[2024-01-24 15:26:04,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a4cf7e5-934c-4124-bc74-bcdf0d576f1e/dqc_reference
[2024-01-24 15:26:07,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,023] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,024] [INFO] Running command: gunzip -c /var/lib/cwl/stga4597fe2-6887-42b7-adeb-ae4b36b7ff32/GCF_001856115.1_ASM185611v1_genomic.fna.gz | prodigal -d GCF_001856115.1_ASM185611v1_genomic.fna/cds.fna -a GCF_001856115.1_ASM185611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:15,077] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:15,077] [INFO] Task started: HMMsearch
[2024-01-24 15:26:15,077] [INFO] Running command: hmmsearch --tblout GCF_001856115.1_ASM185611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a4cf7e5-934c-4124-bc74-bcdf0d576f1e/dqc_reference/reference_markers.hmm GCF_001856115.1_ASM185611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:15,346] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:15,348] [INFO] Found 6/6 markers.
[2024-01-24 15:26:15,386] [INFO] Query marker FASTA was written to GCF_001856115.1_ASM185611v1_genomic.fna/markers.fasta
[2024-01-24 15:26:15,387] [INFO] Task started: Blastn
[2024-01-24 15:26:15,387] [INFO] Running command: blastn -query GCF_001856115.1_ASM185611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a4cf7e5-934c-4124-bc74-bcdf0d576f1e/dqc_reference/reference_markers.fasta -out GCF_001856115.1_ASM185611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:16,062] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:16,066] [INFO] Selected 12 target genomes.
[2024-01-24 15:26:16,067] [INFO] Target genome list was writen to GCF_001856115.1_ASM185611v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:16,073] [INFO] Task started: fastANI
[2024-01-24 15:26:16,073] [INFO] Running command: fastANI --query /var/lib/cwl/stga4597fe2-6887-42b7-adeb-ae4b36b7ff32/GCF_001856115.1_ASM185611v1_genomic.fna.gz --refList GCF_001856115.1_ASM185611v1_genomic.fna/target_genomes.txt --output GCF_001856115.1_ASM185611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:25,189] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:25,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a4cf7e5-934c-4124-bc74-bcdf0d576f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:25,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a4cf7e5-934c-4124-bc74-bcdf0d576f1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:25,202] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:26:25,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:25,202] [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=CECT 8759	GCA_001856115.1	1598147	1598147	suspected-type	True	100.0	1141	1144	95	conclusive
Planococcus faecalis	strain=AJ003	GCA_002009235.1	1598147	1598147	suspected-type	True	99.9473	1105	1144	95	conclusive
Planococcus versutus	strain=L10.15	GCA_001186155.3	1302659	1302659	type	True	84.0297	699	1144	95	below_threshold
Planococcus halocryophilus	strain=DSM 24743	GCA_001687585.2	1215089	1215089	type	True	83.0248	740	1144	95	below_threshold
Planococcus halocryophilus	strain=Or1	GCA_000342445.1	1215089	1215089	type	True	82.934	729	1144	95	below_threshold
Planococcus donghaensis	strain=DSM 22276	GCA_001687665.2	414778	414778	type	True	82.6202	680	1144	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	82.4458	718	1144	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	80.9817	580	1144	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	77.1095	54	1144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:25,205] [INFO] DFAST Taxonomy check result was written to GCF_001856115.1_ASM185611v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:25,206] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:25,206] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:25,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a4cf7e5-934c-4124-bc74-bcdf0d576f1e/dqc_reference/checkm_data
[2024-01-24 15:26:25,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:25,245] [INFO] Task started: CheckM
[2024-01-24 15:26:25,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001856115.1_ASM185611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001856115.1_ASM185611v1_genomic.fna/checkm_input GCF_001856115.1_ASM185611v1_genomic.fna/checkm_result
[2024-01-24 15:26:55,599] [INFO] Task succeeded: CheckM
[2024-01-24 15:26:55,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:26:55,630] [INFO] ===== Completeness check finished =====
[2024-01-24 15:26:55,631] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:26:55,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001856115.1_ASM185611v1_genomic.fna/markers.fasta)
[2024-01-24 15:26:55,632] [INFO] Task started: Blastn
[2024-01-24 15:26:55,632] [INFO] Running command: blastn -query GCF_001856115.1_ASM185611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a4cf7e5-934c-4124-bc74-bcdf0d576f1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001856115.1_ASM185611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:56,672] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:56,675] [INFO] Selected 8 target genomes.
[2024-01-24 15:26:56,675] [INFO] Target genome list was writen to GCF_001856115.1_ASM185611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:26:56,680] [INFO] Task started: fastANI
[2024-01-24 15:26:56,681] [INFO] Running command: fastANI --query /var/lib/cwl/stga4597fe2-6887-42b7-adeb-ae4b36b7ff32/GCF_001856115.1_ASM185611v1_genomic.fna.gz --refList GCF_001856115.1_ASM185611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001856115.1_ASM185611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:03,421] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:03,431] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:03,432] [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	97.9966	1019	1144	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	84.0177	698	1144	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	83.0315	739	1144	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_000785555.1	s__Planococcus sp000785555	82.7574	697	1144	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_000189395.1	s__Planococcus donghaensis_B	82.6263	674	1144	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	82.6225	734	1144	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_001687665.2	s__Planococcus donghaensis	82.6064	682	1144	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	81.1869	626	1144	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 15:27:03,434] [INFO] GTDB search result was written to GCF_001856115.1_ASM185611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:03,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:03,440] [INFO] DFAST_QC result json was written to GCF_001856115.1_ASM185611v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:03,441] [INFO] DFAST_QC completed!
[2024-01-24 15:27:03,441] [INFO] Total running time: 0h0m59s