[2024-01-25 18:09:50,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:50,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:50,682] [INFO] DQC Reference Directory: /var/lib/cwl/stg988412e1-145e-4c4c-b561-feb5e833f22c/dqc_reference
[2024-01-25 18:09:51,827] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:51,827] [INFO] Task started: Prodigal
[2024-01-25 18:09:51,828] [INFO] Running command: gunzip -c /var/lib/cwl/stge799d52e-57e3-4d73-997f-02eb25641e6a/GCF_023061285.1_ASM2306128v1_genomic.fna.gz | prodigal -d GCF_023061285.1_ASM2306128v1_genomic.fna/cds.fna -a GCF_023061285.1_ASM2306128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:01,885] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:01,885] [INFO] Task started: HMMsearch
[2024-01-25 18:10:01,886] [INFO] Running command: hmmsearch --tblout GCF_023061285.1_ASM2306128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg988412e1-145e-4c4c-b561-feb5e833f22c/dqc_reference/reference_markers.hmm GCF_023061285.1_ASM2306128v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:02,185] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:02,186] [INFO] Found 6/6 markers.
[2024-01-25 18:10:02,215] [INFO] Query marker FASTA was written to GCF_023061285.1_ASM2306128v1_genomic.fna/markers.fasta
[2024-01-25 18:10:02,215] [INFO] Task started: Blastn
[2024-01-25 18:10:02,215] [INFO] Running command: blastn -query GCF_023061285.1_ASM2306128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg988412e1-145e-4c4c-b561-feb5e833f22c/dqc_reference/reference_markers.fasta -out GCF_023061285.1_ASM2306128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:03,032] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:03,035] [INFO] Selected 6 target genomes.
[2024-01-25 18:10:03,035] [INFO] Target genome list was writen to GCF_023061285.1_ASM2306128v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:03,040] [INFO] Task started: fastANI
[2024-01-25 18:10:03,040] [INFO] Running command: fastANI --query /var/lib/cwl/stge799d52e-57e3-4d73-997f-02eb25641e6a/GCF_023061285.1_ASM2306128v1_genomic.fna.gz --refList GCF_023061285.1_ASM2306128v1_genomic.fna/target_genomes.txt --output GCF_023061285.1_ASM2306128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:08,187] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:08,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg988412e1-145e-4c4c-b561-feb5e833f22c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:08,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg988412e1-145e-4c4c-b561-feb5e833f22c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:08,193] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:08,193] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:08,193] [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
Chromohalobacter nigrandesensis	strain=DSM 14323	GCA_023061285.1	119863	119863	type	True	100.0	1187	1188	95	conclusive
Chromohalobacter sarecensis	strain=DSM 15547	GCA_023061135.1	245294	245294	type	True	94.9592	1000	1188	95	below_threshold
Chromohalobacter japonicus	strain=CECT 7219	GCA_023061175.1	223900	223900	type	True	89.0196	895	1188	95	below_threshold
Chromohalobacter canadensis	strain=DSM 6769	GCA_023061155.1	141389	141389	suspected-type	True	89.0105	943	1188	95	below_threshold
Chromohalobacter beijerinckii	strain=DSM 7218	GCA_023061185.1	86179	86179	type	True	88.9986	893	1188	95	below_threshold
Chromohalobacter moromii	strain=TMW 2.2308	GCA_023091865.1	2860329	2860329	type	True	88.9058	936	1188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:08,195] [INFO] DFAST Taxonomy check result was written to GCF_023061285.1_ASM2306128v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:08,195] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:08,195] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:08,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg988412e1-145e-4c4c-b561-feb5e833f22c/dqc_reference/checkm_data
[2024-01-25 18:10:08,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:08,234] [INFO] Task started: CheckM
[2024-01-25 18:10:08,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023061285.1_ASM2306128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023061285.1_ASM2306128v1_genomic.fna/checkm_input GCF_023061285.1_ASM2306128v1_genomic.fna/checkm_result
[2024-01-25 18:10:39,533] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:39,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:39,554] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:39,554] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:39,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023061285.1_ASM2306128v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:39,555] [INFO] Task started: Blastn
[2024-01-25 18:10:39,555] [INFO] Running command: blastn -query GCF_023061285.1_ASM2306128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg988412e1-145e-4c4c-b561-feb5e833f22c/dqc_reference/reference_markers_gtdb.fasta -out GCF_023061285.1_ASM2306128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:41,014] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:41,017] [INFO] Selected 6 target genomes.
[2024-01-25 18:10:41,017] [INFO] Target genome list was writen to GCF_023061285.1_ASM2306128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:41,021] [INFO] Task started: fastANI
[2024-01-25 18:10:41,021] [INFO] Running command: fastANI --query /var/lib/cwl/stge799d52e-57e3-4d73-997f-02eb25641e6a/GCF_023061285.1_ASM2306128v1_genomic.fna.gz --refList GCF_023061285.1_ASM2306128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023061285.1_ASM2306128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:45,901] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:45,906] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:10:45,906] [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_900221025.1	s__Chromohalobacter canadensis	88.9365	944	1188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821045.2	s__Chromohalobacter japonicus	88.9357	899	1188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	95.33	95.33	0.87	0.87	2	-
GCF_013393405.1	s__Chromohalobacter salexigens_A	88.8083	896	1188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364315.1	s__Chromohalobacter marismortui	86.3334	947	1188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000761475.1	s__Chromohalobacter israelensis	83.9219	860	1188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	98.07	97.76	0.86	0.85	6	-
GCF_000759345.1	s__Halomonas_A xinjiangensis	78.1208	307	1188	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:45,907] [INFO] GTDB search result was written to GCF_023061285.1_ASM2306128v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:45,908] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:45,910] [INFO] DFAST_QC result json was written to GCF_023061285.1_ASM2306128v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:45,910] [INFO] DFAST_QC completed!
[2024-01-25 18:10:45,910] [INFO] Total running time: 0h0m55s