[2024-01-25 19:32:51,005] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:32:51,007] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:32:51,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg6de328c0-2760-42ac-a22e-5499415e98c3/dqc_reference
[2024-01-25 19:32:52,099] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:32:52,100] [INFO] Task started: Prodigal
[2024-01-25 19:32:52,100] [INFO] Running command: gunzip -c /var/lib/cwl/stge5962fb6-ea95-4312-be07-5f42b5955977/GCF_014652635.1_ASM1465263v1_genomic.fna.gz | prodigal -d GCF_014652635.1_ASM1465263v1_genomic.fna/cds.fna -a GCF_014652635.1_ASM1465263v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:03,106] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:03,107] [INFO] Task started: HMMsearch
[2024-01-25 19:33:03,107] [INFO] Running command: hmmsearch --tblout GCF_014652635.1_ASM1465263v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6de328c0-2760-42ac-a22e-5499415e98c3/dqc_reference/reference_markers.hmm GCF_014652635.1_ASM1465263v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:03,334] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:03,335] [INFO] Found 6/6 markers.
[2024-01-25 19:33:03,370] [INFO] Query marker FASTA was written to GCF_014652635.1_ASM1465263v1_genomic.fna/markers.fasta
[2024-01-25 19:33:03,370] [INFO] Task started: Blastn
[2024-01-25 19:33:03,370] [INFO] Running command: blastn -query GCF_014652635.1_ASM1465263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de328c0-2760-42ac-a22e-5499415e98c3/dqc_reference/reference_markers.fasta -out GCF_014652635.1_ASM1465263v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:04,162] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:04,165] [INFO] Selected 24 target genomes.
[2024-01-25 19:33:04,165] [INFO] Target genome list was writen to GCF_014652635.1_ASM1465263v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:04,172] [INFO] Task started: fastANI
[2024-01-25 19:33:04,172] [INFO] Running command: fastANI --query /var/lib/cwl/stge5962fb6-ea95-4312-be07-5f42b5955977/GCF_014652635.1_ASM1465263v1_genomic.fna.gz --refList GCF_014652635.1_ASM1465263v1_genomic.fna/target_genomes.txt --output GCF_014652635.1_ASM1465263v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:20,849] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:20,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6de328c0-2760-42ac-a22e-5499415e98c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:20,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6de328c0-2760-42ac-a22e-5499415e98c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:20,865] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:33:20,865] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:20,865] [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 pacifica	strain=KCTC 32437	GCA_014652635.1	1335967	1335967	type	True	100.0	1333	1334	95	conclusive
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	77.8904	278	1334	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	77.8892	421	1334	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	77.7658	303	1334	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	77.7242	271	1334	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	77.6909	342	1334	95	below_threshold
Devosia subaequoris	strain=DSM 23447	GCA_014197055.1	395930	395930	type	True	77.6827	269	1334	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	77.6649	343	1334	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	77.5777	315	1334	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	77.5396	285	1334	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	77.5119	310	1334	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	77.4856	300	1334	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	77.4574	292	1334	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	77.4448	283	1334	95	below_threshold
Devosia riboflavina	strain=IFO13584	GCA_000743575.1	46914	46914	type	True	77.4267	307	1334	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	77.3845	273	1334	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	77.3734	272	1334	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	77.3657	314	1334	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	77.351	289	1334	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	77.3358	283	1334	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	77.2601	265	1334	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	77.2509	295	1334	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	76.9432	196	1334	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	75.7522	61	1334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:20,866] [INFO] DFAST Taxonomy check result was written to GCF_014652635.1_ASM1465263v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:20,867] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:20,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:20,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6de328c0-2760-42ac-a22e-5499415e98c3/dqc_reference/checkm_data
[2024-01-25 19:33:20,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:20,910] [INFO] Task started: CheckM
[2024-01-25 19:33:20,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652635.1_ASM1465263v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652635.1_ASM1465263v1_genomic.fna/checkm_input GCF_014652635.1_ASM1465263v1_genomic.fna/checkm_result
[2024-01-25 19:33:54,371] [INFO] Task succeeded: CheckM
[2024-01-25 19:33:54,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:33:54,392] [INFO] ===== Completeness check finished =====
[2024-01-25 19:33:54,392] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:33:54,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652635.1_ASM1465263v1_genomic.fna/markers.fasta)
[2024-01-25 19:33:54,393] [INFO] Task started: Blastn
[2024-01-25 19:33:54,394] [INFO] Running command: blastn -query GCF_014652635.1_ASM1465263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de328c0-2760-42ac-a22e-5499415e98c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652635.1_ASM1465263v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:55,715] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:55,718] [INFO] Selected 24 target genomes.
[2024-01-25 19:33:55,718] [INFO] Target genome list was writen to GCF_014652635.1_ASM1465263v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:33:55,730] [INFO] Task started: fastANI
[2024-01-25 19:33:55,730] [INFO] Running command: fastANI --query /var/lib/cwl/stge5962fb6-ea95-4312-be07-5f42b5955977/GCF_014652635.1_ASM1465263v1_genomic.fna.gz --refList GCF_014652635.1_ASM1465263v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652635.1_ASM1465263v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:34:12,915] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:12,928] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:34:12,929] [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_014652635.1	s__Devosia pacifica	100.0	1331	1334	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_900119845.1	s__Devosia_A enhydra	77.9136	278	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969415.1	s__Devosia geojensis	77.8918	420	1334	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	77.7182	358	1334	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	77.5982	286	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Youhaiella	95.0	99.26	98.52	0.98	0.97	3	-
GCF_001402915.1	s__Devosia_A sp001402915	77.578	295	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735585.1	s__Devosia sp000735585	77.5365	318	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873135.1	s__Devosia_A sp014873135	77.511	283	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	77.502	311	1334	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	77.4959	299	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005222805.1	s__Devosia sp005222805	77.4232	325	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743575.1	s__Devosia riboflavina	77.4174	308	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860165.1	s__Devosia sp014860165	77.4105	347	1334	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	77.4049	287	1334	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	77.3734	272	1334	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	77.3655	314	1334	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	77.3459	302	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Paradevosia	95.0	97.16	97.13	0.92	0.92	4	-
GCA_017307495.1	s__Devosia_A sp017307495	77.3337	266	1334	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_000970465.2	s__Devosia_A insulae	77.2509	295	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971295.1	s__Devosia epidermidihirudinis	77.2109	258	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908315.1	s__Gemmobacter_B sp009908315	75.7522	61	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280725.1	s__UBA7672 sp002280725	75.3545	50	1334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:34:13,069] [INFO] GTDB search result was written to GCF_014652635.1_ASM1465263v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:34:13,070] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:34:13,076] [INFO] DFAST_QC result json was written to GCF_014652635.1_ASM1465263v1_genomic.fna/dqc_result.json
[2024-01-25 19:34:13,076] [INFO] DFAST_QC completed!
[2024-01-25 19:34:13,076] [INFO] Total running time: 0h1m22s