[2023-06-28 20:06:49,474] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:06:49,476] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:06:49,477] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe6a08ee-17b7-4347-9992-f10a2332d1ff/dqc_reference
[2023-06-28 20:06:50,762] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:06:50,763] [INFO] Task started: Prodigal
[2023-06-28 20:06:50,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a6893e6-3311-4a18-a083-2c1753e2238c/GCA_017306945.1_ASM1730694v1_genomic.fna.gz | prodigal -d GCA_017306945.1_ASM1730694v1_genomic.fna/cds.fna -a GCA_017306945.1_ASM1730694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:06:59,913] [INFO] Task succeeded: Prodigal
[2023-06-28 20:06:59,914] [INFO] Task started: HMMsearch
[2023-06-28 20:06:59,914] [INFO] Running command: hmmsearch --tblout GCA_017306945.1_ASM1730694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe6a08ee-17b7-4347-9992-f10a2332d1ff/dqc_reference/reference_markers.hmm GCA_017306945.1_ASM1730694v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:07:00,176] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:07:00,177] [INFO] Found 6/6 markers.
[2023-06-28 20:07:00,210] [INFO] Query marker FASTA was written to GCA_017306945.1_ASM1730694v1_genomic.fna/markers.fasta
[2023-06-28 20:07:00,211] [INFO] Task started: Blastn
[2023-06-28 20:07:00,211] [INFO] Running command: blastn -query GCA_017306945.1_ASM1730694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe6a08ee-17b7-4347-9992-f10a2332d1ff/dqc_reference/reference_markers.fasta -out GCA_017306945.1_ASM1730694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:07:01,270] [INFO] Task succeeded: Blastn
[2023-06-28 20:07:01,275] [INFO] Selected 23 target genomes.
[2023-06-28 20:07:01,276] [INFO] Target genome list was writen to GCA_017306945.1_ASM1730694v1_genomic.fna/target_genomes.txt
[2023-06-28 20:07:01,283] [INFO] Task started: fastANI
[2023-06-28 20:07:01,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a6893e6-3311-4a18-a083-2c1753e2238c/GCA_017306945.1_ASM1730694v1_genomic.fna.gz --refList GCA_017306945.1_ASM1730694v1_genomic.fna/target_genomes.txt --output GCA_017306945.1_ASM1730694v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:07:18,931] [INFO] Task succeeded: fastANI
[2023-06-28 20:07:18,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe6a08ee-17b7-4347-9992-f10a2332d1ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:07:18,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe6a08ee-17b7-4347-9992-f10a2332d1ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:07:18,953] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:07:18,953] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:07:18,953] [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	83.2942	718	1003	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	79.2992	451	1003	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	79.1739	453	1003	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	79.1706	455	1003	95	below_threshold
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	79.0122	374	1003	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	78.7661	388	1003	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	78.5606	360	1003	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	78.4724	342	1003	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.4225	379	1003	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	78.421	328	1003	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	78.3824	383	1003	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	78.1355	370	1003	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	78.0878	376	1003	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	78.0683	320	1003	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	78.0566	328	1003	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	78.0389	284	1003	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	77.9405	259	1003	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	77.7887	297	1003	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	77.5653	251	1003	95	below_threshold
Devosia pacifica	strain=KCTC 32437	GCA_014652635.1	1335967	1335967	type	True	77.3304	207	1003	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.0625	230	1003	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.7816	251	1003	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.7349	255	1003	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:07:18,956] [INFO] DFAST Taxonomy check result was written to GCA_017306945.1_ASM1730694v1_genomic.fna/tc_result.tsv
[2023-06-28 20:07:18,957] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:07:18,957] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:07:18,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe6a08ee-17b7-4347-9992-f10a2332d1ff/dqc_reference/checkm_data
[2023-06-28 20:07:18,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:07:18,998] [INFO] Task started: CheckM
[2023-06-28 20:07:18,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017306945.1_ASM1730694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017306945.1_ASM1730694v1_genomic.fna/checkm_input GCA_017306945.1_ASM1730694v1_genomic.fna/checkm_result
[2023-06-28 20:07:49,722] [INFO] Task succeeded: CheckM
[2023-06-28 20:07:49,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 20:07:49,750] [INFO] ===== Completeness check finished =====
[2023-06-28 20:07:49,750] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:07:49,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017306945.1_ASM1730694v1_genomic.fna/markers.fasta)
[2023-06-28 20:07:49,751] [INFO] Task started: Blastn
[2023-06-28 20:07:49,751] [INFO] Running command: blastn -query GCA_017306945.1_ASM1730694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe6a08ee-17b7-4347-9992-f10a2332d1ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_017306945.1_ASM1730694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:07:51,761] [INFO] Task succeeded: Blastn
[2023-06-28 20:07:51,766] [INFO] Selected 7 target genomes.
[2023-06-28 20:07:51,767] [INFO] Target genome list was writen to GCA_017306945.1_ASM1730694v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:07:51,769] [INFO] Task started: fastANI
[2023-06-28 20:07:51,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a6893e6-3311-4a18-a083-2c1753e2238c/GCA_017306945.1_ASM1730694v1_genomic.fna.gz --refList GCA_017306945.1_ASM1730694v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017306945.1_ASM1730694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:07:59,759] [INFO] Task succeeded: fastANI
[2023-06-28 20:07:59,771] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:07:59,771] [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_017307495.1	s__Devosia_A sp017307495	98.6969	955	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	conclusive
GCA_001899085.1	s__Devosia_A sp001899085	83.6773	775	1003	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_001425235.1	s__Devosia_A sp001425235	83.6447	773	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	97.96	97.96	0.95	0.95	2	-
GCF_001402915.1	s__Devosia_A sp001402915	83.5965	771	1003	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_000970465.2	s__Devosia_A insulae	83.3257	715	1003	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_903842455.1	s__Devosia_A sp903842455	82.0365	631	1003	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_016713105.1	s__Devosia_A sp016713105	81.7263	663	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:07:59,773] [INFO] GTDB search result was written to GCA_017306945.1_ASM1730694v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:07:59,774] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:07:59,778] [INFO] DFAST_QC result json was written to GCA_017306945.1_ASM1730694v1_genomic.fna/dqc_result.json
[2023-06-28 20:07:59,778] [INFO] DFAST_QC completed!
[2023-06-28 20:07:59,778] [INFO] Total running time: 0h1m10s