[2024-01-24 11:12:57,987] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,989] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fbbb1dc-909d-485b-ab93-5cd84c9eec6e/dqc_reference
[2024-01-24 11:12:59,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,297] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,298] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a48d4ac-17e9-45fa-b430-0dbc2eb1c189/GCF_001077815.2_ASM107781v2_genomic.fna.gz | prodigal -d GCF_001077815.2_ASM107781v2_genomic.fna/cds.fna -a GCF_001077815.2_ASM107781v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:10,107] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:10,108] [INFO] Task started: HMMsearch
[2024-01-24 11:13:10,108] [INFO] Running command: hmmsearch --tblout GCF_001077815.2_ASM107781v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fbbb1dc-909d-485b-ab93-5cd84c9eec6e/dqc_reference/reference_markers.hmm GCF_001077815.2_ASM107781v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:10,420] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:10,421] [INFO] Found 6/6 markers.
[2024-01-24 11:13:10,454] [INFO] Query marker FASTA was written to GCF_001077815.2_ASM107781v2_genomic.fna/markers.fasta
[2024-01-24 11:13:10,454] [INFO] Task started: Blastn
[2024-01-24 11:13:10,454] [INFO] Running command: blastn -query GCF_001077815.2_ASM107781v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fbbb1dc-909d-485b-ab93-5cd84c9eec6e/dqc_reference/reference_markers.fasta -out GCF_001077815.2_ASM107781v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:11,221] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:11,224] [INFO] Selected 16 target genomes.
[2024-01-24 11:13:11,224] [INFO] Target genome list was writen to GCF_001077815.2_ASM107781v2_genomic.fna/target_genomes.txt
[2024-01-24 11:13:11,240] [INFO] Task started: fastANI
[2024-01-24 11:13:11,240] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a48d4ac-17e9-45fa-b430-0dbc2eb1c189/GCF_001077815.2_ASM107781v2_genomic.fna.gz --refList GCF_001077815.2_ASM107781v2_genomic.fna/target_genomes.txt --output GCF_001077815.2_ASM107781v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:20,404] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:20,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fbbb1dc-909d-485b-ab93-5cd84c9eec6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:20,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fbbb1dc-909d-485b-ab93-5cd84c9eec6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:20,418] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:20,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:20,418] [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
Aurantiacibacter atlanticus	strain=s21-N3	GCA_001077815.2	1648404	1648404	type	True	100.0	1075	1075	95	conclusive
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	79.6288	394	1075	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.7398	393	1075	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.5421	253	1075	95	below_threshold
Aurantiacibacter marinus	strain=KCTC 23554	GCA_001021555.1	874156	874156	type	True	78.542	394	1075	95	below_threshold
Aurantiacibacter marinus	strain=HWDM-33	GCA_001013305.1	874156	874156	type	True	78.5402	391	1075	95	below_threshold
Aurantiacibacter sediminis	strain=JGD-13	GCA_016019885.1	2793064	2793064	type	True	78.3414	341	1075	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.2281	213	1075	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.2136	343	1075	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.9174	179	1075	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.8758	177	1075	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.8153	194	1075	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	77.8126	199	1075	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	77.7269	193	1075	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.3209	188	1075	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	77.2693	203	1075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,424] [INFO] DFAST Taxonomy check result was written to GCF_001077815.2_ASM107781v2_genomic.fna/tc_result.tsv
[2024-01-24 11:13:20,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:20,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:20,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fbbb1dc-909d-485b-ab93-5cd84c9eec6e/dqc_reference/checkm_data
[2024-01-24 11:13:20,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:20,488] [INFO] Task started: CheckM
[2024-01-24 11:13:20,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001077815.2_ASM107781v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001077815.2_ASM107781v2_genomic.fna/checkm_input GCF_001077815.2_ASM107781v2_genomic.fna/checkm_result
[2024-01-24 11:13:56,339] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:56,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:56,358] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:56,358] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:56,359] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001077815.2_ASM107781v2_genomic.fna/markers.fasta)
[2024-01-24 11:13:56,359] [INFO] Task started: Blastn
[2024-01-24 11:13:56,359] [INFO] Running command: blastn -query GCF_001077815.2_ASM107781v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fbbb1dc-909d-485b-ab93-5cd84c9eec6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001077815.2_ASM107781v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:57,678] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:57,682] [INFO] Selected 14 target genomes.
[2024-01-24 11:13:57,682] [INFO] Target genome list was writen to GCF_001077815.2_ASM107781v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:57,692] [INFO] Task started: fastANI
[2024-01-24 11:13:57,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a48d4ac-17e9-45fa-b430-0dbc2eb1c189/GCF_001077815.2_ASM107781v2_genomic.fna.gz --refList GCF_001077815.2_ASM107781v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001077815.2_ASM107781v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:05,837] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:05,855] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:05,855] [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_001077815.2	s__Alteraurantiacibacter atlanticus	100.0	1074	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002367375.1	s__Alteraurantiacibacter sp002367375	78.8668	360	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	78.7508	392	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498745.1	s__Alteraurantiacibacter sp902498745	78.6235	374	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	78.5737	330	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021555.1	s__Alteraurantiacibacter marinus	78.543	394	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001008165.2	s__Croceibacterium atlanticum	78.5142	253	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016019885.1	s__Alteraurantiacibacter sp016019885	78.3374	342	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	78.2283	343	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827405.1	s__Alteraurantiacibacter aestuarii	78.2281	213	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	78.2207	270	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.0445	240	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	77.7221	194	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003660445.1	s__Croceibacterium ferulae	77.1695	166	1075	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:05,860] [INFO] GTDB search result was written to GCF_001077815.2_ASM107781v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:05,860] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:05,864] [INFO] DFAST_QC result json was written to GCF_001077815.2_ASM107781v2_genomic.fna/dqc_result.json
[2024-01-24 11:14:05,864] [INFO] DFAST_QC completed!
[2024-01-24 11:14:05,864] [INFO] Total running time: 0h1m8s