30e58be10ae/dqc_reference/checkm_data
[2023-06-28 20:07:26,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:07:26,098] [INFO] Task started: CheckM
[2023-06-28 20:07:26,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020402265.1_ASM2040226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020402265.1_ASM2040226v1_genomic.fna/checkm_input GCA_020402265.1_ASM2040226v1_genomic.fna/checkm_result
[2023-06-28 20:07:49,525] [INFO] Task succeeded: CheckM
[2023-06-28 20:07:49,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:07:49,551] [INFO] ===== Completeness check finished =====
[2023-06-28 20:07:49,551] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:07:49,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020402265.1_ASM2040226v1_genomic.fna/markers.fasta)
[2023-06-28 20:07:49,552] [INFO] Task started: Blastn
[2023-06-28 20:07:49,552] [INFO] Running command: blastn -query GCA_020402265.1_ASM2040226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85d25cb3-b631-41ce-a8b8-d30e58be10ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_020402265.1_ASM2040226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:07:50,825] [INFO] Task succeeded: Blastn
[2023-06-28 20:07:50,829] [INFO] Selected 14 target genomes.
[2023-06-28 20:07:50,829] [INFO] Target genome list was writen to GCA_020402265.1_ASM2040226v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:07:50,836] [INFO] Task started: fastANI
[2023-06-28 20:07:50,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6c728c8-b606-42e8-9c69-89a863a710bf/GCA_020402265.1_ASM2040226v1_genomic.fna.gz --refList GCA_020402265.1_ASM2040226v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020402265.1_ASM2040226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:08:00,589] [INFO] Task succeeded: fastANI
[2023-06-28 20:08:00,602] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:08:00,602] [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_903842425.1	s__Phenylobacterium sp903842425	86.0103	482	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003150835.1	s__Phenylobacterium parvum	85.8355	611	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912465.1	s__Phenylobacterium sp903912465	83.8803	486	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903933475.1	s__Phenylobacterium sp903933475	83.6798	490	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.29	99.29	0.84	0.84	2	-
GCA_013911965.1	s__Phenylobacterium sp013911965	79.5118	357	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_018001015.1	s__Phenylobacterium sp018001015	79.3739	369	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCF_016772415.1	s__Phenylobacterium sp016772415	79.307	386	740	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	79.2536	354	740	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	79.1061	269	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	79.0979	340	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001824475.1	s__Phenylobacterium sp001824475	78.872	334	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	96.46	96.46	0.87	0.87	2	-
GCA_017418605.1	s__CAISGS01 sp017418605	78.5658	306	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931565.1	s__Caulobacter sp003931565	78.235	279	740	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	78.213	283	740	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:08:00,605] [INFO] GTDB search result was written to GCA_020402265.1_ASM2040226v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:08:00,605] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:08:00,610] [INFO] DFAST_QC result json was written to GCA_020402265.1_ASM2040226v1_genomic.fna/dqc_result.json
[2023-06-28 20:08:00,611] [INFO] DFAST_QC completed!
[2023-06-28 20:08:00,611] [INFO] Total running time: 0h0m53s