[2024-01-24 13:01:39,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,720] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1f91fb7-b66b-45da-af68-f9c62764972f/dqc_reference
[2024-01-24 13:01:41,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,376] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg7396003b-9d01-4e51-a5f2-c368b655e71d/GCF_003428865.1_ASM342886v1_genomic.fna.gz | prodigal -d GCF_003428865.1_ASM342886v1_genomic.fna/cds.fna -a GCF_003428865.1_ASM342886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:50,285] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:50,286] [INFO] Task started: HMMsearch
[2024-01-24 13:01:50,286] [INFO] Running command: hmmsearch --tblout GCF_003428865.1_ASM342886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1f91fb7-b66b-45da-af68-f9c62764972f/dqc_reference/reference_markers.hmm GCF_003428865.1_ASM342886v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:50,612] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:50,613] [INFO] Found 6/6 markers.
[2024-01-24 13:01:50,648] [INFO] Query marker FASTA was written to GCF_003428865.1_ASM342886v1_genomic.fna/markers.fasta
[2024-01-24 13:01:50,648] [INFO] Task started: Blastn
[2024-01-24 13:01:50,648] [INFO] Running command: blastn -query GCF_003428865.1_ASM342886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f91fb7-b66b-45da-af68-f9c62764972f/dqc_reference/reference_markers.fasta -out GCF_003428865.1_ASM342886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:51,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:51,337] [INFO] Selected 15 target genomes.
[2024-01-24 13:01:51,338] [INFO] Target genome list was writen to GCF_003428865.1_ASM342886v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:51,344] [INFO] Task started: fastANI
[2024-01-24 13:01:51,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg7396003b-9d01-4e51-a5f2-c368b655e71d/GCF_003428865.1_ASM342886v1_genomic.fna.gz --refList GCF_003428865.1_ASM342886v1_genomic.fna/target_genomes.txt --output GCF_003428865.1_ASM342886v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:04,630] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:04,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1f91fb7-b66b-45da-af68-f9c62764972f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:04,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1f91fb7-b66b-45da-af68-f9c62764972f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:04,646] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:02:04,647] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:04,647] [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
Planococcus salinarum	strain=ISL-16	GCA_003428865.1	622695	622695	type	True	100.0	1049	1051	95	conclusive
Planococcus salinarum	strain=KCTC 13584	GCA_007004625.1	622695	622695	type	True	99.9932	1048	1051	95	conclusive
Planococcus salinarum	strain=DSM 23820	GCA_001856085.1	622695	622695	type	True	98.8456	263	1051	95	conclusive
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	79.0702	337	1051	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	78.9904	335	1051	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	78.7807	297	1051	95	below_threshold
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	78.7719	319	1051	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	78.7249	339	1051	95	below_threshold
Planococcus glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	78.6762	342	1051	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	78.6061	283	1051	95	below_threshold
Planococcus maitriensis	strain=S1	GCA_003289925.1	221799	221799	type	True	78.1547	272	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:04,649] [INFO] DFAST Taxonomy check result was written to GCF_003428865.1_ASM342886v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:04,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:04,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:04,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1f91fb7-b66b-45da-af68-f9c62764972f/dqc_reference/checkm_data
[2024-01-24 13:02:04,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:04,697] [INFO] Task started: CheckM
[2024-01-24 13:02:04,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003428865.1_ASM342886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003428865.1_ASM342886v1_genomic.fna/checkm_input GCF_003428865.1_ASM342886v1_genomic.fna/checkm_result
[2024-01-24 13:02:38,631] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:38,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:38,658] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:38,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:38,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003428865.1_ASM342886v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:38,660] [INFO] Task started: Blastn
[2024-01-24 13:02:38,660] [INFO] Running command: blastn -query GCF_003428865.1_ASM342886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f91fb7-b66b-45da-af68-f9c62764972f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003428865.1_ASM342886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:39,511] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:39,515] [INFO] Selected 9 target genomes.
[2024-01-24 13:02:39,515] [INFO] Target genome list was writen to GCF_003428865.1_ASM342886v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:39,522] [INFO] Task started: fastANI
[2024-01-24 13:02:39,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg7396003b-9d01-4e51-a5f2-c368b655e71d/GCF_003428865.1_ASM342886v1_genomic.fna.gz --refList GCF_003428865.1_ASM342886v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003428865.1_ASM342886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:46,915] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:46,924] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:46,924] [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_007004625.1	s__Planococcus salinarum	99.9932	1048	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003289955.1	s__Planococcus halotolerans	82.9286	716	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.14	99.14	0.94	0.94	2	-
GCF_003668635.1	s__Planococcus sp003668635	82.7012	721	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428875.1	s__Planococcus okeanokoites	82.5805	666	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.50	97.25	0.88	0.87	3	-
GCF_017873465.1	s__Planococcus mcmeekinii	82.259	654	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775575.1	s__Planococcus sp000775575	81.3778	518	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820495.1	s__Planococcus sp016820495	80.9808	548	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613655.1	s__Planococcus sp018613655	78.4981	288	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003289925.1	s__Planococcus maitriensis	78.1683	271	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:46,926] [INFO] GTDB search result was written to GCF_003428865.1_ASM342886v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:46,927] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:46,930] [INFO] DFAST_QC result json was written to GCF_003428865.1_ASM342886v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:46,930] [INFO] DFAST_QC completed!
[2024-01-24 13:02:46,930] [INFO] Total running time: 0h1m7s