[2023-06-05 07:16:06,739] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:16:06,742] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:16:06,742] [INFO] DQC Reference Directory: /var/lib/cwl/stg0951e146-efeb-4185-ba31-85715b99d134/dqc_reference
[2023-06-05 07:16:08,221] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:16:08,223] [INFO] Task started: Prodigal
[2023-06-05 07:16:08,224] [INFO] Running command: gunzip -c /var/lib/cwl/stgfba782a9-b95f-47bb-ab90-b77b9fa9531e/GCA_004297265.1_ASM429726v1_genomic.fna.gz | prodigal -d GCA_004297265.1_ASM429726v1_genomic.fna/cds.fna -a GCA_004297265.1_ASM429726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:16:25,634] [INFO] Task succeeded: Prodigal
[2023-06-05 07:16:25,634] [INFO] Task started: HMMsearch
[2023-06-05 07:16:25,634] [INFO] Running command: hmmsearch --tblout GCA_004297265.1_ASM429726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0951e146-efeb-4185-ba31-85715b99d134/dqc_reference/reference_markers.hmm GCA_004297265.1_ASM429726v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:16:26,027] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:16:26,029] [INFO] Found 6/6 markers.
[2023-06-05 07:16:26,085] [INFO] Query marker FASTA was written to GCA_004297265.1_ASM429726v1_genomic.fna/markers.fasta
[2023-06-05 07:16:26,085] [INFO] Task started: Blastn
[2023-06-05 07:16:26,085] [INFO] Running command: blastn -query GCA_004297265.1_ASM429726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0951e146-efeb-4185-ba31-85715b99d134/dqc_reference/reference_markers.fasta -out GCA_004297265.1_ASM429726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:16:27,178] [INFO] Task succeeded: Blastn
[2023-06-05 07:16:27,182] [INFO] Selected 13 target genomes.
[2023-06-05 07:16:27,183] [INFO] Target genome list was writen to GCA_004297265.1_ASM429726v1_genomic.fna/target_genomes.txt
[2023-06-05 07:16:27,186] [INFO] Task started: fastANI
[2023-06-05 07:16:27,186] [INFO] Running command: fastANI --query /var/lib/cwl/stgfba782a9-b95f-47bb-ab90-b77b9fa9531e/GCA_004297265.1_ASM429726v1_genomic.fna.gz --refList GCA_004297265.1_ASM429726v1_genomic.fna/target_genomes.txt --output GCA_004297265.1_ASM429726v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:16:43,380] [INFO] Task succeeded: fastANI
[2023-06-05 07:16:43,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0951e146-efeb-4185-ba31-85715b99d134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:16:43,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0951e146-efeb-4185-ba31-85715b99d134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:16:43,395] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:16:43,395] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:16:43,396] [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
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	87.405	1511	1974	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	83.4707	1240	1974	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	82.7337	1308	1974	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	78.6708	857	1974	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.7077	481	1974	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.6628	419	1974	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.3568	345	1974	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.345	227	1974	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.3171	383	1974	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.3051	270	1974	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.2719	207	1974	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.9734	210	1974	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	75.847	200	1974	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:16:43,398] [INFO] DFAST Taxonomy check result was written to GCA_004297265.1_ASM429726v1_genomic.fna/tc_result.tsv
[2023-06-05 07:16:43,399] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:16:43,399] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:16:43,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0951e146-efeb-4185-ba31-85715b99d134/dqc_reference/checkm_data
[2023-06-05 07:16:43,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:16:43,485] [INFO] Task started: CheckM
[2023-06-05 07:16:43,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004297265.1_ASM429726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004297265.1_ASM429726v1_genomic.fna/checkm_input GCA_004297265.1_ASM429726v1_genomic.fna/checkm_result
[2023-06-05 07:17:34,673] [INFO] Task succeeded: CheckM
[2023-06-05 07:17:34,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:17:34,698] [INFO] ===== Completeness check finished =====
[2023-06-05 07:17:34,698] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:17:34,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004297265.1_ASM429726v1_genomic.fna/markers.fasta)
[2023-06-05 07:17:34,699] [INFO] Task started: Blastn
[2023-06-05 07:17:34,699] [INFO] Running command: blastn -query GCA_004297265.1_ASM429726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0951e146-efeb-4185-ba31-85715b99d134/dqc_reference/reference_markers_gtdb.fasta -out GCA_004297265.1_ASM429726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:17:36,759] [INFO] Task succeeded: Blastn
[2023-06-05 07:17:36,764] [INFO] Selected 7 target genomes.
[2023-06-05 07:17:36,764] [INFO] Target genome list was writen to GCA_004297265.1_ASM429726v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:17:36,772] [INFO] Task started: fastANI
[2023-06-05 07:17:36,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgfba782a9-b95f-47bb-ab90-b77b9fa9531e/GCA_004297265.1_ASM429726v1_genomic.fna.gz --refList GCA_004297265.1_ASM429726v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004297265.1_ASM429726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:17:47,775] [INFO] Task succeeded: fastANI
[2023-06-05 07:17:47,787] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:17:47,788] [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
GCA_004297265.1	s__Reyranella sp004297265	100.0	1968	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009772935.1	s__Reyranella sp009772935	90.0816	1574	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017990895.1	s__Reyranella sp017990895	89.4045	1147	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281855.1	s__Reyranella sp002281855	89.0738	1546	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.99	99.99	0.99	0.99	3	-
GCF_019039055.1	s__Reyranella sp019039055	87.7698	1493	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001557035.1	s__Reyranella sp001557035	87.7694	1273	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205335.1	s__Reyranella sp013205335	87.588	1077	1974	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 07:17:47,790] [INFO] GTDB search result was written to GCA_004297265.1_ASM429726v1_genomic.fna/result_gtdb.tsv
[2023-06-05 07:17:47,790] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:17:47,794] [INFO] DFAST_QC result json was written to GCA_004297265.1_ASM429726v1_genomic.fna/dqc_result.json
[2023-06-05 07:17:47,794] [INFO] DFAST_QC completed!
[2023-06-05 07:17:47,794] [INFO] Total running time: 0h1m41s