[2024-01-25 19:38:05,915] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:05,918] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:05,918] [INFO] DQC Reference Directory: /var/lib/cwl/stg4828f35e-bb35-4bc7-983a-b47ebc808678/dqc_reference
[2024-01-25 19:38:07,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:07,145] [INFO] Task started: Prodigal
[2024-01-25 19:38:07,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg415df6d6-9271-4499-981a-1a09c8fc792b/GCF_016820615.1_ASM1682061v1_genomic.fna.gz | prodigal -d GCF_016820615.1_ASM1682061v1_genomic.fna/cds.fna -a GCF_016820615.1_ASM1682061v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:16,269] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:16,269] [INFO] Task started: HMMsearch
[2024-01-25 19:38:16,269] [INFO] Running command: hmmsearch --tblout GCF_016820615.1_ASM1682061v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4828f35e-bb35-4bc7-983a-b47ebc808678/dqc_reference/reference_markers.hmm GCF_016820615.1_ASM1682061v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:16,502] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:16,503] [INFO] Found 6/6 markers.
[2024-01-25 19:38:16,530] [INFO] Query marker FASTA was written to GCF_016820615.1_ASM1682061v1_genomic.fna/markers.fasta
[2024-01-25 19:38:16,530] [INFO] Task started: Blastn
[2024-01-25 19:38:16,530] [INFO] Running command: blastn -query GCF_016820615.1_ASM1682061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4828f35e-bb35-4bc7-983a-b47ebc808678/dqc_reference/reference_markers.fasta -out GCF_016820615.1_ASM1682061v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:17,096] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:17,098] [INFO] Selected 12 target genomes.
[2024-01-25 19:38:17,099] [INFO] Target genome list was writen to GCF_016820615.1_ASM1682061v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:17,104] [INFO] Task started: fastANI
[2024-01-25 19:38:17,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg415df6d6-9271-4499-981a-1a09c8fc792b/GCF_016820615.1_ASM1682061v1_genomic.fna.gz --refList GCF_016820615.1_ASM1682061v1_genomic.fna/target_genomes.txt --output GCF_016820615.1_ASM1682061v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:25,281] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:25,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4828f35e-bb35-4bc7-983a-b47ebc808678/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:25,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4828f35e-bb35-4bc7-983a-b47ebc808678/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:25,288] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:38:25,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:25,289] [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 wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	97.1644	1113	1229	95	conclusive
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	82.6788	880	1229	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_001687565.2	161360	161360	type	True	81.6908	786	1229	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	81.6259	777	1229	95	below_threshold
Planococcus faecalis	strain=AJ003	GCA_002009235.1	1598147	1598147	suspected-type	True	80.9452	609	1229	95	below_threshold
Planococcus donghaensis	strain=DSM 22276	GCA_001687665.2	414778	414778	type	True	80.9088	559	1229	95	below_threshold
Planococcus halocryophilus	strain=Or1	GCA_000342445.1	1215089	1215089	type	True	80.7054	596	1229	95	below_threshold
Planococcus halocryophilus	strain=DSM 24743	GCA_001687585.2	1215089	1215089	type	True	80.6854	605	1229	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	79.4493	401	1229	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	79.4181	415	1229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:25,290] [INFO] DFAST Taxonomy check result was written to GCF_016820615.1_ASM1682061v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:25,290] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:25,290] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:25,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4828f35e-bb35-4bc7-983a-b47ebc808678/dqc_reference/checkm_data
[2024-01-25 19:38:25,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:25,330] [INFO] Task started: CheckM
[2024-01-25 19:38:25,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016820615.1_ASM1682061v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016820615.1_ASM1682061v1_genomic.fna/checkm_input GCF_016820615.1_ASM1682061v1_genomic.fna/checkm_result
[2024-01-25 19:38:55,902] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:55,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:55,926] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:55,926] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:55,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016820615.1_ASM1682061v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:55,927] [INFO] Task started: Blastn
[2024-01-25 19:38:55,927] [INFO] Running command: blastn -query GCF_016820615.1_ASM1682061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4828f35e-bb35-4bc7-983a-b47ebc808678/dqc_reference/reference_markers_gtdb.fasta -out GCF_016820615.1_ASM1682061v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:56,709] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:56,712] [INFO] Selected 6 target genomes.
[2024-01-25 19:38:56,712] [INFO] Target genome list was writen to GCF_016820615.1_ASM1682061v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:56,719] [INFO] Task started: fastANI
[2024-01-25 19:38:56,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg415df6d6-9271-4499-981a-1a09c8fc792b/GCF_016820615.1_ASM1682061v1_genomic.fna.gz --refList GCF_016820615.1_ASM1682061v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016820615.1_ASM1682061v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:02,151] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:02,157] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:02,157] [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_014836985.1	s__Planococcus sp014836985	97.1644	1113	1229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.16	97.16	0.91	0.91	2	conclusive
GCF_018613575.1	s__Planococcus sp018613575	83.0944	842	1229	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_016881065.1	s__Planococcus soli	82.6775	878	1229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007859295.1	s__Planococcus sp007859295	82.5767	853	1229	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	81.6643	789	1229	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_001687585.2	s__Planococcus halocryophilus	80.6749	606	1229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.95	99.95	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:02,159] [INFO] GTDB search result was written to GCF_016820615.1_ASM1682061v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:02,160] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:02,162] [INFO] DFAST_QC result json was written to GCF_016820615.1_ASM1682061v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:02,163] [INFO] DFAST_QC completed!
[2024-01-25 19:39:02,163] [INFO] Total running time: 0h0m56s