[2024-01-24 14:46:55,815] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,823] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc09bde3-989b-461e-8782-5f61f77a3ea3/dqc_reference
[2024-01-24 14:46:58,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,018] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg64cc4081-5314-4a23-8577-da9ea9fc148a/GCF_018069895.1_ASM1806989v1_genomic.fna.gz | prodigal -d GCF_018069895.1_ASM1806989v1_genomic.fna/cds.fna -a GCF_018069895.1_ASM1806989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:12,311] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:12,311] [INFO] Task started: HMMsearch
[2024-01-24 14:47:12,311] [INFO] Running command: hmmsearch --tblout GCF_018069895.1_ASM1806989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc09bde3-989b-461e-8782-5f61f77a3ea3/dqc_reference/reference_markers.hmm GCF_018069895.1_ASM1806989v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:12,617] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:12,618] [INFO] Found 6/6 markers.
[2024-01-24 14:47:12,659] [INFO] Query marker FASTA was written to GCF_018069895.1_ASM1806989v1_genomic.fna/markers.fasta
[2024-01-24 14:47:12,659] [INFO] Task started: Blastn
[2024-01-24 14:47:12,659] [INFO] Running command: blastn -query GCF_018069895.1_ASM1806989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc09bde3-989b-461e-8782-5f61f77a3ea3/dqc_reference/reference_markers.fasta -out GCF_018069895.1_ASM1806989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:13,727] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:13,731] [INFO] Selected 23 target genomes.
[2024-01-24 14:47:13,731] [INFO] Target genome list was writen to GCF_018069895.1_ASM1806989v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:13,742] [INFO] Task started: fastANI
[2024-01-24 14:47:13,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg64cc4081-5314-4a23-8577-da9ea9fc148a/GCF_018069895.1_ASM1806989v1_genomic.fna.gz --refList GCF_018069895.1_ASM1806989v1_genomic.fna/target_genomes.txt --output GCF_018069895.1_ASM1806989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:31,249] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:31,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc09bde3-989b-461e-8782-5f61f77a3ea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:31,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc09bde3-989b-461e-8782-5f61f77a3ea3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:31,268] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:31,268] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:31,268] [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
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	81.6978	725	1188	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	81.1727	694	1188	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	80.9678	664	1188	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	80.559	635	1188	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.1481	513	1188	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.9346	469	1188	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.7984	467	1188	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	78.6752	478	1188	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.6727	451	1188	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.4658	495	1188	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	78.4608	464	1188	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.4427	475	1188	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.3851	450	1188	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.2896	454	1188	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	78.2247	442	1188	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.1154	350	1188	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.1004	430	1188	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.0788	416	1188	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.8975	361	1188	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.7733	390	1188	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.6401	382	1188	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.5872	348	1188	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.4547	304	1188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:31,270] [INFO] DFAST Taxonomy check result was written to GCF_018069895.1_ASM1806989v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:31,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:31,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:31,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc09bde3-989b-461e-8782-5f61f77a3ea3/dqc_reference/checkm_data
[2024-01-24 14:47:31,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:31,320] [INFO] Task started: CheckM
[2024-01-24 14:47:31,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018069895.1_ASM1806989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018069895.1_ASM1806989v1_genomic.fna/checkm_input GCF_018069895.1_ASM1806989v1_genomic.fna/checkm_result
[2024-01-24 14:48:16,050] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:16,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:16,071] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:16,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:16,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018069895.1_ASM1806989v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:16,072] [INFO] Task started: Blastn
[2024-01-24 14:48:16,073] [INFO] Running command: blastn -query GCF_018069895.1_ASM1806989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc09bde3-989b-461e-8782-5f61f77a3ea3/dqc_reference/reference_markers_gtdb.fasta -out GCF_018069895.1_ASM1806989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:17,948] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:17,951] [INFO] Selected 11 target genomes.
[2024-01-24 14:48:17,952] [INFO] Target genome list was writen to GCF_018069895.1_ASM1806989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:17,961] [INFO] Task started: fastANI
[2024-01-24 14:48:17,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg64cc4081-5314-4a23-8577-da9ea9fc148a/GCF_018069895.1_ASM1806989v1_genomic.fna.gz --refList GCF_018069895.1_ASM1806989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018069895.1_ASM1806989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:26,772] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:26,792] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:26,793] [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_018069895.1	s__Roseovarius sp018069895	100.0	1183	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	conclusive
GCA_002842985.1	s__Roseovarius sp002842985	86.5844	853	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428225.1	s__Roseovarius sp002428225	86.1825	508	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.12	96.12	0.88	0.88	2	-
GCA_002720475.1	s__Roseovarius sp002720475	84.56	588	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCA_014359765.1	s__Roseovarius sp014359765	84.5105	665	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421985.1	s__Roseovarius sp002421985	83.0429	612	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	81.8223	591	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002072155.1	s__Roseovarius sp002072155	81.2243	717	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	81.1971	691	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_004339675.1	s__Rhodovulum steppense	78.2933	453	1188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	77.4515	322	1188	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 14:48:26,795] [INFO] GTDB search result was written to GCF_018069895.1_ASM1806989v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:26,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:26,801] [INFO] DFAST_QC result json was written to GCF_018069895.1_ASM1806989v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:26,801] [INFO] DFAST_QC completed!
[2024-01-24 14:48:26,801] [INFO] Total running time: 0h1m31s