[2024-01-24 13:01:26,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e49cbfe-8e31-4342-87f7-5b57a0582071/dqc_reference
[2024-01-24 13:01:27,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,915] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg85a56e30-140c-4ecc-8e59-6717cef96ff6/GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/cds.fna -a GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:39,739] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:39,739] [INFO] Task started: HMMsearch
[2024-01-24 13:01:39,739] [INFO] Running command: hmmsearch --tblout GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e49cbfe-8e31-4342-87f7-5b57a0582071/dqc_reference/reference_markers.hmm GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:40,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:40,038] [INFO] Found 6/6 markers.
[2024-01-24 13:01:40,070] [INFO] Query marker FASTA was written to GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:40,070] [INFO] Task started: Blastn
[2024-01-24 13:01:40,070] [INFO] Running command: blastn -query GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e49cbfe-8e31-4342-87f7-5b57a0582071/dqc_reference/reference_markers.fasta -out GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:40,940] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:40,945] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:40,946] [INFO] Target genome list was writen to GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:40,957] [INFO] Task started: fastANI
[2024-01-24 13:01:40,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg85a56e30-140c-4ecc-8e59-6717cef96ff6/GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna.gz --refList GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:55,496] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:55,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e49cbfe-8e31-4342-87f7-5b57a0582071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:55,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e49cbfe-8e31-4342-87f7-5b57a0582071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:55,511] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:55,511] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:55,511] [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 crocina	strain=IPL20	GCA_900116545.1	429728	429728	type	True	100.0	1238	1238	95	conclusive
Devosia riboflavina	strain=IFO13584	GCA_000743575.1	46914	46914	type	True	81.4187	732	1238	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	81.053	724	1238	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	80.5913	603	1238	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.2887	598	1238	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	80.1567	609	1238	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	80.0642	549	1238	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	79.9468	585	1238	95	below_threshold
Devosia aurantiaca	strain=H239	GCA_011058215.1	2714858	2714858	type	True	79.9461	564	1238	95	below_threshold
Devosia lucknowensis	strain=L15	GCA_900177655.1	1096929	1096929	type	True	79.889	568	1238	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	79.779	557	1238	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	79.6498	509	1238	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	79.6271	559	1238	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.3443	522	1238	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.2115	497	1238	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	79.1941	547	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:55,513] [INFO] DFAST Taxonomy check result was written to GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:01:55,514] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:55,514] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:55,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e49cbfe-8e31-4342-87f7-5b57a0582071/dqc_reference/checkm_data
[2024-01-24 13:01:55,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:55,565] [INFO] Task started: CheckM
[2024-01-24 13:01:55,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/checkm_input GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:32,583] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:32,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:32,609] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:32,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:32,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:32,610] [INFO] Task started: Blastn
[2024-01-24 13:02:32,610] [INFO] Running command: blastn -query GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e49cbfe-8e31-4342-87f7-5b57a0582071/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:33,930] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:33,936] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:33,936] [INFO] Target genome list was writen to GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:33,950] [INFO] Task started: fastANI
[2024-01-24 13:02:33,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg85a56e30-140c-4ecc-8e59-6717cef96ff6/GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna.gz --refList GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:46,831] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:46,851] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:46,851] [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_900116545.1	s__Devosia crocina	100.0	1238	1238	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_000743575.1	s__Devosia riboflavina	81.4324	731	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427875.1	s__Devosia sp001427875	81.4272	728	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744655.1	s__Devosia sp017744655	81.3894	731	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307565.1	s__Devosia sp017307565	81.0994	600	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425445.1	s__Devosia sp001425445	81.0896	698	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	96.74	96.74	0.91	0.91	2	-
GCF_000970455.1	s__Devosia soli	81.0467	725	1238	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	80.6018	602	1238	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	80.2832	599	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698665.1	s__Devosia sp016698665	80.055	550	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058215.1	s__Devosia aurantiaca	79.9654	562	1238	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	79.9276	587	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	98.09	98.08	0.92	0.92	4	-
GCF_900177655.1	s__Devosia lucknowensis	79.9234	564	1238	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	79.7887	556	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000969445.1	s__Devosia chinhatensis	79.6117	562	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012799265.1	s__Devosia sp012799265	79.1112	404	1238	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:46,853] [INFO] GTDB search result was written to GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:46,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:46,858] [INFO] DFAST_QC result json was written to GCF_900116545.1_IMG-taxon_2675903690_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:46,858] [INFO] DFAST_QC completed!
[2024-01-24 13:02:46,858] [INFO] Total running time: 0h1m20s