[2024-01-24 10:47:06,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgea7f112d-b296-4149-b40c-397b3b690110/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg7859574f-c9f7-4ab2-8175-179412f101f7/GCF_014651915.1_ASM1465191v1_genomic.fna.gz | prodigal -d GCF_014651915.1_ASM1465191v1_genomic.fna/cds.fna -a GCF_014651915.1_ASM1465191v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:20,454] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:20,455] [INFO] Task started: HMMsearch
[2024-01-24 10:47:20,455] [INFO] Running command: hmmsearch --tblout GCF_014651915.1_ASM1465191v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea7f112d-b296-4149-b40c-397b3b690110/dqc_reference/reference_markers.hmm GCF_014651915.1_ASM1465191v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:20,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:20,685] [INFO] Found 6/6 markers.
[2024-01-24 10:47:20,716] [INFO] Query marker FASTA was written to GCF_014651915.1_ASM1465191v1_genomic.fna/markers.fasta
[2024-01-24 10:47:20,716] [INFO] Task started: Blastn
[2024-01-24 10:47:20,716] [INFO] Running command: blastn -query GCF_014651915.1_ASM1465191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea7f112d-b296-4149-b40c-397b3b690110/dqc_reference/reference_markers.fasta -out GCF_014651915.1_ASM1465191v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:21,666] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:21,670] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:21,670] [INFO] Target genome list was writen to GCF_014651915.1_ASM1465191v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:21,741] [INFO] Task started: fastANI
[2024-01-24 10:47:21,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg7859574f-c9f7-4ab2-8175-179412f101f7/GCF_014651915.1_ASM1465191v1_genomic.fna.gz --refList GCF_014651915.1_ASM1465191v1_genomic.fna/target_genomes.txt --output GCF_014651915.1_ASM1465191v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:36,262] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:36,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea7f112d-b296-4149-b40c-397b3b690110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:36,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea7f112d-b296-4149-b40c-397b3b690110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:36,277] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:36,277] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:36,278] [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
Parvularcula lutaonensis	strain=KCTC 22245	GCA_014651915.1	491923	491923	type	True	100.0	981	981	95	conclusive
Parvularcula mediterranea	strain=ZS-1/3	GCA_013085255.1	2732508	2732508	type	True	79.6084	509	981	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	77.7554	258	981	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	77.5463	216	981	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	77.3126	138	981	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	77.2152	151	981	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	77.181	156	981	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	76.8716	76	981	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.8367	93	981	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	76.5197	67	981	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.4899	97	981	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	76.4326	69	981	95	below_threshold
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	76.3168	118	981	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	76.2878	102	981	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	76.26	73	981	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.0302	94	981	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.9962	98	981	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.908	70	981	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	75.8221	57	981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:36,279] [INFO] DFAST Taxonomy check result was written to GCF_014651915.1_ASM1465191v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:36,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:36,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:36,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea7f112d-b296-4149-b40c-397b3b690110/dqc_reference/checkm_data
[2024-01-24 10:47:36,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:36,313] [INFO] Task started: CheckM
[2024-01-24 10:47:36,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651915.1_ASM1465191v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651915.1_ASM1465191v1_genomic.fna/checkm_input GCF_014651915.1_ASM1465191v1_genomic.fna/checkm_result
[2024-01-24 10:48:05,791] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:05,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:05,808] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:05,808] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:05,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651915.1_ASM1465191v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:05,809] [INFO] Task started: Blastn
[2024-01-24 10:48:05,809] [INFO] Running command: blastn -query GCF_014651915.1_ASM1465191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea7f112d-b296-4149-b40c-397b3b690110/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651915.1_ASM1465191v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:07,475] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:07,479] [INFO] Selected 15 target genomes.
[2024-01-24 10:48:07,479] [INFO] Target genome list was writen to GCF_014651915.1_ASM1465191v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:07,544] [INFO] Task started: fastANI
[2024-01-24 10:48:07,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg7859574f-c9f7-4ab2-8175-179412f101f7/GCF_014651915.1_ASM1465191v1_genomic.fna.gz --refList GCF_014651915.1_ASM1465191v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651915.1_ASM1465191v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:17,878] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:17,890] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:17,890] [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_014651915.1	s__Parvularcula lutaonensis	100.0	981	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013085255.1	s__Parvularcula mediterranea	79.6086	509	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733125.1	s__Parvularcula oceani	77.7437	259	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215175.1	s__Parvularcula sp013215175	77.7095	207	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199615.1	s__Parvularcula dongshanensis	77.5604	215	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399445.1	s__Parvularcula sp003399445	77.3126	138	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640095.1	s__Aquisalinus flavus	77.2135	155	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900185715.1	s__Bosea sp900185715	76.589	98	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952425.1	s__Mesorhizobium sp003952425	76.4476	95	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.51	95.02	0.90	0.84	19	-
GCA_016125425.1	s__Amphiplicatus sp016125425	76.4049	75	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442815.1	s__Mesorhizobium sp006442815	76.3665	95	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002943565.1	s__Marinicaulis flavus	76.3168	118	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898115.1	s__Bosea sp001898115	76.2535	77	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.21	98.43	0.96	0.93	3	-
GCA_019137195.1	s__Hyphomicrobium sp019137195	76.2367	55	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026145.1	s__Hyphomicrobium_A sp009026145	76.1928	63	981	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:17,891] [INFO] GTDB search result was written to GCF_014651915.1_ASM1465191v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:17,892] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:17,896] [INFO] DFAST_QC result json was written to GCF_014651915.1_ASM1465191v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:17,896] [INFO] DFAST_QC completed!
[2024-01-24 10:48:17,896] [INFO] Total running time: 0h1m11s