[2024-01-24 14:15:34,241] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,248] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg50be5678-d2ba-44b5-97ee-7610c328720a/dqc_reference
[2024-01-24 14:15:35,624] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,624] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,625] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d90712c-b82b-42be-a48b-3a188b7b8793/GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/cds.fna -a GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:50,640] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:50,641] [INFO] Task started: HMMsearch
[2024-01-24 14:15:50,641] [INFO] Running command: hmmsearch --tblout GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50be5678-d2ba-44b5-97ee-7610c328720a/dqc_reference/reference_markers.hmm GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:50,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:50,942] [INFO] Found 6/6 markers.
[2024-01-24 14:15:50,983] [INFO] Query marker FASTA was written to GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:15:50,983] [INFO] Task started: Blastn
[2024-01-24 14:15:50,983] [INFO] Running command: blastn -query GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg50be5678-d2ba-44b5-97ee-7610c328720a/dqc_reference/reference_markers.fasta -out GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:51,815] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:51,819] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:51,820] [INFO] Target genome list was writen to GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:15:51,827] [INFO] Task started: fastANI
[2024-01-24 14:15:51,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d90712c-b82b-42be-a48b-3a188b7b8793/GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna.gz --refList GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:06,794] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:06,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50be5678-d2ba-44b5-97ee-7610c328720a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:06,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50be5678-d2ba-44b5-97ee-7610c328720a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:06,809] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:16:06,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:06,810] [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 limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	100.0	1421	1422	95	conclusive
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	99.9702	1383	1422	95	conclusive
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	81.3639	758	1422	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	80.9033	673	1422	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	80.8899	689	1422	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	80.7622	666	1422	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	80.7194	697	1422	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	80.6989	711	1422	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.342	651	1422	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	80.2867	662	1422	95	below_threshold
Devosia riboflavina	strain=IFO13584	GCA_000743575.1	46914	46914	type	True	80.1942	659	1422	95	below_threshold
Devosia submarina	strain=JCM 18935	GCA_003056345.1	1173082	1173082	type	True	79.4944	556	1422	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.2414	564	1422	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	78.9207	568	1422	95	below_threshold
Devosia crocina	strain=IPL20	GCA_900116545.1	429728	429728	type	True	78.9099	491	1422	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	77.3977	298	1422	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.1217	169	1422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:06,812] [INFO] DFAST Taxonomy check result was written to GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:16:06,813] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:06,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:06,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50be5678-d2ba-44b5-97ee-7610c328720a/dqc_reference/checkm_data
[2024-01-24 14:16:06,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:06,861] [INFO] Task started: CheckM
[2024-01-24 14:16:06,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/checkm_input GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:16:51,530] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:51,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:51,555] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:51,555] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:51,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:16:51,556] [INFO] Task started: Blastn
[2024-01-24 14:16:51,556] [INFO] Running command: blastn -query GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg50be5678-d2ba-44b5-97ee-7610c328720a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:53,024] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:53,028] [INFO] Selected 14 target genomes.
[2024-01-24 14:16:53,028] [INFO] Target genome list was writen to GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:53,038] [INFO] Task started: fastANI
[2024-01-24 14:16:53,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d90712c-b82b-42be-a48b-3a188b7b8793/GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna.gz --refList GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:06,372] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:06,388] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:06,388] [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_900128975.1	s__Devosia limi	100.0	1421	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.98	99.98	0.97	0.97	2	conclusive
GCA_018828145.1	s__Devosia sp018828145	82.4703	829	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCA_014860165.1	s__Devosia sp014860165	81.7081	740	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470445.1	s__Devosia sp900470445	81.6348	760	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	95.41	95.41	0.81	0.81	2	-
GCF_900110945.1	s__Devosia sp900110945	81.5199	734	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735585.1	s__Devosia sp000735585	81.4029	757	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014926585.1	s__Devosia sp014926585	81.3648	758	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222805.1	s__Devosia sp005222805	81.3469	721	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971295.1	s__Devosia epidermidihirudinis	80.9003	674	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698645.1	s__Devosia sp016698645	80.8787	690	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056355.1	s__Devosia naphthalenivorans	80.7555	667	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971275.1	s__Devosia psychrophila	80.7194	697	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.97	99.97	0.98	0.98	2	-
GCF_004005995.1	s__Devosia sp004005995	79.7869	597	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.21	97.18	0.88	0.88	3	-
GCF_014837245.1	s__Devosia sp014837245	78.827	524	1422	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 14:17:06,390] [INFO] GTDB search result was written to GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:06,390] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:06,394] [INFO] DFAST_QC result json was written to GCF_900128975.1_IMG-taxon_2582580747_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:17:06,395] [INFO] DFAST_QC completed!
[2024-01-24 14:17:06,395] [INFO] Total running time: 0h1m32s