[2024-01-24 13:48:59,080] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg986a29ec-bad9-45f8-9674-6d1b87412c6b/dqc_reference
[2024-01-24 13:49:00,404] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,405] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,405] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd96879d-8d2f-4f8c-ab08-daeab6c5fbef/GCF_000342445.1_PlanoHalo1.0_genomic.fna.gz | prodigal -d GCF_000342445.1_PlanoHalo1.0_genomic.fna/cds.fna -a GCF_000342445.1_PlanoHalo1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:08,233] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:08,234] [INFO] Task started: HMMsearch
[2024-01-24 13:49:08,234] [INFO] Running command: hmmsearch --tblout GCF_000342445.1_PlanoHalo1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg986a29ec-bad9-45f8-9674-6d1b87412c6b/dqc_reference/reference_markers.hmm GCF_000342445.1_PlanoHalo1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:08,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:08,527] [INFO] Found 6/6 markers.
[2024-01-24 13:49:08,567] [INFO] Query marker FASTA was written to GCF_000342445.1_PlanoHalo1.0_genomic.fna/markers.fasta
[2024-01-24 13:49:08,568] [INFO] Task started: Blastn
[2024-01-24 13:49:08,568] [INFO] Running command: blastn -query GCF_000342445.1_PlanoHalo1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg986a29ec-bad9-45f8-9674-6d1b87412c6b/dqc_reference/reference_markers.fasta -out GCF_000342445.1_PlanoHalo1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:09,204] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:09,208] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:09,209] [INFO] Target genome list was writen to GCF_000342445.1_PlanoHalo1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:49:09,237] [INFO] Task started: fastANI
[2024-01-24 13:49:09,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd96879d-8d2f-4f8c-ab08-daeab6c5fbef/GCF_000342445.1_PlanoHalo1.0_genomic.fna.gz --refList GCF_000342445.1_PlanoHalo1.0_genomic.fna/target_genomes.txt --output GCF_000342445.1_PlanoHalo1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:17,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:17,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg986a29ec-bad9-45f8-9674-6d1b87412c6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:17,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg986a29ec-bad9-45f8-9674-6d1b87412c6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:18,005] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:18,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:18,005] [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 halocryophilus	strain=Or1	GCA_000342445.1	1215089	1215089	type	True	100.0	1124	1126	95	conclusive
Planococcus halocryophilus	strain=DSM 24743	GCA_001687585.2	1215089	1215089	type	True	99.9545	1106	1126	95	conclusive
Planococcus donghaensis	strain=DSM 22276	GCA_001687665.2	414778	414778	type	True	88.9868	964	1126	95	below_threshold
Planococcus faecalis	strain=CECT 8759	GCA_001856115.1	1598147	1598147	suspected-type	True	82.8366	741	1126	95	below_threshold
Planococcus faecalis	strain=AJ003	GCA_002009235.1	1598147	1598147	suspected-type	True	82.833	754	1126	95	below_threshold
Planococcus versutus	strain=L10.15	GCA_001186155.3	1302659	1302659	type	True	82.1909	699	1126	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	81.1472	666	1126	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	80.838	587	1126	95	below_threshold
Lysinibacillus contaminans	strain=DSM 25560	GCA_001278945.1	1293441	1293441	type	True	76.5826	58	1126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:18,007] [INFO] DFAST Taxonomy check result was written to GCF_000342445.1_PlanoHalo1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:49:18,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:18,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:18,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg986a29ec-bad9-45f8-9674-6d1b87412c6b/dqc_reference/checkm_data
[2024-01-24 13:49:18,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:18,049] [INFO] Task started: CheckM
[2024-01-24 13:49:18,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000342445.1_PlanoHalo1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000342445.1_PlanoHalo1.0_genomic.fna/checkm_input GCF_000342445.1_PlanoHalo1.0_genomic.fna/checkm_result
[2024-01-24 13:49:46,817] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:46,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:46,838] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:46,839] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:46,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000342445.1_PlanoHalo1.0_genomic.fna/markers.fasta)
[2024-01-24 13:49:46,840] [INFO] Task started: Blastn
[2024-01-24 13:49:46,840] [INFO] Running command: blastn -query GCF_000342445.1_PlanoHalo1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg986a29ec-bad9-45f8-9674-6d1b87412c6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000342445.1_PlanoHalo1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:47,767] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:47,770] [INFO] Selected 6 target genomes.
[2024-01-24 13:49:47,771] [INFO] Target genome list was writen to GCF_000342445.1_PlanoHalo1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:47,800] [INFO] Task started: fastANI
[2024-01-24 13:49:47,800] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd96879d-8d2f-4f8c-ab08-daeab6c5fbef/GCF_000342445.1_PlanoHalo1.0_genomic.fna.gz --refList GCF_000342445.1_PlanoHalo1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000342445.1_PlanoHalo1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:53,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:53,034] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:53,034] [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_001687585.2	s__Planococcus halocryophilus	99.9545	1106	1126	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.95	99.95	0.98	0.98	2	conclusive
GCF_000189395.1	s__Planococcus donghaensis_B	89.902	948	1126	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_001687665.2	s__Planococcus donghaensis	88.9868	964	1126	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	86.6892	902	1126	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_001465835.2	s__Planococcus kocurii	82.9846	760	1126	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	98.39	98.00	0.92	0.89	4	-
GCF_001186155.3	s__Planococcus versutus	82.1976	698	1126	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 13:49:53,036] [INFO] GTDB search result was written to GCF_000342445.1_PlanoHalo1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:53,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:53,040] [INFO] DFAST_QC result json was written to GCF_000342445.1_PlanoHalo1.0_genomic.fna/dqc_result.json
[2024-01-24 13:49:53,040] [INFO] DFAST_QC completed!
[2024-01-24 13:49:53,040] [INFO] Total running time: 0h0m54s