[2024-01-24 11:59:35,652] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg33393711-83f0-4039-9e11-9501714eecb7/dqc_reference
[2024-01-24 11:59:36,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,874] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a4e0ec7-19db-4d45-886b-cd041c435f7b/GCF_003576245.1_ASM357624v1_genomic.fna.gz | prodigal -d GCF_003576245.1_ASM357624v1_genomic.fna/cds.fna -a GCF_003576245.1_ASM357624v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:46,114] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:46,115] [INFO] Task started: HMMsearch
[2024-01-24 11:59:46,115] [INFO] Running command: hmmsearch --tblout GCF_003576245.1_ASM357624v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33393711-83f0-4039-9e11-9501714eecb7/dqc_reference/reference_markers.hmm GCF_003576245.1_ASM357624v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:46,423] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:46,424] [INFO] Found 6/6 markers.
[2024-01-24 11:59:46,452] [INFO] Query marker FASTA was written to GCF_003576245.1_ASM357624v1_genomic.fna/markers.fasta
[2024-01-24 11:59:46,453] [INFO] Task started: Blastn
[2024-01-24 11:59:46,453] [INFO] Running command: blastn -query GCF_003576245.1_ASM357624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33393711-83f0-4039-9e11-9501714eecb7/dqc_reference/reference_markers.fasta -out GCF_003576245.1_ASM357624v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:47,319] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:47,323] [INFO] Selected 14 target genomes.
[2024-01-24 11:59:47,324] [INFO] Target genome list was writen to GCF_003576245.1_ASM357624v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:47,392] [INFO] Task started: fastANI
[2024-01-24 11:59:47,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a4e0ec7-19db-4d45-886b-cd041c435f7b/GCF_003576245.1_ASM357624v1_genomic.fna.gz --refList GCF_003576245.1_ASM357624v1_genomic.fna/target_genomes.txt --output GCF_003576245.1_ASM357624v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:57,706] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:57,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33393711-83f0-4039-9e11-9501714eecb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:57,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33393711-83f0-4039-9e11-9501714eecb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:57,727] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:57,728] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:57,728] [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 algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	100.0	1063	1065	95	conclusive
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	85.7525	917	1065	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	81.6974	756	1065	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	79.3536	526	1065	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	79.327	542	1065	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	79.3029	483	1065	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	79.2617	474	1065	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	79.2316	521	1065	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.4918	205	1065	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	77.4317	219	1065	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.4715	89	1065	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.0635	60	1065	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.5771	90	1065	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.3441	64	1065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:57,730] [INFO] DFAST Taxonomy check result was written to GCF_003576245.1_ASM357624v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:57,730] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:57,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:57,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33393711-83f0-4039-9e11-9501714eecb7/dqc_reference/checkm_data
[2024-01-24 11:59:57,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:57,763] [INFO] Task started: CheckM
[2024-01-24 11:59:57,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003576245.1_ASM357624v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003576245.1_ASM357624v1_genomic.fna/checkm_input GCF_003576245.1_ASM357624v1_genomic.fna/checkm_result
[2024-01-24 12:00:29,536] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:29,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:29,560] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:29,560] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:29,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003576245.1_ASM357624v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:29,561] [INFO] Task started: Blastn
[2024-01-24 12:00:29,561] [INFO] Running command: blastn -query GCF_003576245.1_ASM357624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33393711-83f0-4039-9e11-9501714eecb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003576245.1_ASM357624v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:31,246] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:31,250] [INFO] Selected 9 target genomes.
[2024-01-24 12:00:31,250] [INFO] Target genome list was writen to GCF_003576245.1_ASM357624v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:31,268] [INFO] Task started: fastANI
[2024-01-24 12:00:31,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a4e0ec7-19db-4d45-886b-cd041c435f7b/GCF_003576245.1_ASM357624v1_genomic.fna.gz --refList GCF_003576245.1_ASM357624v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003576245.1_ASM357624v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:38,033] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:38,045] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:38,045] [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_003576245.1	s__Henriciella algicola	100.0	1063	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012960415.1	s__Henriciella sp012960415	89.5853	923	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_003576345.1	s__Henriciella barbarensis	85.7585	916	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376805.1	s__Henriciella marina	81.6878	757	1065	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	81.5639	684	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	-
GCF_002088935.1	s__Henriciella litoralis	79.368	524	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088945.1	s__Henriciella pelagia	79.2571	474	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000961795.1	s__Hyphomonas sp000961795	77.4001	220	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830285.1	s__Hyphomonas sp018830285	76.9317	221	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:38,046] [INFO] GTDB search result was written to GCF_003576245.1_ASM357624v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:38,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:38,052] [INFO] DFAST_QC result json was written to GCF_003576245.1_ASM357624v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:38,052] [INFO] DFAST_QC completed!
[2024-01-24 12:00:38,052] [INFO] Total running time: 0h1m2s