[2024-01-24 12:44:52,555] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:52,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:52,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg52fe6842-146d-4bba-8ed2-eb696ba07e1d/dqc_reference
[2024-01-24 12:44:53,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:53,798] [INFO] Task started: Prodigal
[2024-01-24 12:44:53,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg095d9259-9b00-4fe3-afae-eedf8da3820d/GCF_000685635.1_ASM68563v1_genomic.fna.gz | prodigal -d GCF_000685635.1_ASM68563v1_genomic.fna/cds.fna -a GCF_000685635.1_ASM68563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:14,354] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:14,354] [INFO] Task started: HMMsearch
[2024-01-24 12:45:14,354] [INFO] Running command: hmmsearch --tblout GCF_000685635.1_ASM68563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52fe6842-146d-4bba-8ed2-eb696ba07e1d/dqc_reference/reference_markers.hmm GCF_000685635.1_ASM68563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:14,607] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:14,609] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg095d9259-9b00-4fe3-afae-eedf8da3820d/GCF_000685635.1_ASM68563v1_genomic.fna.gz]
[2024-01-24 12:45:14,648] [INFO] Query marker FASTA was written to GCF_000685635.1_ASM68563v1_genomic.fna/markers.fasta
[2024-01-24 12:45:14,648] [INFO] Task started: Blastn
[2024-01-24 12:45:14,649] [INFO] Running command: blastn -query GCF_000685635.1_ASM68563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52fe6842-146d-4bba-8ed2-eb696ba07e1d/dqc_reference/reference_markers.fasta -out GCF_000685635.1_ASM68563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:15,185] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:15,190] [INFO] Selected 7 target genomes.
[2024-01-24 12:45:15,191] [INFO] Target genome list was writen to GCF_000685635.1_ASM68563v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:15,198] [INFO] Task started: fastANI
[2024-01-24 12:45:15,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg095d9259-9b00-4fe3-afae-eedf8da3820d/GCF_000685635.1_ASM68563v1_genomic.fna.gz --refList GCF_000685635.1_ASM68563v1_genomic.fna/target_genomes.txt --output GCF_000685635.1_ASM68563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:22,208] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:22,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52fe6842-146d-4bba-8ed2-eb696ba07e1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:22,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52fe6842-146d-4bba-8ed2-eb696ba07e1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:22,221] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:45:22,221] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:22,222] [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
Haloferax mediterranei	strain=ATCC 33500	GCA_000685635.1	2252	2252	type	True	99.9971	1297	1300	95	conclusive
Haloferax mediterranei	strain=ATCC 33500	GCA_000337295.1	2252	2252	type	True	99.9753	1287	1300	95	conclusive
Haloferax mediterranei	strain=CGMCC 1.2087	GCA_000306765.2	2252	2252	type	True	99.965	1291	1300	95	conclusive
Haloferax mediterranei	strain=ATCC 33500	GCA_005406325.1	2252	2252	type	True	99.9637	1293	1300	95	conclusive
Haloferax mucosum	strain=ATCC BAA-1512	GCA_000337815.1	403181	403181	type	True	86.0277	914	1300	95	below_threshold
Haloferax massiliensis	strain=Arc-Hr	GCA_001368915.1	1476858	1476858	type	True	84.3437	828	1300	95	below_threshold
Haloferax elongans	strain=ATCC BAA-1513	GCA_000336755.1	403191	403191	type	True	83.3191	789	1300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:22,223] [INFO] DFAST Taxonomy check result was written to GCF_000685635.1_ASM68563v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:22,224] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:22,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:22,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52fe6842-146d-4bba-8ed2-eb696ba07e1d/dqc_reference/checkm_data
[2024-01-24 12:45:22,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:22,268] [INFO] Task started: CheckM
[2024-01-24 12:45:22,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000685635.1_ASM68563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000685635.1_ASM68563v1_genomic.fna/checkm_input GCF_000685635.1_ASM68563v1_genomic.fna/checkm_result
[2024-01-24 12:46:19,552] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:19,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:19,575] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:19,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:19,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000685635.1_ASM68563v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:19,577] [INFO] Task started: Blastn
[2024-01-24 12:46:19,577] [INFO] Running command: blastn -query GCF_000685635.1_ASM68563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52fe6842-146d-4bba-8ed2-eb696ba07e1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000685635.1_ASM68563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:20,077] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:20,080] [INFO] Selected 12 target genomes.
[2024-01-24 12:46:20,081] [INFO] Target genome list was writen to GCF_000685635.1_ASM68563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:20,119] [INFO] Task started: fastANI
[2024-01-24 12:46:20,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg095d9259-9b00-4fe3-afae-eedf8da3820d/GCF_000685635.1_ASM68563v1_genomic.fna.gz --refList GCF_000685635.1_ASM68563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000685635.1_ASM68563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:30,610] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:30,625] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:30,626] [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_000306765.2	s__Haloferax mediterranei	99.965	1291	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	99.99	99.97	1.00	0.99	4	conclusive
GCF_000337815.1	s__Haloferax mucosum	86.0455	913	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469875.2	s__Haloferax marisrubri	84.7312	816	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	95.85	95.85	0.83	0.83	2	-
GCF_000336775.1	s__Haloferax gibbonsii	84.4851	833	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_001482285.1	s__Haloferax sp001482285	84.4001	832	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001368915.1	s__Haloferax massiliensis	84.3724	825	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.2845	98.47	96.94	0.94	0.88	3	-
GCF_000336815.1	s__Haloferax prahovense	84.3467	836	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	99.29	99.22	0.91	0.91	5	-
GCF_000025685.1	s__Haloferax volcanii	84.1848	831	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	98.27	96.62	0.93	0.89	21	-
GCF_001469865.1	s__Haloferax profundi	83.6745	674	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336955.1	s__Haloferax larsenii	83.5647	798	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	96.49	96.49	0.91	0.91	2	-
GCF_009674585.1	s__Haloferax sp009674585	83.4417	719	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000336755.1	s__Haloferax elongans	83.3155	790	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:30,628] [INFO] GTDB search result was written to GCF_000685635.1_ASM68563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:30,629] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:30,634] [INFO] DFAST_QC result json was written to GCF_000685635.1_ASM68563v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:30,634] [INFO] DFAST_QC completed!
[2024-01-24 12:46:30,634] [INFO] Total running time: 0h1m38s