[2024-01-25 18:09:35,975] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:35,977] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:35,977] [INFO] DQC Reference Directory: /var/lib/cwl/stg3013e2d9-6ab8-4a1d-9bb0-f44e20a021b6/dqc_reference
[2024-01-25 18:09:37,114] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:37,114] [INFO] Task started: Prodigal
[2024-01-25 18:09:37,115] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cd4f923-eb06-45d7-95e7-d341285a9f6b/GCF_002906165.1_ASM290616v1_genomic.fna.gz | prodigal -d GCF_002906165.1_ASM290616v1_genomic.fna/cds.fna -a GCF_002906165.1_ASM290616v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:54,496] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:54,496] [INFO] Task started: HMMsearch
[2024-01-25 18:09:54,496] [INFO] Running command: hmmsearch --tblout GCF_002906165.1_ASM290616v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3013e2d9-6ab8-4a1d-9bb0-f44e20a021b6/dqc_reference/reference_markers.hmm GCF_002906165.1_ASM290616v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:54,793] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:54,794] [INFO] Found 6/6 markers.
[2024-01-25 18:09:54,841] [INFO] Query marker FASTA was written to GCF_002906165.1_ASM290616v1_genomic.fna/markers.fasta
[2024-01-25 18:09:54,842] [INFO] Task started: Blastn
[2024-01-25 18:09:54,842] [INFO] Running command: blastn -query GCF_002906165.1_ASM290616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3013e2d9-6ab8-4a1d-9bb0-f44e20a021b6/dqc_reference/reference_markers.fasta -out GCF_002906165.1_ASM290616v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:55,752] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:55,755] [INFO] Selected 19 target genomes.
[2024-01-25 18:09:55,756] [INFO] Target genome list was writen to GCF_002906165.1_ASM290616v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:55,765] [INFO] Task started: fastANI
[2024-01-25 18:09:55,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cd4f923-eb06-45d7-95e7-d341285a9f6b/GCF_002906165.1_ASM290616v1_genomic.fna.gz --refList GCF_002906165.1_ASM290616v1_genomic.fna/target_genomes.txt --output GCF_002906165.1_ASM290616v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:14,174] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:14,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3013e2d9-6ab8-4a1d-9bb0-f44e20a021b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:14,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3013e2d9-6ab8-4a1d-9bb0-f44e20a021b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:14,186] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:14,187] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:14,187] [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
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	100.0	2002	2004	95	conclusive
Roseibium aggregatum	strain=IAM 12614	GCA_000168975.1	187304	187304	suspected-type	True	80.2438	956	2004	95	below_threshold
Roseibium aestuarii	strain=SYSU M00256-3	GCA_008477545.1	2600299	2600299	type	True	78.7552	517	2004	95	below_threshold
Roseibium album	strain=CECT 5095	GCA_001404515.1	311410	311410	type	True	78.5266	633	2004	95	below_threshold
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	78.4946	499	2004	95	below_threshold
Roseibium alexandrii	strain=DFL-11	GCA_000158095.2	388408	388408	type	True	78.3202	491	2004	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	78.3184	434	2004	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	78.3009	436	2004	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	78.1665	467	2004	95	below_threshold
Roseibium denhamense	strain=JCM 10543	GCA_009711415.1	76305	76305	type	True	78.1289	474	2004	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	78.0577	462	2004	95	below_threshold
Roseibium limicola	strain=CAU 1637	GCA_017313085.1	2816037	2816037	type	True	77.5433	404	2004	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.7294	250	2004	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.7091	265	2004	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.6218	168	2004	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	76.5721	121	2004	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.4377	184	2004	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.1609	185	2004	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	75.8792	112	2004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:14,189] [INFO] DFAST Taxonomy check result was written to GCF_002906165.1_ASM290616v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:14,189] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:14,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:14,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3013e2d9-6ab8-4a1d-9bb0-f44e20a021b6/dqc_reference/checkm_data
[2024-01-25 18:10:14,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:14,247] [INFO] Task started: CheckM
[2024-01-25 18:10:14,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002906165.1_ASM290616v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002906165.1_ASM290616v1_genomic.fna/checkm_input GCF_002906165.1_ASM290616v1_genomic.fna/checkm_result
[2024-01-25 18:11:03,506] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:03,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:03,532] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:03,532] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:03,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002906165.1_ASM290616v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:03,533] [INFO] Task started: Blastn
[2024-01-25 18:11:03,533] [INFO] Running command: blastn -query GCF_002906165.1_ASM290616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3013e2d9-6ab8-4a1d-9bb0-f44e20a021b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002906165.1_ASM290616v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:05,367] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:05,370] [INFO] Selected 10 target genomes.
[2024-01-25 18:11:05,370] [INFO] Target genome list was writen to GCF_002906165.1_ASM290616v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:05,385] [INFO] Task started: fastANI
[2024-01-25 18:11:05,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cd4f923-eb06-45d7-95e7-d341285a9f6b/GCF_002906165.1_ASM290616v1_genomic.fna.gz --refList GCF_002906165.1_ASM290616v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002906165.1_ASM290616v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:18,543] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:18,551] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:18,552] [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_002906165.1	s__Roseibium marinum	100.0	2002	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001624695.1	s__Roseibium sp001624695	88.1379	1439	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075075.1	s__Roseibium sp003075075	86.1437	1327	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000168975.1	s__Roseibium aggregatum	80.265	952	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309185.1	s__Roseibium aggregatum_B	80.0942	904	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999245.1	s__Roseibium aggregatum_A	79.9847	976	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	97.61	96.85	0.93	0.89	16	-
GCF_002237595.1	s__Roseibium sp002237595	79.9121	906	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008107755.1	s__Roseibium sp008107755	79.5438	840	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643925.1	s__Roseibium sp017643925	78.9856	676	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014842915.1	s__Roseibium litorale	78.4949	499	2004	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:18,553] [INFO] GTDB search result was written to GCF_002906165.1_ASM290616v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:18,554] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:18,560] [INFO] DFAST_QC result json was written to GCF_002906165.1_ASM290616v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:18,561] [INFO] DFAST_QC completed!
[2024-01-25 18:11:18,561] [INFO] Total running time: 0h1m43s