[2024-01-24 13:28:29,251] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:29,253] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:29,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ea5c785-5340-4e4a-abe6-b9b8dfffebf3/dqc_reference
[2024-01-24 13:28:30,452] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,453] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,453] [INFO] Running command: gunzip -c /var/lib/cwl/stgecd87875-3e02-400e-9810-2232995a1383/GCF_014904795.1_ASM1490479v1_genomic.fna.gz | prodigal -d GCF_014904795.1_ASM1490479v1_genomic.fna/cds.fna -a GCF_014904795.1_ASM1490479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:44,381] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:44,382] [INFO] Task started: HMMsearch
[2024-01-24 13:28:44,382] [INFO] Running command: hmmsearch --tblout GCF_014904795.1_ASM1490479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ea5c785-5340-4e4a-abe6-b9b8dfffebf3/dqc_reference/reference_markers.hmm GCF_014904795.1_ASM1490479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:44,671] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:44,672] [INFO] Found 6/6 markers.
[2024-01-24 13:28:44,714] [INFO] Query marker FASTA was written to GCF_014904795.1_ASM1490479v1_genomic.fna/markers.fasta
[2024-01-24 13:28:44,714] [INFO] Task started: Blastn
[2024-01-24 13:28:44,715] [INFO] Running command: blastn -query GCF_014904795.1_ASM1490479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea5c785-5340-4e4a-abe6-b9b8dfffebf3/dqc_reference/reference_markers.fasta -out GCF_014904795.1_ASM1490479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:45,574] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:45,579] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:45,579] [INFO] Target genome list was writen to GCF_014904795.1_ASM1490479v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:45,584] [INFO] Task started: fastANI
[2024-01-24 13:28:45,584] [INFO] Running command: fastANI --query /var/lib/cwl/stgecd87875-3e02-400e-9810-2232995a1383/GCF_014904795.1_ASM1490479v1_genomic.fna.gz --refList GCF_014904795.1_ASM1490479v1_genomic.fna/target_genomes.txt --output GCF_014904795.1_ASM1490479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:58,197] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:58,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ea5c785-5340-4e4a-abe6-b9b8dfffebf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:58,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ea5c785-5340-4e4a-abe6-b9b8dfffebf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:58,207] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:58,207] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:58,207] [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
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	100.0	1566	1570	95	conclusive
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	92.2707	1356	1570	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	81.4716	963	1570	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	81.2338	954	1570	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.3946	363	1570	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.9574	232	1570	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.1301	192	1570	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.0696	136	1570	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.9378	153	1570	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	75.8974	161	1570	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.7882	119	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:58,209] [INFO] DFAST Taxonomy check result was written to GCF_014904795.1_ASM1490479v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:58,209] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:58,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:58,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ea5c785-5340-4e4a-abe6-b9b8dfffebf3/dqc_reference/checkm_data
[2024-01-24 13:28:58,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:58,254] [INFO] Task started: CheckM
[2024-01-24 13:28:58,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014904795.1_ASM1490479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014904795.1_ASM1490479v1_genomic.fna/checkm_input GCF_014904795.1_ASM1490479v1_genomic.fna/checkm_result
[2024-01-24 13:29:41,612] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:41,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:41,629] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:41,629] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:41,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014904795.1_ASM1490479v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:41,630] [INFO] Task started: Blastn
[2024-01-24 13:29:41,630] [INFO] Running command: blastn -query GCF_014904795.1_ASM1490479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ea5c785-5340-4e4a-abe6-b9b8dfffebf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014904795.1_ASM1490479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:43,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:43,281] [INFO] Selected 11 target genomes.
[2024-01-24 13:29:43,281] [INFO] Target genome list was writen to GCF_014904795.1_ASM1490479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:43,289] [INFO] Task started: fastANI
[2024-01-24 13:29:43,289] [INFO] Running command: fastANI --query /var/lib/cwl/stgecd87875-3e02-400e-9810-2232995a1383/GCF_014904795.1_ASM1490479v1_genomic.fna.gz --refList GCF_014904795.1_ASM1490479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014904795.1_ASM1490479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:54,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:54,017] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:54,017] [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_014904795.1	s__Nisaea nitritireducens	100.0	1566	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000426505.1	s__Nisaea denitrificans	92.2707	1356	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	81.4743	962	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	81.4029	915	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	77.5064	387	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_000171835.1	s__Thalassobaculum_A sp000171835	76.7714	257	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780745.1	s__JADHLJ01 sp016780745	76.5269	179	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JADHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	76.3378	194	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869375.1	s__SHVZ01 sp016869375	76.3324	167	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107285.1	s__Roseomonas sp016107285	76.0188	131	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379805.1	s__Magnetospirillum sp014379805	75.4609	58	1570	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:54,019] [INFO] GTDB search result was written to GCF_014904795.1_ASM1490479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:54,019] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:54,023] [INFO] DFAST_QC result json was written to GCF_014904795.1_ASM1490479v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:54,023] [INFO] DFAST_QC completed!
[2024-01-24 13:29:54,023] [INFO] Total running time: 0h1m25s