[2024-01-24 10:57:26,597] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,608] [INFO] DQC Reference Directory: /var/lib/cwl/stgea648b6d-7238-47f0-aefe-3965fc8a8e2c/dqc_reference
[2024-01-24 10:57:28,048] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,053] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,053] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a4d8075-9fa1-4419-afaf-078a746e73fd/GCF_001663155.1_ASM166315v1_genomic.fna.gz | prodigal -d GCF_001663155.1_ASM166315v1_genomic.fna/cds.fna -a GCF_001663155.1_ASM166315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:36,664] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:36,665] [INFO] Task started: HMMsearch
[2024-01-24 10:57:36,665] [INFO] Running command: hmmsearch --tblout GCF_001663155.1_ASM166315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea648b6d-7238-47f0-aefe-3965fc8a8e2c/dqc_reference/reference_markers.hmm GCF_001663155.1_ASM166315v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:36,931] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:36,932] [INFO] Found 6/6 markers.
[2024-01-24 10:57:36,967] [INFO] Query marker FASTA was written to GCF_001663155.1_ASM166315v1_genomic.fna/markers.fasta
[2024-01-24 10:57:36,968] [INFO] Task started: Blastn
[2024-01-24 10:57:36,968] [INFO] Running command: blastn -query GCF_001663155.1_ASM166315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea648b6d-7238-47f0-aefe-3965fc8a8e2c/dqc_reference/reference_markers.fasta -out GCF_001663155.1_ASM166315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:37,714] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:37,718] [INFO] Selected 18 target genomes.
[2024-01-24 10:57:37,718] [INFO] Target genome list was writen to GCF_001663155.1_ASM166315v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:37,756] [INFO] Task started: fastANI
[2024-01-24 10:57:37,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a4d8075-9fa1-4419-afaf-078a746e73fd/GCF_001663155.1_ASM166315v1_genomic.fna.gz --refList GCF_001663155.1_ASM166315v1_genomic.fna/target_genomes.txt --output GCF_001663155.1_ASM166315v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:48,675] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:48,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea648b6d-7238-47f0-aefe-3965fc8a8e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:48,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea648b6d-7238-47f0-aefe-3965fc8a8e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:48,695] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:48,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:48,696] [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
Altererythrobacter ishigakiensis	strain=NBRC 107699	GCA_001663155.1	476157	476157	type	True	100.0	891	891	95	conclusive
Altererythrobacter ishigakiensis	strain=ATCC BAA-2084	GCA_007830695.1	476157	476157	type	True	99.9999	888	891	95	conclusive
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	78.3009	272	891	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	78.1261	201	891	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.902	210	891	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.852	215	891	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	77.7862	221	891	95	below_threshold
Erythrobacter rubeus	strain=KMU-140	GCA_014705715.1	2760803	2760803	type	True	77.7114	238	891	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	77.5832	242	891	95	below_threshold
Erythrobacter sanguineus	strain=DSM 11032	GCA_900143235.1	198312	198312	type	True	77.5489	239	891	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.4409	173	891	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	77.4111	219	891	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	77.3298	221	891	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	77.3198	219	891	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.303	165	891	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	77.288	226	891	95	below_threshold
Erythrobacter insulae	strain=JBTF-M21	GCA_007004095.1	2584124	2584124	type	True	77.251	179	891	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	76.8394	82	891	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:48,700] [INFO] DFAST Taxonomy check result was written to GCF_001663155.1_ASM166315v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:48,702] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:48,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:48,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea648b6d-7238-47f0-aefe-3965fc8a8e2c/dqc_reference/checkm_data
[2024-01-24 10:57:48,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:48,733] [INFO] Task started: CheckM
[2024-01-24 10:57:48,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001663155.1_ASM166315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001663155.1_ASM166315v1_genomic.fna/checkm_input GCF_001663155.1_ASM166315v1_genomic.fna/checkm_result
[2024-01-24 10:58:18,719] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:18,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:18,736] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:18,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:18,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001663155.1_ASM166315v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:18,737] [INFO] Task started: Blastn
[2024-01-24 10:58:18,737] [INFO] Running command: blastn -query GCF_001663155.1_ASM166315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea648b6d-7238-47f0-aefe-3965fc8a8e2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001663155.1_ASM166315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:20,095] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:20,099] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:20,099] [INFO] Target genome list was writen to GCF_001663155.1_ASM166315v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:20,128] [INFO] Task started: fastANI
[2024-01-24 10:58:20,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a4d8075-9fa1-4419-afaf-078a746e73fd/GCF_001663155.1_ASM166315v1_genomic.fna.gz --refList GCF_001663155.1_ASM166315v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001663155.1_ASM166315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:29,906] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:29,919] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:29,919] [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_001663155.1	s__Erythrobacter ishigakiensis	100.0	891	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	97.03	96.25	0.95	0.94	6	conclusive
GCA_003149575.1	s__Erythrobacter sp003149575	81.5892	515	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	98.16	98.16	0.93	0.93	2	-
GCA_013002295.1	s__Erythrobacter sp013002295	81.3916	396	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.14	98.90	0.85	0.82	4	-
GCF_011047315.1	s__Erythrobacter sp011047315	78.9253	395	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	78.586	297	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001515985.1	s__Erythrobacter sp001515985	78.3024	272	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371495.1	s__Erythrobacter sp013371495	78.3009	272	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	78.2325	246	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152865.1	s__Erythrobacter sp000152865	78.0011	253	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	77.8225	161	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542875.1	s__Erythrobacter sp001542875	77.7922	180	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905735.1	s__Erythrobacter sp009905735	77.716	211	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	77.6703	158	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001296025.1	s__Erythrobacter sp001296025	77.5275	215	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828055.1	s__Erythrobacter ramosus	77.3198	219	891	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:29,921] [INFO] GTDB search result was written to GCF_001663155.1_ASM166315v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:29,922] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:29,926] [INFO] DFAST_QC result json was written to GCF_001663155.1_ASM166315v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:29,926] [INFO] DFAST_QC completed!
[2024-01-24 10:58:29,926] [INFO] Total running time: 0h1m3s