[2024-01-24 12:39:41,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg244ea132-3329-46c7-9b36-b21fac2da2ad/dqc_reference
[2024-01-24 12:39:42,913] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:42,914] [INFO] Task started: Prodigal
[2024-01-24 12:39:42,914] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a94ef1c-073b-41c8-bc9c-da802b3c342f/GCF_002088935.1_ASM208893v1_genomic.fna.gz | prodigal -d GCF_002088935.1_ASM208893v1_genomic.fna/cds.fna -a GCF_002088935.1_ASM208893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:54,202] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:54,202] [INFO] Task started: HMMsearch
[2024-01-24 12:39:54,202] [INFO] Running command: hmmsearch --tblout GCF_002088935.1_ASM208893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg244ea132-3329-46c7-9b36-b21fac2da2ad/dqc_reference/reference_markers.hmm GCF_002088935.1_ASM208893v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:54,493] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:54,495] [INFO] Found 6/6 markers.
[2024-01-24 12:39:54,532] [INFO] Query marker FASTA was written to GCF_002088935.1_ASM208893v1_genomic.fna/markers.fasta
[2024-01-24 12:39:54,532] [INFO] Task started: Blastn
[2024-01-24 12:39:54,533] [INFO] Running command: blastn -query GCF_002088935.1_ASM208893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg244ea132-3329-46c7-9b36-b21fac2da2ad/dqc_reference/reference_markers.fasta -out GCF_002088935.1_ASM208893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:55,412] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:55,418] [INFO] Selected 18 target genomes.
[2024-01-24 12:39:55,419] [INFO] Target genome list was writen to GCF_002088935.1_ASM208893v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:55,427] [INFO] Task started: fastANI
[2024-01-24 12:39:55,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a94ef1c-073b-41c8-bc9c-da802b3c342f/GCF_002088935.1_ASM208893v1_genomic.fna.gz --refList GCF_002088935.1_ASM208893v1_genomic.fna/target_genomes.txt --output GCF_002088935.1_ASM208893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:11,540] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:11,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg244ea132-3329-46c7-9b36-b21fac2da2ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:11,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg244ea132-3329-46c7-9b36-b21fac2da2ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:11,555] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:11,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:11,555] [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
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	100.0	1254	1255	95	conclusive
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	80.5442	481	1255	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	80.3745	499	1255	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	79.7414	529	1255	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	79.4868	526	1255	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	79.3153	528	1255	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	79.2792	524	1255	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	79.0659	478	1255	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	77.0952	205	1255	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.1785	50	1255	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.1151	62	1255	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	76.0486	53	1255	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.6556	61	1255	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.5635	54	1255	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	75.5162	67	1255	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.4206	53	1255	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.3846	51	1255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:11,557] [INFO] DFAST Taxonomy check result was written to GCF_002088935.1_ASM208893v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:11,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:11,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:11,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg244ea132-3329-46c7-9b36-b21fac2da2ad/dqc_reference/checkm_data
[2024-01-24 12:40:11,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:11,604] [INFO] Task started: CheckM
[2024-01-24 12:40:11,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002088935.1_ASM208893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002088935.1_ASM208893v1_genomic.fna/checkm_input GCF_002088935.1_ASM208893v1_genomic.fna/checkm_result
[2024-01-24 12:40:48,981] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:48,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:49,005] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:49,006] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:49,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002088935.1_ASM208893v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:49,007] [INFO] Task started: Blastn
[2024-01-24 12:40:49,007] [INFO] Running command: blastn -query GCF_002088935.1_ASM208893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg244ea132-3329-46c7-9b36-b21fac2da2ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_002088935.1_ASM208893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:50,317] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:50,320] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:50,320] [INFO] Target genome list was writen to GCF_002088935.1_ASM208893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:50,347] [INFO] Task started: fastANI
[2024-01-24 12:40:50,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a94ef1c-073b-41c8-bc9c-da802b3c342f/GCF_002088935.1_ASM208893v1_genomic.fna.gz --refList GCF_002088935.1_ASM208893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002088935.1_ASM208893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:59,915] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:59,930] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:59,931] [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_002088935.1	s__Henriciella litoralis	100.0	1254	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002088945.1	s__Henriciella pelagia	80.5442	481	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017792385.1	s__Hyphomonas sp017792385	79.9629	244	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088975.1	s__Henriciella aquimarina	79.7414	529	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576285.1	s__Henriciella sp003576285	79.7102	511	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCA_012960415.1	s__Henriciella sp012960415	79.6026	508	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_000376805.1	s__Henriciella marina	79.4962	525	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576245.1	s__Henriciella algicola	79.3153	528	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733705.1	s__Henriciella sp002733705	79.1755	477	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_003576345.1	s__Henriciella barbarensis	79.0622	476	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763715.1	s__Hyphomonas sp014763715	77.2737	224	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018413645.1	s__Roseococcus sp018413645	75.6556	61	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791365.1	s__Terricaulis sp016791365	75.5681	52	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005855.1	s__Rhodovarius sp004005855	75.3846	51	1255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:59,932] [INFO] GTDB search result was written to GCF_002088935.1_ASM208893v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:59,933] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:59,937] [INFO] DFAST_QC result json was written to GCF_002088935.1_ASM208893v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:59,938] [INFO] DFAST_QC completed!
[2024-01-24 12:40:59,938] [INFO] Total running time: 0h1m18s