[2024-01-25 20:13:05,761] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:05,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:05,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d63942f-68c4-4370-a18d-063fd7aca336/dqc_reference
[2024-01-25 20:13:06,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:06,874] [INFO] Task started: Prodigal
[2024-01-25 20:13:06,874] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3e2fc89-52a2-4a5d-8b44-c77a9c801d1d/GCF_030160115.1_ASM3016011v1_genomic.fna.gz | prodigal -d GCF_030160115.1_ASM3016011v1_genomic.fna/cds.fna -a GCF_030160115.1_ASM3016011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:22,015] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:22,015] [INFO] Task started: HMMsearch
[2024-01-25 20:13:22,015] [INFO] Running command: hmmsearch --tblout GCF_030160115.1_ASM3016011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d63942f-68c4-4370-a18d-063fd7aca336/dqc_reference/reference_markers.hmm GCF_030160115.1_ASM3016011v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:22,341] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:22,342] [INFO] Found 6/6 markers.
[2024-01-25 20:13:22,387] [INFO] Query marker FASTA was written to GCF_030160115.1_ASM3016011v1_genomic.fna/markers.fasta
[2024-01-25 20:13:22,387] [INFO] Task started: Blastn
[2024-01-25 20:13:22,387] [INFO] Running command: blastn -query GCF_030160115.1_ASM3016011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d63942f-68c4-4370-a18d-063fd7aca336/dqc_reference/reference_markers.fasta -out GCF_030160115.1_ASM3016011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:23,333] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:23,336] [INFO] Selected 20 target genomes.
[2024-01-25 20:13:23,336] [INFO] Target genome list was writen to GCF_030160115.1_ASM3016011v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:23,344] [INFO] Task started: fastANI
[2024-01-25 20:13:23,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3e2fc89-52a2-4a5d-8b44-c77a9c801d1d/GCF_030160115.1_ASM3016011v1_genomic.fna.gz --refList GCF_030160115.1_ASM3016011v1_genomic.fna/target_genomes.txt --output GCF_030160115.1_ASM3016011v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:39,955] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:39,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d63942f-68c4-4370-a18d-063fd7aca336/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:39,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d63942f-68c4-4370-a18d-063fd7aca336/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:39,967] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:13:39,967] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:13:39,967] [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 geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	83.1285	991	1830	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	78.6835	528	1830	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	78.5918	573	1830	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	78.5491	528	1830	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	78.5098	512	1830	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	78.4731	503	1830	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	78.3951	512	1830	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.3112	529	1830	95	below_threshold
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	78.2255	435	1830	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	78.1964	445	1830	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	78.1659	412	1830	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	78.0647	531	1830	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	78.0342	403	1830	95	below_threshold
Devosia riboflavina	strain=IFO13584	GCA_000743575.1	46914	46914	type	True	77.8893	492	1830	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	77.8641	399	1830	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	77.7304	458	1830	95	below_threshold
Devosia crocina	strain=IPL20	GCA_900116545.1	429728	429728	type	True	77.6689	373	1830	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	77.6592	478	1830	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	76.5947	230	1830	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.3217	245	1830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:39,969] [INFO] DFAST Taxonomy check result was written to GCF_030160115.1_ASM3016011v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:39,969] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:39,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:39,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d63942f-68c4-4370-a18d-063fd7aca336/dqc_reference/checkm_data
[2024-01-25 20:13:39,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:40,032] [INFO] Task started: CheckM
[2024-01-25 20:13:40,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160115.1_ASM3016011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160115.1_ASM3016011v1_genomic.fna/checkm_input GCF_030160115.1_ASM3016011v1_genomic.fna/checkm_result
[2024-01-25 20:14:22,394] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:22,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:22,420] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:22,421] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:22,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160115.1_ASM3016011v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:22,422] [INFO] Task started: Blastn
[2024-01-25 20:14:22,422] [INFO] Running command: blastn -query GCF_030160115.1_ASM3016011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d63942f-68c4-4370-a18d-063fd7aca336/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160115.1_ASM3016011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:24,206] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:24,210] [INFO] Selected 19 target genomes.
[2024-01-25 20:14:24,210] [INFO] Target genome list was writen to GCF_030160115.1_ASM3016011v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:24,219] [INFO] Task started: fastANI
[2024-01-25 20:14:24,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3e2fc89-52a2-4a5d-8b44-c77a9c801d1d/GCF_030160115.1_ASM3016011v1_genomic.fna.gz --refList GCF_030160115.1_ASM3016011v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160115.1_ASM3016011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:41,785] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:41,796] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:14:41,797] [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_000969415.1	s__Devosia geojensis	83.1593	988	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426345.1	s__Devosia sp001426345	78.6869	543	1830	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	78.5572	527	1830	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	78.5197	572	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_008000755.1	s__Youhaiella tibetensis	78.4872	512	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Youhaiella	95.0	99.26	98.52	0.98	0.97	3	-
GCF_016698645.1	s__Devosia sp016698645	78.403	511	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307495.1	s__Devosia_A sp017307495	78.3589	474	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCF_001402915.1	s__Devosia_A sp001402915	78.2526	513	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899075.1	s__Devosia_A sp001899075	78.2523	496	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900128975.1	s__Devosia limi	78.2501	525	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.98	99.98	0.97	0.97	2	-
GCF_003056405.1	s__Devosia indica	78.2073	443	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900110945.1	s__Devosia sp900110945	78.2048	513	1830	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	78.173	526	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801025.1	s__Paradevosia shaoguanensis	78.1365	514	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Paradevosia	95.0	97.16	97.13	0.92	0.92	4	-
GCF_001425235.1	s__Devosia_A sp001425235	78.1089	566	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	97.96	97.96	0.95	0.95	2	-
GCA_001899085.1	s__Devosia_A sp001899085	78.0932	537	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.98	99.97	0.99	0.99	3	-
GCF_015158295.1	s__Devosia sp015158295	78.0345	399	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234425.1	s__Devosia sp015234425	78.0165	439	1830	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	77.78	409	1830	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	96.74	96.74	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:41,798] [INFO] GTDB search result was written to GCF_030160115.1_ASM3016011v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:41,799] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:41,802] [INFO] DFAST_QC result json was written to GCF_030160115.1_ASM3016011v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:41,803] [INFO] DFAST_QC completed!
[2024-01-25 20:14:41,803] [INFO] Total running time: 0h1m36s