[2024-01-25 17:48:20,504] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:20,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:20,506] [INFO] DQC Reference Directory: /var/lib/cwl/stg579df953-2b11-4e7b-abfd-ffd65b4f57fb/dqc_reference
[2024-01-25 17:48:21,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:21,689] [INFO] Task started: Prodigal
[2024-01-25 17:48:21,690] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbdb7c99-ee2d-49ef-b355-f575dc763944/GCF_016698665.1_ASM1669866v1_genomic.fna.gz | prodigal -d GCF_016698665.1_ASM1669866v1_genomic.fna/cds.fna -a GCF_016698665.1_ASM1669866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:31,468] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:31,468] [INFO] Task started: HMMsearch
[2024-01-25 17:48:31,469] [INFO] Running command: hmmsearch --tblout GCF_016698665.1_ASM1669866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg579df953-2b11-4e7b-abfd-ffd65b4f57fb/dqc_reference/reference_markers.hmm GCF_016698665.1_ASM1669866v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:31,698] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:31,699] [INFO] Found 6/6 markers.
[2024-01-25 17:48:31,727] [INFO] Query marker FASTA was written to GCF_016698665.1_ASM1669866v1_genomic.fna/markers.fasta
[2024-01-25 17:48:31,727] [INFO] Task started: Blastn
[2024-01-25 17:48:31,727] [INFO] Running command: blastn -query GCF_016698665.1_ASM1669866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg579df953-2b11-4e7b-abfd-ffd65b4f57fb/dqc_reference/reference_markers.fasta -out GCF_016698665.1_ASM1669866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:32,505] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:32,511] [INFO] Selected 14 target genomes.
[2024-01-25 17:48:32,511] [INFO] Target genome list was writen to GCF_016698665.1_ASM1669866v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:32,524] [INFO] Task started: fastANI
[2024-01-25 17:48:32,525] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbdb7c99-ee2d-49ef-b355-f575dc763944/GCF_016698665.1_ASM1669866v1_genomic.fna.gz --refList GCF_016698665.1_ASM1669866v1_genomic.fna/target_genomes.txt --output GCF_016698665.1_ASM1669866v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:44,608] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:44,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg579df953-2b11-4e7b-abfd-ffd65b4f57fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:44,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg579df953-2b11-4e7b-abfd-ffd65b4f57fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:44,618] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:44,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:44,618] [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
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	100.0	1174	1174	95	conclusive
Devosia aurantiaca	strain=H239	GCA_011058215.1	2714858	2714858	type	True	91.1792	918	1174	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	81.6036	731	1174	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	81.066	678	1174	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	81.0338	681	1174	95	below_threshold
Devosia lucknowensis	strain=L15	GCA_900177655.1	1096929	1096929	type	True	80.7656	674	1174	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	80.5216	614	1174	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	80.1601	614	1174	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	80.1508	637	1174	95	below_threshold
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	80.0048	607	1174	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	79.9403	611	1174	95	below_threshold
Devosia crocina	strain=IPL20	GCA_900116545.1	429728	429728	type	True	79.9296	545	1174	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.7831	588	1174	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.7707	577	1174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:44,622] [INFO] DFAST Taxonomy check result was written to GCF_016698665.1_ASM1669866v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:44,623] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:44,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:44,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg579df953-2b11-4e7b-abfd-ffd65b4f57fb/dqc_reference/checkm_data
[2024-01-25 17:48:44,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:44,661] [INFO] Task started: CheckM
[2024-01-25 17:48:44,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016698665.1_ASM1669866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016698665.1_ASM1669866v1_genomic.fna/checkm_input GCF_016698665.1_ASM1669866v1_genomic.fna/checkm_result
[2024-01-25 17:49:15,598] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:15,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:15,611] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:15,611] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:15,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016698665.1_ASM1669866v1_genomic.fna/markers.fasta)
[2024-01-25 17:49:15,612] [INFO] Task started: Blastn
[2024-01-25 17:49:15,612] [INFO] Running command: blastn -query GCF_016698665.1_ASM1669866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg579df953-2b11-4e7b-abfd-ffd65b4f57fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016698665.1_ASM1669866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:17,042] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:17,050] [INFO] Selected 14 target genomes.
[2024-01-25 17:49:17,050] [INFO] Target genome list was writen to GCF_016698665.1_ASM1669866v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:17,059] [INFO] Task started: fastANI
[2024-01-25 17:49:17,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbdb7c99-ee2d-49ef-b355-f575dc763944/GCF_016698665.1_ASM1669866v1_genomic.fna.gz --refList GCF_016698665.1_ASM1669866v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016698665.1_ASM1669866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:29,289] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:29,298] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:29,298] [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_016698665.1	s__Devosia sp016698665	100.0	1174	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011058215.1	s__Devosia aurantiaca	91.1669	919	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016411825.1	s__Devosia sp016411825	81.5842	733	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	81.0624	678	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177655.1	s__Devosia lucknowensis	80.7905	671	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969445.1	s__Devosia chinhatensis	80.5078	615	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015158295.1	s__Devosia sp015158295	80.4748	587	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631955.1	s__Devosia sp001899045	80.4285	652	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	98.09	98.08	0.92	0.92	4	-
GCF_001427875.1	s__Devosia sp001427875	80.2568	666	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	80.2087	649	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCA_017744655.1	s__Devosia sp017744655	80.1525	667	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056405.1	s__Devosia indica	80.1419	638	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009758415.1	s__Devosia marina	79.9956	608	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
GCF_900116545.1	s__Devosia crocina	79.9278	546	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:29,299] [INFO] GTDB search result was written to GCF_016698665.1_ASM1669866v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:29,301] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:29,304] [INFO] DFAST_QC result json was written to GCF_016698665.1_ASM1669866v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:29,304] [INFO] DFAST_QC completed!
[2024-01-25 17:49:29,304] [INFO] Total running time: 0h1m9s