[2024-01-24 15:26:52,157] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:52,159] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:52,160] [INFO] DQC Reference Directory: /var/lib/cwl/stg05c99d45-0861-412a-892a-1ed5c9e1b1c2/dqc_reference
[2024-01-24 15:26:53,389] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:53,390] [INFO] Task started: Prodigal
[2024-01-24 15:26:53,390] [INFO] Running command: gunzip -c /var/lib/cwl/stg9aaad605-2e05-4b19-8b77-aa32dfbfb24d/GCF_010119205.1_ASM1011920v1_genomic.fna.gz | prodigal -d GCF_010119205.1_ASM1011920v1_genomic.fna/cds.fna -a GCF_010119205.1_ASM1011920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:11,950] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:11,950] [INFO] Task started: HMMsearch
[2024-01-24 15:27:11,950] [INFO] Running command: hmmsearch --tblout GCF_010119205.1_ASM1011920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05c99d45-0861-412a-892a-1ed5c9e1b1c2/dqc_reference/reference_markers.hmm GCF_010119205.1_ASM1011920v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:12,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:12,217] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9aaad605-2e05-4b19-8b77-aa32dfbfb24d/GCF_010119205.1_ASM1011920v1_genomic.fna.gz]
[2024-01-24 15:27:12,250] [INFO] Query marker FASTA was written to GCF_010119205.1_ASM1011920v1_genomic.fna/markers.fasta
[2024-01-24 15:27:12,250] [INFO] Task started: Blastn
[2024-01-24 15:27:12,250] [INFO] Running command: blastn -query GCF_010119205.1_ASM1011920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05c99d45-0861-412a-892a-1ed5c9e1b1c2/dqc_reference/reference_markers.fasta -out GCF_010119205.1_ASM1011920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:12,799] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:12,803] [INFO] Selected 6 target genomes.
[2024-01-24 15:27:12,803] [INFO] Target genome list was writen to GCF_010119205.1_ASM1011920v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:12,806] [INFO] Task started: fastANI
[2024-01-24 15:27:12,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaad605-2e05-4b19-8b77-aa32dfbfb24d/GCF_010119205.1_ASM1011920v1_genomic.fna.gz --refList GCF_010119205.1_ASM1011920v1_genomic.fna/target_genomes.txt --output GCF_010119205.1_ASM1011920v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:20,537] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:20,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05c99d45-0861-412a-892a-1ed5c9e1b1c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:20,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05c99d45-0861-412a-892a-1ed5c9e1b1c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:20,545] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:20,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:20,545] [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
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	100.0	1298	1298	95	conclusive
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	93.037	1090	1298	95	below_threshold
Halomicroarcula amylolytica	strain=LR21	GCA_004681185.1	2562280	2562280	type	True	89.7382	1090	1298	95	below_threshold
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	84.0061	864	1298	95	below_threshold
Halomicroarcula pellucida	strain=JCM 17820	GCA_014647235.1	1427151	1427151	type	True	83.6244	837	1298	95	below_threshold
Halomicroarcula pellucida	strain=CECT 7537	GCA_019599515.1	1427151	1427151	type	True	83.5919	840	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:20,547] [INFO] DFAST Taxonomy check result was written to GCF_010119205.1_ASM1011920v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:20,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:20,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:20,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05c99d45-0861-412a-892a-1ed5c9e1b1c2/dqc_reference/checkm_data
[2024-01-24 15:27:20,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:20,588] [INFO] Task started: CheckM
[2024-01-24 15:27:20,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119205.1_ASM1011920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119205.1_ASM1011920v1_genomic.fna/checkm_input GCF_010119205.1_ASM1011920v1_genomic.fna/checkm_result
[2024-01-24 15:28:09,974] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:09,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:10,000] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:10,000] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:10,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119205.1_ASM1011920v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:10,001] [INFO] Task started: Blastn
[2024-01-24 15:28:10,001] [INFO] Running command: blastn -query GCF_010119205.1_ASM1011920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05c99d45-0861-412a-892a-1ed5c9e1b1c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119205.1_ASM1011920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:10,515] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:10,519] [INFO] Selected 7 target genomes.
[2024-01-24 15:28:10,519] [INFO] Target genome list was writen to GCF_010119205.1_ASM1011920v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:10,525] [INFO] Task started: fastANI
[2024-01-24 15:28:10,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aaad605-2e05-4b19-8b77-aa32dfbfb24d/GCF_010119205.1_ASM1011920v1_genomic.fna.gz --refList GCF_010119205.1_ASM1011920v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119205.1_ASM1011920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:16,999] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:17,005] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:17,006] [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_010119205.1	s__Halomicroarcula limicola	100.0	1298	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004681185.1	s__Halomicroarcula amylolytica	89.7177	1092	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647235.1	s__Halomicroarcula pellucida	83.6143	838	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	96.63	96.63	0.87	0.87	2	-
GCF_010119195.1	s__Haloarcula salina	82.7319	736	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003021755.1	s__Halomicroarcula sp003021755	82.148	400	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005406125.1	s__Haloarcula sp005406125	81.1696	648	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844335.1	s__Haloarcula taiwanensis	80.9293	620	1298	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.00	98.44	0.94	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:17,007] [INFO] GTDB search result was written to GCF_010119205.1_ASM1011920v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:17,008] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:17,010] [INFO] DFAST_QC result json was written to GCF_010119205.1_ASM1011920v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:17,011] [INFO] DFAST_QC completed!
[2024-01-24 15:28:17,011] [INFO] Total running time: 0h1m25s