[2024-01-24 11:05:28,090] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,093] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,093] [INFO] DQC Reference Directory: /var/lib/cwl/stga0444f36-d66a-46bc-8920-01390214498b/dqc_reference
[2024-01-24 11:05:29,552] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,553] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg8db68fb9-17c0-482c-9105-5dcaaecf8137/GCF_000970465.2_ASM97046v2_genomic.fna.gz | prodigal -d GCF_000970465.2_ASM97046v2_genomic.fna/cds.fna -a GCF_000970465.2_ASM97046v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:46,059] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:46,059] [INFO] Task started: HMMsearch
[2024-01-24 11:05:46,059] [INFO] Running command: hmmsearch --tblout GCF_000970465.2_ASM97046v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0444f36-d66a-46bc-8920-01390214498b/dqc_reference/reference_markers.hmm GCF_000970465.2_ASM97046v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:46,385] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:46,386] [INFO] Found 6/6 markers.
[2024-01-24 11:05:46,437] [INFO] Query marker FASTA was written to GCF_000970465.2_ASM97046v2_genomic.fna/markers.fasta
[2024-01-24 11:05:46,437] [INFO] Task started: Blastn
[2024-01-24 11:05:46,438] [INFO] Running command: blastn -query GCF_000970465.2_ASM97046v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga0444f36-d66a-46bc-8920-01390214498b/dqc_reference/reference_markers.fasta -out GCF_000970465.2_ASM97046v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:47,512] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:47,515] [INFO] Selected 20 target genomes.
[2024-01-24 11:05:47,516] [INFO] Target genome list was writen to GCF_000970465.2_ASM97046v2_genomic.fna/target_genomes.txt
[2024-01-24 11:05:47,523] [INFO] Task started: fastANI
[2024-01-24 11:05:47,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg8db68fb9-17c0-482c-9105-5dcaaecf8137/GCF_000970465.2_ASM97046v2_genomic.fna.gz --refList GCF_000970465.2_ASM97046v2_genomic.fna/target_genomes.txt --output GCF_000970465.2_ASM97046v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:07,631] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:07,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0444f36-d66a-46bc-8920-01390214498b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:07,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0444f36-d66a-46bc-8920-01390214498b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:07,649] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:07,649] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:07,649] [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 insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	100.0	1695	1712	95	conclusive
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	79.0111	595	1712	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	78.9524	590	1712	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	78.8794	587	1712	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	78.8071	551	1712	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	78.7226	490	1712	95	below_threshold
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	78.6422	495	1712	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.6191	528	1712	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	78.6143	458	1712	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	78.5572	509	1712	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	78.5181	466	1712	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	78.4163	391	1712	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	78.2015	414	1712	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	78.0734	386	1712	95	below_threshold
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	78.0388	353	1712	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	77.917	317	1712	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.2318	256	1712	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	77.2299	287	1712	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.1964	307	1712	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	75.9562	238	1712	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:07,651] [INFO] DFAST Taxonomy check result was written to GCF_000970465.2_ASM97046v2_genomic.fna/tc_result.tsv
[2024-01-24 11:06:07,652] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:07,652] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:07,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0444f36-d66a-46bc-8920-01390214498b/dqc_reference/checkm_data
[2024-01-24 11:06:07,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:07,718] [INFO] Task started: CheckM
[2024-01-24 11:06:07,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000970465.2_ASM97046v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000970465.2_ASM97046v2_genomic.fna/checkm_input GCF_000970465.2_ASM97046v2_genomic.fna/checkm_result
[2024-01-24 11:06:55,526] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:55,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:55,550] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:55,551] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:55,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000970465.2_ASM97046v2_genomic.fna/markers.fasta)
[2024-01-24 11:06:55,552] [INFO] Task started: Blastn
[2024-01-24 11:06:55,552] [INFO] Running command: blastn -query GCF_000970465.2_ASM97046v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga0444f36-d66a-46bc-8920-01390214498b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000970465.2_ASM97046v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:57,498] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:57,502] [INFO] Selected 5 target genomes.
[2024-01-24 11:06:57,502] [INFO] Target genome list was writen to GCF_000970465.2_ASM97046v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:57,507] [INFO] Task started: fastANI
[2024-01-24 11:06:57,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg8db68fb9-17c0-482c-9105-5dcaaecf8137/GCF_000970465.2_ASM97046v2_genomic.fna.gz --refList GCF_000970465.2_ASM97046v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000970465.2_ASM97046v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:06,702] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:06,713] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:06,714] [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_000970465.2	s__Devosia_A insulae	100.0	1695	1712	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001425235.1	s__Devosia_A sp001425235	92.2667	1454	1712	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	88.7696	1315	1712	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_001402915.1	s__Devosia_A sp001402915	87.8167	1263	1712	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_017307495.1	s__Devosia_A sp017307495	83.4194	877	1712	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:06,715] [INFO] GTDB search result was written to GCF_000970465.2_ASM97046v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:06,716] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:06,720] [INFO] DFAST_QC result json was written to GCF_000970465.2_ASM97046v2_genomic.fna/dqc_result.json
[2024-01-24 11:07:06,720] [INFO] DFAST_QC completed!
[2024-01-24 11:07:06,721] [INFO] Total running time: 0h1m39s