[2023-07-01 06:19:07,972] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:19:07,989] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:19:07,990] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3f393a9-2e26-4fb7-99ea-d9fe8fd3b544/dqc_reference
[2023-07-01 06:19:09,582] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:19:09,583] [INFO] Task started: Prodigal
[2023-07-01 06:19:09,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg8385bd05-c0c4-4aab-8eac-dcb03ed7c36e/GCA_024508875.1_ASM2450887v1_genomic.fna.gz | prodigal -d GCA_024508875.1_ASM2450887v1_genomic.fna/cds.fna -a GCA_024508875.1_ASM2450887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:19:21,110] [INFO] Task succeeded: Prodigal
[2023-07-01 06:19:21,110] [INFO] Task started: HMMsearch
[2023-07-01 06:19:21,111] [INFO] Running command: hmmsearch --tblout GCA_024508875.1_ASM2450887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3f393a9-2e26-4fb7-99ea-d9fe8fd3b544/dqc_reference/reference_markers.hmm GCA_024508875.1_ASM2450887v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:19:21,398] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:19:21,400] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8385bd05-c0c4-4aab-8eac-dcb03ed7c36e/GCA_024508875.1_ASM2450887v1_genomic.fna.gz]
[2023-07-01 06:19:21,455] [INFO] Query marker FASTA was written to GCA_024508875.1_ASM2450887v1_genomic.fna/markers.fasta
[2023-07-01 06:19:21,456] [INFO] Task started: Blastn
[2023-07-01 06:19:21,456] [INFO] Running command: blastn -query GCA_024508875.1_ASM2450887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f393a9-2e26-4fb7-99ea-d9fe8fd3b544/dqc_reference/reference_markers.fasta -out GCA_024508875.1_ASM2450887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:19:24,013] [INFO] Task succeeded: Blastn
[2023-07-01 06:19:24,035] [INFO] Selected 12 target genomes.
[2023-07-01 06:19:24,035] [INFO] Target genome list was writen to GCA_024508875.1_ASM2450887v1_genomic.fna/target_genomes.txt
[2023-07-01 06:19:24,040] [INFO] Task started: fastANI
[2023-07-01 06:19:24,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg8385bd05-c0c4-4aab-8eac-dcb03ed7c36e/GCA_024508875.1_ASM2450887v1_genomic.fna.gz --refList GCA_024508875.1_ASM2450887v1_genomic.fna/target_genomes.txt --output GCA_024508875.1_ASM2450887v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:19:34,723] [INFO] Task succeeded: fastANI
[2023-07-01 06:19:34,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3f393a9-2e26-4fb7-99ea-d9fe8fd3b544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:19:34,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3f393a9-2e26-4fb7-99ea-d9fe8fd3b544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:19:34,742] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:19:34,742] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 06:19:34,743] [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 kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	82.6956	856	1410	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	81.8835	764	1410	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	81.0422	660	1410	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.9183	665	1410	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	79.5934	520	1410	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.4487	583	1410	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.3946	656	1410	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	78.8649	536	1410	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.5676	551	1410	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	77.8149	342	1410	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	77.6711	346	1410	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.774	221	1410	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 06:19:34,745] [INFO] DFAST Taxonomy check result was written to GCA_024508875.1_ASM2450887v1_genomic.fna/tc_result.tsv
[2023-07-01 06:19:34,745] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:19:34,745] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:19:34,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3f393a9-2e26-4fb7-99ea-d9fe8fd3b544/dqc_reference/checkm_data
[2023-07-01 06:19:34,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:19:34,800] [INFO] Task started: CheckM
[2023-07-01 06:19:34,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024508875.1_ASM2450887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024508875.1_ASM2450887v1_genomic.fna/checkm_input GCA_024508875.1_ASM2450887v1_genomic.fna/checkm_result
[2023-07-01 06:20:10,264] [INFO] Task succeeded: CheckM
[2023-07-01 06:20:10,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.86%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 06:20:10,287] [INFO] ===== Completeness check finished =====
[2023-07-01 06:20:10,287] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:20:10,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024508875.1_ASM2450887v1_genomic.fna/markers.fasta)
[2023-07-01 06:20:10,288] [INFO] Task started: Blastn
[2023-07-01 06:20:10,288] [INFO] Running command: blastn -query GCA_024508875.1_ASM2450887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f393a9-2e26-4fb7-99ea-d9fe8fd3b544/dqc_reference/reference_markers_gtdb.fasta -out GCA_024508875.1_ASM2450887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:20:12,297] [INFO] Task succeeded: Blastn
[2023-07-01 06:20:12,306] [INFO] Selected 11 target genomes.
[2023-07-01 06:20:12,306] [INFO] Target genome list was writen to GCA_024508875.1_ASM2450887v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:20:12,335] [INFO] Task started: fastANI
[2023-07-01 06:20:12,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg8385bd05-c0c4-4aab-8eac-dcb03ed7c36e/GCA_024508875.1_ASM2450887v1_genomic.fna.gz --refList GCA_024508875.1_ASM2450887v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024508875.1_ASM2450887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:20:24,561] [INFO] Task succeeded: fastANI
[2023-07-01 06:20:24,576] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 06:20:24,576] [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_001557235.1	s__Phenylobacterium sp001557235	84.5027	930	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.95	99.95	0.94	0.94	2	-
GCA_001824475.1	s__Phenylobacterium sp001824475	84.4256	1000	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	96.46	96.46	0.87	0.87	2	-
GCA_004297125.1	s__Phenylobacterium sp004297125	84.4115	1043	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018821435.1	s__Phenylobacterium sp018821435	84.1872	1025	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	0.99	0.99	6	-
GCF_003254525.1	s__Phenylobacterium kunshanense	82.6844	858	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299445.1	s__Phenylobacterium sp004299445	82.604	888	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793285.1	s__Phenylobacterium sp016793285	82.5175	846	1410	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	82.034	861	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793225.1	s__Phenylobacterium sp016793225	81.9129	833	1410	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	81.8965	763	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_001724605.1	s__Phenylobacterium sp001724605	81.7541	817	1410	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 06:20:24,578] [INFO] GTDB search result was written to GCA_024508875.1_ASM2450887v1_genomic.fna/result_gtdb.tsv
[2023-07-01 06:20:24,579] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:20:24,584] [INFO] DFAST_QC result json was written to GCA_024508875.1_ASM2450887v1_genomic.fna/dqc_result.json
[2023-07-01 06:20:24,584] [INFO] DFAST_QC completed!
[2023-07-01 06:20:24,584] [INFO] Total running time: 0h1m17s