[2024-01-24 13:25:47,781] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,783] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,783] [INFO] DQC Reference Directory: /var/lib/cwl/stg5395833b-1a99-44a6-8601-0a5c38bb7f25/dqc_reference
[2024-01-24 13:25:49,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:49,099] [INFO] Task started: Prodigal
[2024-01-24 13:25:49,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d527474-9d5d-4c8b-af81-9e8053594c71/GCF_006861665.1_ASM686166v1_genomic.fna.gz | prodigal -d GCF_006861665.1_ASM686166v1_genomic.fna/cds.fna -a GCF_006861665.1_ASM686166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:03,611] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:03,612] [INFO] Task started: HMMsearch
[2024-01-24 13:26:03,612] [INFO] Running command: hmmsearch --tblout GCF_006861665.1_ASM686166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5395833b-1a99-44a6-8601-0a5c38bb7f25/dqc_reference/reference_markers.hmm GCF_006861665.1_ASM686166v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:03,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:03,847] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1d527474-9d5d-4c8b-af81-9e8053594c71/GCF_006861665.1_ASM686166v1_genomic.fna.gz]
[2024-01-24 13:26:03,874] [INFO] Query marker FASTA was written to GCF_006861665.1_ASM686166v1_genomic.fna/markers.fasta
[2024-01-24 13:26:03,874] [INFO] Task started: Blastn
[2024-01-24 13:26:03,874] [INFO] Running command: blastn -query GCF_006861665.1_ASM686166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5395833b-1a99-44a6-8601-0a5c38bb7f25/dqc_reference/reference_markers.fasta -out GCF_006861665.1_ASM686166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:04,387] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:04,391] [INFO] Selected 7 target genomes.
[2024-01-24 13:26:04,391] [INFO] Target genome list was writen to GCF_006861665.1_ASM686166v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:04,396] [INFO] Task started: fastANI
[2024-01-24 13:26:04,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d527474-9d5d-4c8b-af81-9e8053594c71/GCF_006861665.1_ASM686166v1_genomic.fna.gz --refList GCF_006861665.1_ASM686166v1_genomic.fna/target_genomes.txt --output GCF_006861665.1_ASM686166v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:10,051] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:10,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5395833b-1a99-44a6-8601-0a5c38bb7f25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:10,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5395833b-1a99-44a6-8601-0a5c38bb7f25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:10,059] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:10,059] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:10,059] [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
Halonotius terrestris	strain=F15B	GCA_006861665.1	2487750	2487750	type	True	100.0	934	936	95	conclusive
Halonotius roseus	strain=F9-27	GCA_006861655.1	2511997	2511997	type	True	84.1422	586	936	95	below_threshold
Halonotius aquaticus	strain=F13-13	GCA_003605575.1	2216978	2216978	type	True	83.526	531	936	95	below_threshold
Halonotius pteroides	strain=CECT 7525	GCA_003605635.1	268735	268735	type	True	82.2498	500	936	95	below_threshold
Halohasta litchfieldiae	strain=tADL	GCA_002788215.1	1073996	1073996	type	True	78.7102	389	936	95	below_threshold
Halogranum salarium	strain=B-1	GCA_000283335.1	693851	693851	type	True	77.2876	263	936	95	below_threshold
Halogranum rubrum	strain=CGMCC 1.7738	GCA_900114455.1	553466	553466	type	True	77.1098	272	936	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:10,060] [INFO] DFAST Taxonomy check result was written to GCF_006861665.1_ASM686166v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:10,061] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:10,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:10,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5395833b-1a99-44a6-8601-0a5c38bb7f25/dqc_reference/checkm_data
[2024-01-24 13:26:10,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:10,090] [INFO] Task started: CheckM
[2024-01-24 13:26:10,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006861665.1_ASM686166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006861665.1_ASM686166v1_genomic.fna/checkm_input GCF_006861665.1_ASM686166v1_genomic.fna/checkm_result
[2024-01-24 13:26:52,976] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:52,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:52,998] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:52,999] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:52,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006861665.1_ASM686166v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:52,999] [INFO] Task started: Blastn
[2024-01-24 13:26:53,000] [INFO] Running command: blastn -query GCF_006861665.1_ASM686166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5395833b-1a99-44a6-8601-0a5c38bb7f25/dqc_reference/reference_markers_gtdb.fasta -out GCF_006861665.1_ASM686166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:53,505] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:53,509] [INFO] Selected 6 target genomes.
[2024-01-24 13:26:53,509] [INFO] Target genome list was writen to GCF_006861665.1_ASM686166v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:53,515] [INFO] Task started: fastANI
[2024-01-24 13:26:53,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d527474-9d5d-4c8b-af81-9e8053594c71/GCF_006861665.1_ASM686166v1_genomic.fna.gz --refList GCF_006861665.1_ASM686166v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006861665.1_ASM686166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:57,929] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:57,940] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:57,940] [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_006861665.1	s__Halonotius terrestris	100.0	934	936	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006861655.1	s__Halonotius roseus	84.1409	586	936	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605575.1	s__Halonotius sp003605575	83.5307	531	936	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000496215.1	s__Halonotius sp000496215	82.5557	494	936	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	96.16	96.16	0.87	0.87	2	-
GCF_003605635.1	s__Halonotius pteroides	82.2573	499	936	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114455.1	s__Halogranum rubrum	77.075	276	936	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	97.00	97.00	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:57,941] [INFO] GTDB search result was written to GCF_006861665.1_ASM686166v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:57,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:57,944] [INFO] DFAST_QC result json was written to GCF_006861665.1_ASM686166v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:57,944] [INFO] DFAST_QC completed!
[2024-01-24 13:26:57,945] [INFO] Total running time: 0h1m10s