[2024-01-25 20:20:05,999] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:06,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:06,001] [INFO] DQC Reference Directory: /var/lib/cwl/stga001660f-a907-4e80-8ce0-ca3bdb2109d8/dqc_reference
[2024-01-25 20:20:07,139] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:07,145] [INFO] Task started: Prodigal
[2024-01-25 20:20:07,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg03919a27-381e-4ae8-92dc-5e5f8df543d0/GCF_003675875.1_ASM367587v1_genomic.fna.gz | prodigal -d GCF_003675875.1_ASM367587v1_genomic.fna/cds.fna -a GCF_003675875.1_ASM367587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:23,123] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:23,123] [INFO] Task started: HMMsearch
[2024-01-25 20:20:23,123] [INFO] Running command: hmmsearch --tblout GCF_003675875.1_ASM367587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga001660f-a907-4e80-8ce0-ca3bdb2109d8/dqc_reference/reference_markers.hmm GCF_003675875.1_ASM367587v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:23,429] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:23,430] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg03919a27-381e-4ae8-92dc-5e5f8df543d0/GCF_003675875.1_ASM367587v1_genomic.fna.gz]
[2024-01-25 20:20:23,463] [INFO] Query marker FASTA was written to GCF_003675875.1_ASM367587v1_genomic.fna/markers.fasta
[2024-01-25 20:20:23,464] [INFO] Task started: Blastn
[2024-01-25 20:20:23,464] [INFO] Running command: blastn -query GCF_003675875.1_ASM367587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga001660f-a907-4e80-8ce0-ca3bdb2109d8/dqc_reference/reference_markers.fasta -out GCF_003675875.1_ASM367587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:23,982] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:23,984] [INFO] Selected 8 target genomes.
[2024-01-25 20:20:23,985] [INFO] Target genome list was writen to GCF_003675875.1_ASM367587v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:23,990] [INFO] Task started: fastANI
[2024-01-25 20:20:23,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg03919a27-381e-4ae8-92dc-5e5f8df543d0/GCF_003675875.1_ASM367587v1_genomic.fna.gz --refList GCF_003675875.1_ASM367587v1_genomic.fna/target_genomes.txt --output GCF_003675875.1_ASM367587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:32,203] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:32,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga001660f-a907-4e80-8ce0-ca3bdb2109d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:32,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga001660f-a907-4e80-8ce0-ca3bdb2109d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:32,211] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:32,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:32,211] [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
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	100.0	1365	1367	95	conclusive
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	84.1395	782	1367	95	below_threshold
Halostella salina	strain=CBA1114	GCA_003675855.1	1547897	1547897	type	True	83.5645	769	1367	95	below_threshold
Natronoarchaeum rubrum	strain=GX48	GCA_024494695.1	755311	755311	type	True	79.6125	597	1367	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	79.1756	609	1367	95	below_threshold
Halorussus marinus	strain=LYG-36	GCA_004765795.1	2505976	2505976	type	True	78.9811	557	1367	95	below_threshold
Halegenticoccus soli	strain=SYSU A9-0	GCA_002844195.1	1985678	1985678	type	True	78.8452	600	1367	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	78.6653	590	1367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:32,212] [INFO] DFAST Taxonomy check result was written to GCF_003675875.1_ASM367587v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:32,213] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:32,213] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:32,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga001660f-a907-4e80-8ce0-ca3bdb2109d8/dqc_reference/checkm_data
[2024-01-25 20:20:32,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:32,256] [INFO] Task started: CheckM
[2024-01-25 20:20:32,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003675875.1_ASM367587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003675875.1_ASM367587v1_genomic.fna/checkm_input GCF_003675875.1_ASM367587v1_genomic.fna/checkm_result
[2024-01-25 20:21:15,701] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:15,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:15,720] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:15,720] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:15,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003675875.1_ASM367587v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:15,721] [INFO] Task started: Blastn
[2024-01-25 20:21:15,721] [INFO] Running command: blastn -query GCF_003675875.1_ASM367587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga001660f-a907-4e80-8ce0-ca3bdb2109d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003675875.1_ASM367587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:16,288] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:16,291] [INFO] Selected 7 target genomes.
[2024-01-25 20:21:16,292] [INFO] Target genome list was writen to GCF_003675875.1_ASM367587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:16,297] [INFO] Task started: fastANI
[2024-01-25 20:21:16,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg03919a27-381e-4ae8-92dc-5e5f8df543d0/GCF_003675875.1_ASM367587v1_genomic.fna.gz --refList GCF_003675875.1_ASM367587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003675875.1_ASM367587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:23,384] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:23,390] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:23,390] [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_003675875.1	s__Halostella sp003675875	100.0	1365	1367	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_003023565.1	s__Halostella sp003023565	88.4599	810	1367	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785955.1	s__Halostella litorea	84.1737	779	1367	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675855.1	s__Halostella salina	83.6428	762	1367	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005954745.1	s__Halostella pelagica	82.7688	780	1367	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	98.54	98.54	0.89	0.89	2	-
GCF_003369835.1	s__Halorussus rarus	79.173	607	1367	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004698125.1	s__Halosimplex halophilum	78.6275	595	1367	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:23,392] [INFO] GTDB search result was written to GCF_003675875.1_ASM367587v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:23,392] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:23,394] [INFO] DFAST_QC result json was written to GCF_003675875.1_ASM367587v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:23,394] [INFO] DFAST_QC completed!
[2024-01-25 20:21:23,395] [INFO] Total running time: 0h1m17s