[2024-01-24 14:39:14,564] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,567] [INFO] DQC Reference Directory: /var/lib/cwl/stgdce6a9f1-37f6-4e7b-ad6f-9a6263fa77da/dqc_reference
[2024-01-24 14:39:15,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:15,827] [INFO] Task started: Prodigal
[2024-01-24 14:39:15,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cbf0d54-d8a9-4b7e-af38-05ed92fcd5e8/GCF_018219815.1_ASM1821981v1_genomic.fna.gz | prodigal -d GCF_018219815.1_ASM1821981v1_genomic.fna/cds.fna -a GCF_018219815.1_ASM1821981v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:28,660] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:28,660] [INFO] Task started: HMMsearch
[2024-01-24 14:39:28,660] [INFO] Running command: hmmsearch --tblout GCF_018219815.1_ASM1821981v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdce6a9f1-37f6-4e7b-ad6f-9a6263fa77da/dqc_reference/reference_markers.hmm GCF_018219815.1_ASM1821981v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:28,964] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:28,966] [INFO] Found 6/6 markers.
[2024-01-24 14:39:29,015] [INFO] Query marker FASTA was written to GCF_018219815.1_ASM1821981v1_genomic.fna/markers.fasta
[2024-01-24 14:39:29,015] [INFO] Task started: Blastn
[2024-01-24 14:39:29,015] [INFO] Running command: blastn -query GCF_018219815.1_ASM1821981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdce6a9f1-37f6-4e7b-ad6f-9a6263fa77da/dqc_reference/reference_markers.fasta -out GCF_018219815.1_ASM1821981v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:29,939] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:29,943] [INFO] Selected 14 target genomes.
[2024-01-24 14:39:29,944] [INFO] Target genome list was writen to GCF_018219815.1_ASM1821981v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:29,951] [INFO] Task started: fastANI
[2024-01-24 14:39:29,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbf0d54-d8a9-4b7e-af38-05ed92fcd5e8/GCF_018219815.1_ASM1821981v1_genomic.fna.gz --refList GCF_018219815.1_ASM1821981v1_genomic.fna/target_genomes.txt --output GCF_018219815.1_ASM1821981v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:41,321] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:41,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdce6a9f1-37f6-4e7b-ad6f-9a6263fa77da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:41,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdce6a9f1-37f6-4e7b-ad6f-9a6263fa77da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:41,339] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:41,339] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:41,339] [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
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	100.0	1407	1412	95	conclusive
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	88.7716	1065	1412	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	82.0692	887	1412	95	below_threshold
Thalassobius gelatinovorus	strain=CECT 4357	GCA_001458355.1	53501	53501	type	True	82.0659	887	1412	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.3985	531	1412	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.1679	541	1412	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.0848	515	1412	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.0512	558	1412	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	79.0395	585	1412	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4465	449	1412	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.303	473	1412	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.1953	420	1412	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.9894	404	1412	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6074	383	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:41,342] [INFO] DFAST Taxonomy check result was written to GCF_018219815.1_ASM1821981v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:41,343] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:41,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:41,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdce6a9f1-37f6-4e7b-ad6f-9a6263fa77da/dqc_reference/checkm_data
[2024-01-24 14:39:41,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:41,389] [INFO] Task started: CheckM
[2024-01-24 14:39:41,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018219815.1_ASM1821981v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018219815.1_ASM1821981v1_genomic.fna/checkm_input GCF_018219815.1_ASM1821981v1_genomic.fna/checkm_result
[2024-01-24 14:40:22,734] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:22,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:22,759] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:22,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:22,760] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018219815.1_ASM1821981v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:22,761] [INFO] Task started: Blastn
[2024-01-24 14:40:22,761] [INFO] Running command: blastn -query GCF_018219815.1_ASM1821981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdce6a9f1-37f6-4e7b-ad6f-9a6263fa77da/dqc_reference/reference_markers_gtdb.fasta -out GCF_018219815.1_ASM1821981v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:24,342] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:24,345] [INFO] Selected 16 target genomes.
[2024-01-24 14:40:24,345] [INFO] Target genome list was writen to GCF_018219815.1_ASM1821981v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:24,356] [INFO] Task started: fastANI
[2024-01-24 14:40:24,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbf0d54-d8a9-4b7e-af38-05ed92fcd5e8/GCF_018219815.1_ASM1821981v1_genomic.fna.gz --refList GCF_018219815.1_ASM1821981v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018219815.1_ASM1821981v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:38,770] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:38,784] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:38,784] [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_018219815.1	s__Thalassobius aquimarinus	100.0	1407	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009857745.1	s__Thalassobius mangrovi	88.7698	1066	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458355.1	s__Thalassobius gelatinovorus	82.0602	888	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	99.99	0.99	0.99	3	-
GCF_900142185.1	s__Lutimaribacter pacificus	80.4101	660	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004799325.1	s__Thalassobius vesicularis	80.3152	664	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	79.9781	612	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	79.3797	533	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.2252	501	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001507595.1	s__Ruegeria marisrubri	79.1344	545	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	79.0671	519	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_001458255.1	s__Thalassobius autumnalis	79.0163	588	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900109035.1	s__Cribrihabitans marinus	79.0118	559	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005938215.1	s__Ruegeria sediminis	78.9703	531	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182725.1	s__Thalassobius litoralis	78.8677	542	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	78.1595	538	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.774	363	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:38,789] [INFO] GTDB search result was written to GCF_018219815.1_ASM1821981v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:38,790] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:38,796] [INFO] DFAST_QC result json was written to GCF_018219815.1_ASM1821981v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:38,796] [INFO] DFAST_QC completed!
[2024-01-24 14:40:38,796] [INFO] Total running time: 0h1m24s