[2024-01-24 14:28:15,644] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg1feed2d4-8497-4c8f-b98a-daea3998e897/dqc_reference
[2024-01-24 14:28:17,077] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,078] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,078] [INFO] Running command: gunzip -c /var/lib/cwl/stgb90e3645-a9ac-4372-af86-3f1bebdac8eb/GCF_023061185.1_ASM2306118v1_genomic.fna.gz | prodigal -d GCF_023061185.1_ASM2306118v1_genomic.fna/cds.fna -a GCF_023061185.1_ASM2306118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:28,273] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:28,273] [INFO] Task started: HMMsearch
[2024-01-24 14:28:28,273] [INFO] Running command: hmmsearch --tblout GCF_023061185.1_ASM2306118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1feed2d4-8497-4c8f-b98a-daea3998e897/dqc_reference/reference_markers.hmm GCF_023061185.1_ASM2306118v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:28,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:28,623] [INFO] Found 6/6 markers.
[2024-01-24 14:28:28,655] [INFO] Query marker FASTA was written to GCF_023061185.1_ASM2306118v1_genomic.fna/markers.fasta
[2024-01-24 14:28:28,655] [INFO] Task started: Blastn
[2024-01-24 14:28:28,655] [INFO] Running command: blastn -query GCF_023061185.1_ASM2306118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1feed2d4-8497-4c8f-b98a-daea3998e897/dqc_reference/reference_markers.fasta -out GCF_023061185.1_ASM2306118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:29,614] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:29,618] [INFO] Selected 6 target genomes.
[2024-01-24 14:28:29,618] [INFO] Target genome list was writen to GCF_023061185.1_ASM2306118v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:29,624] [INFO] Task started: fastANI
[2024-01-24 14:28:29,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgb90e3645-a9ac-4372-af86-3f1bebdac8eb/GCF_023061185.1_ASM2306118v1_genomic.fna.gz --refList GCF_023061185.1_ASM2306118v1_genomic.fna/target_genomes.txt --output GCF_023061185.1_ASM2306118v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:34,759] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:34,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1feed2d4-8497-4c8f-b98a-daea3998e897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:34,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1feed2d4-8497-4c8f-b98a-daea3998e897/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:34,766] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:34,766] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:28:34,766] [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 beijerinckii	strain=DSM 7218	GCA_023061185.1	86179	86179	type	True	100.0	1086	1088	95	inconclusive
Chromohalobacter japonicus	strain=CECT 7219	GCA_023061175.1	223900	223900	type	True	97.3564	986	1088	95	inconclusive
Chromohalobacter moromii	strain=TMW 2.2308	GCA_023091865.1	2860329	2860329	type	True	94.0339	975	1088	95	below_threshold
Chromohalobacter canadensis	strain=DSM 6769	GCA_023061155.1	141389	141389	suspected-type	True	92.9252	961	1088	95	below_threshold
Chromohalobacter sarecensis	strain=DSM 15547	GCA_023061135.1	245294	245294	type	True	89.3164	931	1088	95	below_threshold
Chromohalobacter nigrandesensis	strain=DSM 14323	GCA_023061285.1	119863	119863	type	True	88.8788	897	1088	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:34,768] [INFO] DFAST Taxonomy check result was written to GCF_023061185.1_ASM2306118v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:34,769] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:34,769] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:34,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1feed2d4-8497-4c8f-b98a-daea3998e897/dqc_reference/checkm_data
[2024-01-24 14:28:34,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:34,808] [INFO] Task started: CheckM
[2024-01-24 14:28:34,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023061185.1_ASM2306118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023061185.1_ASM2306118v1_genomic.fna/checkm_input GCF_023061185.1_ASM2306118v1_genomic.fna/checkm_result
[2024-01-24 14:29:09,607] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:09,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:09,629] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:09,630] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:09,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023061185.1_ASM2306118v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:09,630] [INFO] Task started: Blastn
[2024-01-24 14:29:09,631] [INFO] Running command: blastn -query GCF_023061185.1_ASM2306118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1feed2d4-8497-4c8f-b98a-daea3998e897/dqc_reference/reference_markers_gtdb.fasta -out GCF_023061185.1_ASM2306118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:11,204] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:11,209] [INFO] Selected 7 target genomes.
[2024-01-24 14:29:11,209] [INFO] Target genome list was writen to GCF_023061185.1_ASM2306118v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:11,215] [INFO] Task started: fastANI
[2024-01-24 14:29:11,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgb90e3645-a9ac-4372-af86-3f1bebdac8eb/GCF_023061185.1_ASM2306118v1_genomic.fna.gz --refList GCF_023061185.1_ASM2306118v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023061185.1_ASM2306118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:17,305] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:17,312] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:17,312] [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_000821045.2	s__Chromohalobacter japonicus	96.5304	985	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	95.33	95.33	0.87	0.87	2	conclusive
GCF_013393405.1	s__Chromohalobacter salexigens_A	93.7631	962	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900221025.1	s__Chromohalobacter canadensis	92.6835	969	1088	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	87.8575	913	1088	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	85.639	907	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	98.07	97.76	0.86	0.85	6	-
GCF_004117855.1	s__Halomonas_C coralii	79.3839	487	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731955.1	s__Halomonas_C zincidurans	79.3826	467	1088	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:17,314] [INFO] GTDB search result was written to GCF_023061185.1_ASM2306118v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:17,315] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:17,317] [INFO] DFAST_QC result json was written to GCF_023061185.1_ASM2306118v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:17,318] [INFO] DFAST_QC completed!
[2024-01-24 14:29:17,318] [INFO] Total running time: 0h1m2s