[2024-01-24 13:40:29,975] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:29,977] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:29,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg21e107b1-2341-4312-90a1-7a6d908d1338/dqc_reference
[2024-01-24 13:40:31,413] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,414] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,414] [INFO] Running command: gunzip -c /var/lib/cwl/stg56a9d95d-98b6-4d70-a6d2-8af0de9533e4/GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/cds.fna -a GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:44,787] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:44,787] [INFO] Task started: HMMsearch
[2024-01-24 13:40:44,787] [INFO] Running command: hmmsearch --tblout GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21e107b1-2341-4312-90a1-7a6d908d1338/dqc_reference/reference_markers.hmm GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:45,069] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:45,070] [INFO] Found 6/6 markers.
[2024-01-24 13:40:45,109] [INFO] Query marker FASTA was written to GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:40:45,110] [INFO] Task started: Blastn
[2024-01-24 13:40:45,110] [INFO] Running command: blastn -query GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e107b1-2341-4312-90a1-7a6d908d1338/dqc_reference/reference_markers.fasta -out GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,220] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,224] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:46,225] [INFO] Target genome list was writen to GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,229] [INFO] Task started: fastANI
[2024-01-24 13:40:46,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg56a9d95d-98b6-4d70-a6d2-8af0de9533e4/GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna.gz --refList GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:56,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:56,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21e107b1-2341-4312-90a1-7a6d908d1338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:56,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21e107b1-2341-4312-90a1-7a6d908d1338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:56,654] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:56,654] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:56,654] [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
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	100.0	1494	1495	95	conclusive
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	99.9935	1468	1495	95	conclusive
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	83.9165	962	1495	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	83.8591	959	1495	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	81.2759	816	1495	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.7109	598	1495	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	79.2114	595	1495	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.127	495	1495	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.0984	430	1495	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0442	390	1495	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.5721	317	1495	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:56,656] [INFO] DFAST Taxonomy check result was written to GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:40:56,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:56,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:56,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21e107b1-2341-4312-90a1-7a6d908d1338/dqc_reference/checkm_data
[2024-01-24 13:40:56,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:56,707] [INFO] Task started: CheckM
[2024-01-24 13:40:56,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/checkm_input GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 13:41:43,996] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:43,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,017] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:44,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:44,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:41:44,018] [INFO] Task started: Blastn
[2024-01-24 13:41:44,018] [INFO] Running command: blastn -query GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg21e107b1-2341-4312-90a1-7a6d908d1338/dqc_reference/reference_markers_gtdb.fasta -out GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:46,146] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:46,150] [INFO] Selected 8 target genomes.
[2024-01-24 13:41:46,150] [INFO] Target genome list was writen to GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:46,156] [INFO] Task started: fastANI
[2024-01-24 13:41:46,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg56a9d95d-98b6-4d70-a6d2-8af0de9533e4/GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna.gz --refList GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:54,894] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:54,909] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:54,909] [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_002786295.1	s__Pseudooceanicola marinus	99.9935	1468	1495	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_018222585.1	s__Pseudooceanicola sp018222585	83.9773	1010	1495	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	83.8686	958	1495	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	83.8366	894	1495	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	81.3268	796	1495	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_011806405.1	s__Pseudooceanicola sp011806405	80.7274	725	1495	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	79.8565	632	1495	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_004959925.1	s__Pseudooceanicola onchidii	79.7109	598	1495	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:54,911] [INFO] GTDB search result was written to GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:54,912] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:54,915] [INFO] DFAST_QC result json was written to GCF_900172385.1_Ps.marinus_CECT7751_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:41:54,916] [INFO] DFAST_QC completed!
[2024-01-24 13:41:54,916] [INFO] Total running time: 0h1m25s