[2023-06-28 15:54:00,096] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:54:00,098] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:54:00,098] [INFO] DQC Reference Directory: /var/lib/cwl/stg35845b9c-1b3c-4ce2-b51e-ee9532f2450d/dqc_reference
[2023-06-28 15:54:01,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:54:01,285] [INFO] Task started: Prodigal
[2023-06-28 15:54:01,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg7129062f-9b34-4a4b-9640-e231622f6d0b/GCA_020402585.1_ASM2040258v1_genomic.fna.gz | prodigal -d GCA_020402585.1_ASM2040258v1_genomic.fna/cds.fna -a GCA_020402585.1_ASM2040258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:54:07,874] [INFO] Task succeeded: Prodigal
[2023-06-28 15:54:07,874] [INFO] Task started: HMMsearch
[2023-06-28 15:54:07,874] [INFO] Running command: hmmsearch --tblout GCA_020402585.1_ASM2040258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35845b9c-1b3c-4ce2-b51e-ee9532f2450d/dqc_reference/reference_markers.hmm GCA_020402585.1_ASM2040258v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:54:08,071] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:54:08,072] [INFO] Found 6/6 markers.
[2023-06-28 15:54:08,098] [INFO] Query marker FASTA was written to GCA_020402585.1_ASM2040258v1_genomic.fna/markers.fasta
[2023-06-28 15:54:08,098] [INFO] Task started: Blastn
[2023-06-28 15:54:08,098] [INFO] Running command: blastn -query GCA_020402585.1_ASM2040258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35845b9c-1b3c-4ce2-b51e-ee9532f2450d/dqc_reference/reference_markers.fasta -out GCA_020402585.1_ASM2040258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:54:08,966] [INFO] Task succeeded: Blastn
[2023-06-28 15:54:08,970] [INFO] Selected 14 target genomes.
[2023-06-28 15:54:08,971] [INFO] Target genome list was writen to GCA_020402585.1_ASM2040258v1_genomic.fna/target_genomes.txt
[2023-06-28 15:54:08,971] [INFO] Task started: fastANI
[2023-06-28 15:54:08,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg7129062f-9b34-4a4b-9640-e231622f6d0b/GCA_020402585.1_ASM2040258v1_genomic.fna.gz --refList GCA_020402585.1_ASM2040258v1_genomic.fna/target_genomes.txt --output GCA_020402585.1_ASM2040258v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:54:20,455] [INFO] Task succeeded: fastANI
[2023-06-28 15:54:20,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35845b9c-1b3c-4ce2-b51e-ee9532f2450d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:54:20,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35845b9c-1b3c-4ce2-b51e-ee9532f2450d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:54:20,467] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:54:20,468] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 15:54:20,468] [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	88.302	752	882	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.8839	494	882	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.5573	458	882	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.5454	420	882	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	79.4805	423	882	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	79.3342	420	882	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.1253	402	882	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	78.8165	428	882	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	78.717	327	882	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	78.3882	365	882	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.3542	361	882	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	78.1374	368	882	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	77.7905	198	882	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.2335	183	882	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:54:20,472] [INFO] DFAST Taxonomy check result was written to GCA_020402585.1_ASM2040258v1_genomic.fna/tc_result.tsv
[2023-06-28 15:54:20,472] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:54:20,472] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:54:20,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35845b9c-1b3c-4ce2-b51e-ee9532f2450d/dqc_reference/checkm_data
[2023-06-28 15:54:20,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:54:20,504] [INFO] Task started: CheckM
[2023-06-28 15:54:20,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020402585.1_ASM2040258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020402585.1_ASM2040258v1_genomic.fna/checkm_input GCA_020402585.1_ASM2040258v1_genomic.fna/checkm_result
[2023-06-28 15:54:45,034] [INFO] Task succeeded: CheckM
[2023-06-28 15:54:45,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:54:45,054] [INFO] ===== Completeness check finished =====
[2023-06-28 15:54:45,054] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:54:45,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020402585.1_ASM2040258v1_genomic.fna/markers.fasta)
[2023-06-28 15:54:45,055] [INFO] Task started: Blastn
[2023-06-28 15:54:45,055] [INFO] Running command: blastn -query GCA_020402585.1_ASM2040258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35845b9c-1b3c-4ce2-b51e-ee9532f2450d/dqc_reference/reference_markers_gtdb.fasta -out GCA_020402585.1_ASM2040258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:54:46,608] [INFO] Task succeeded: Blastn
[2023-06-28 15:54:46,612] [INFO] Selected 15 target genomes.
[2023-06-28 15:54:46,612] [INFO] Target genome list was writen to GCA_020402585.1_ASM2040258v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:54:46,613] [INFO] Task started: fastANI
[2023-06-28 15:54:46,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg7129062f-9b34-4a4b-9640-e231622f6d0b/GCA_020402585.1_ASM2040258v1_genomic.fna.gz --refList GCA_020402585.1_ASM2040258v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020402585.1_ASM2040258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:54:57,880] [INFO] Task succeeded: fastANI
[2023-06-28 15:54:57,893] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 15:54:57,893] [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_003150835.1	s__Phenylobacterium parvum	88.2689	754	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842425.1	s__Phenylobacterium sp903842425	86.7561	535	882	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	84.8703	569	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.29	99.29	0.84	0.84	2	-
GCA_903912465.1	s__Phenylobacterium sp903912465	84.7737	551	882	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	79.5443	420	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_018001015.1	s__Phenylobacterium sp018001015	79.5233	440	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCA_002363865.1	s__Phenylobacterium sp002363865	79.3137	424	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.98	99.98	0.95	0.91	3	-
GCA_004799515.1	s__Phenylobacterium sp004799515	79.2675	411	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	78.7161	399	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467375.1	s__Caulobacter sp016467375	78.6277	305	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745545.1	s__Caulobacter henricii_C	78.4041	373	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.38	99.38	0.95	0.95	2	-
GCF_000712075.1	s__Caulobacter sp000712075	78.3502	404	882	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	78.1513	367	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144935.1	s__Caulobacter sp004144935	78.0906	293	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000733915.1	s__PMMR1 sp000733915	77.6314	232	882	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__PMMR1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:54:57,895] [INFO] GTDB search result was written to GCA_020402585.1_ASM2040258v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:54:57,896] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:54:57,900] [INFO] DFAST_QC result json was written to GCA_020402585.1_ASM2040258v1_genomic.fna/dqc_result.json
[2023-06-28 15:54:57,900] [INFO] DFAST_QC completed!
[2023-06-28 15:54:57,900] [INFO] Total running time: 0h0m58s