[2024-01-24 12:36:58,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg4234c532-6878-4223-ab10-29707400a92b/dqc_reference
[2024-01-24 12:37:00,073] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:00,074] [INFO] Task started: Prodigal
[2024-01-24 12:37:00,074] [INFO] Running command: gunzip -c /var/lib/cwl/stg3917373e-19c0-449f-8cdc-85a273b03d3a/GCF_002009235.1_ASM200923v1_genomic.fna.gz | prodigal -d GCF_002009235.1_ASM200923v1_genomic.fna/cds.fna -a GCF_002009235.1_ASM200923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:08,831] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:08,832] [INFO] Task started: HMMsearch
[2024-01-24 12:37:08,832] [INFO] Running command: hmmsearch --tblout GCF_002009235.1_ASM200923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4234c532-6878-4223-ab10-29707400a92b/dqc_reference/reference_markers.hmm GCF_002009235.1_ASM200923v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:09,160] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:09,162] [INFO] Found 6/6 markers.
[2024-01-24 12:37:09,204] [INFO] Query marker FASTA was written to GCF_002009235.1_ASM200923v1_genomic.fna/markers.fasta
[2024-01-24 12:37:09,204] [INFO] Task started: Blastn
[2024-01-24 12:37:09,205] [INFO] Running command: blastn -query GCF_002009235.1_ASM200923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4234c532-6878-4223-ab10-29707400a92b/dqc_reference/reference_markers.fasta -out GCF_002009235.1_ASM200923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:09,846] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:09,849] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:09,849] [INFO] Target genome list was writen to GCF_002009235.1_ASM200923v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:09,860] [INFO] Task started: fastANI
[2024-01-24 12:37:09,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg3917373e-19c0-449f-8cdc-85a273b03d3a/GCF_002009235.1_ASM200923v1_genomic.fna.gz --refList GCF_002009235.1_ASM200923v1_genomic.fna/target_genomes.txt --output GCF_002009235.1_ASM200923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:19,068] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:19,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4234c532-6878-4223-ab10-29707400a92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:19,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4234c532-6878-4223-ab10-29707400a92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:19,077] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:19,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:19,077] [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 faecalis	strain=AJ003	GCA_002009235.1	1598147	1598147	suspected-type	True	100.0	1164	1165	95	conclusive
Planococcus faecalis	strain=CECT 8759	GCA_001856115.1	1598147	1598147	suspected-type	True	99.9205	1099	1165	95	conclusive
Planococcus versutus	strain=L10.15	GCA_001186155.3	1302659	1302659	type	True	83.8342	748	1165	95	below_threshold
Planococcus halocryophilus	strain=DSM 24743	GCA_001687585.2	1215089	1215089	type	True	83.1087	753	1165	95	below_threshold
Planococcus halocryophilus	strain=Or1	GCA_000342445.1	1215089	1215089	type	True	82.8605	762	1165	95	below_threshold
Planococcus donghaensis	strain=DSM 22276	GCA_001687665.2	414778	414778	type	True	82.8497	683	1165	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	82.4493	753	1165	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	80.9978	616	1165	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	76.7628	65	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:19,079] [INFO] DFAST Taxonomy check result was written to GCF_002009235.1_ASM200923v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:19,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:19,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:19,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4234c532-6878-4223-ab10-29707400a92b/dqc_reference/checkm_data
[2024-01-24 12:37:19,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:19,117] [INFO] Task started: CheckM
[2024-01-24 12:37:19,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002009235.1_ASM200923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002009235.1_ASM200923v1_genomic.fna/checkm_input GCF_002009235.1_ASM200923v1_genomic.fna/checkm_result
[2024-01-24 12:37:50,989] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:50,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:51,015] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:51,015] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:51,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002009235.1_ASM200923v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:51,016] [INFO] Task started: Blastn
[2024-01-24 12:37:51,017] [INFO] Running command: blastn -query GCF_002009235.1_ASM200923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4234c532-6878-4223-ab10-29707400a92b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002009235.1_ASM200923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:51,817] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:51,821] [INFO] Selected 8 target genomes.
[2024-01-24 12:37:51,822] [INFO] Target genome list was writen to GCF_002009235.1_ASM200923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:51,837] [INFO] Task started: fastANI
[2024-01-24 12:37:51,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg3917373e-19c0-449f-8cdc-85a273b03d3a/GCF_002009235.1_ASM200923v1_genomic.fna.gz --refList GCF_002009235.1_ASM200923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002009235.1_ASM200923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:58,810] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:58,818] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:58,818] [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_001465835.2	s__Planococcus kocurii	98.0754	1074	1165	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	98.39	98.00	0.92	0.89	4	conclusive
GCF_001186155.3	s__Planococcus versutus	83.8335	748	1165	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_001687585.2	s__Planococcus halocryophilus	83.131	754	1165	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.95	99.95	0.98	0.98	2	-
GCF_001687665.2	s__Planococcus donghaensis	82.8246	686	1165	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_000785555.1	s__Planococcus sp000785555	82.8116	719	1165	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_001687565.2	s__Planococcus antarcticus	82.7483	762	1165	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.42	99.42	0.95	0.95	2	-
GCF_000189395.1	s__Planococcus donghaensis_B	82.6669	699	1165	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_018613575.1	s__Planococcus sp018613575	81.2225	658	1165	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 12:37:58,820] [INFO] GTDB search result was written to GCF_002009235.1_ASM200923v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:58,820] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:58,823] [INFO] DFAST_QC result json was written to GCF_002009235.1_ASM200923v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:58,824] [INFO] DFAST_QC completed!
[2024-01-24 12:37:58,824] [INFO] Total running time: 0h1m0s