[2024-01-24 14:22:15,367] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:15,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:15,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg908b0d4b-de6a-4a6a-9280-ec7ae19aeffd/dqc_reference
[2024-01-24 14:22:16,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:16,834] [INFO] Task started: Prodigal
[2024-01-24 14:22:16,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f9e6d94-6abc-4eac-9987-0c71d0901600/GCF_004761975.1_ASM476197v1_genomic.fna.gz | prodigal -d GCF_004761975.1_ASM476197v1_genomic.fna/cds.fna -a GCF_004761975.1_ASM476197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:26,660] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:26,660] [INFO] Task started: HMMsearch
[2024-01-24 14:22:26,660] [INFO] Running command: hmmsearch --tblout GCF_004761975.1_ASM476197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg908b0d4b-de6a-4a6a-9280-ec7ae19aeffd/dqc_reference/reference_markers.hmm GCF_004761975.1_ASM476197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:26,969] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:26,971] [INFO] Found 6/6 markers.
[2024-01-24 14:22:27,004] [INFO] Query marker FASTA was written to GCF_004761975.1_ASM476197v1_genomic.fna/markers.fasta
[2024-01-24 14:22:27,005] [INFO] Task started: Blastn
[2024-01-24 14:22:27,005] [INFO] Running command: blastn -query GCF_004761975.1_ASM476197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg908b0d4b-de6a-4a6a-9280-ec7ae19aeffd/dqc_reference/reference_markers.fasta -out GCF_004761975.1_ASM476197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:27,648] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:27,652] [INFO] Selected 15 target genomes.
[2024-01-24 14:22:27,652] [INFO] Target genome list was writen to GCF_004761975.1_ASM476197v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:27,661] [INFO] Task started: fastANI
[2024-01-24 14:22:27,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9e6d94-6abc-4eac-9987-0c71d0901600/GCF_004761975.1_ASM476197v1_genomic.fna.gz --refList GCF_004761975.1_ASM476197v1_genomic.fna/target_genomes.txt --output GCF_004761975.1_ASM476197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:38,140] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:38,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg908b0d4b-de6a-4a6a-9280-ec7ae19aeffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:38,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg908b0d4b-de6a-4a6a-9280-ec7ae19aeffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:38,150] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:38,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:38,151] [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 koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	100.0	1096	1102	95	conclusive
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	99.9899	1097	1102	95	conclusive
Planococcus glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	79.9471	504	1102	95	below_threshold
Planococcus massiliensis	strain=ES2	GCA_000821325.2	1499687	1499687	type	True	79.8353	407	1102	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	79.7324	411	1102	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	79.2745	379	1102	95	below_threshold
Planococcus rifietoensis	strain=M8	GCA_001465795.2	200991	200991	type	True	78.9668	338	1102	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_001687565.2	161360	161360	type	True	78.7941	322	1102	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	78.6789	307	1102	95	below_threshold
Planococcus salinus	strain=LCB217	GCA_003719725.1	1848460	1848460	type	True	78.4412	290	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:38,153] [INFO] DFAST Taxonomy check result was written to GCF_004761975.1_ASM476197v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:38,153] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:38,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:38,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg908b0d4b-de6a-4a6a-9280-ec7ae19aeffd/dqc_reference/checkm_data
[2024-01-24 14:22:38,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:38,193] [INFO] Task started: CheckM
[2024-01-24 14:22:38,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004761975.1_ASM476197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004761975.1_ASM476197v1_genomic.fna/checkm_input GCF_004761975.1_ASM476197v1_genomic.fna/checkm_result
[2024-01-24 14:23:11,734] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:11,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:11,752] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:11,753] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:11,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004761975.1_ASM476197v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:11,753] [INFO] Task started: Blastn
[2024-01-24 14:23:11,753] [INFO] Running command: blastn -query GCF_004761975.1_ASM476197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg908b0d4b-de6a-4a6a-9280-ec7ae19aeffd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004761975.1_ASM476197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:12,557] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:12,560] [INFO] Selected 18 target genomes.
[2024-01-24 14:23:12,560] [INFO] Target genome list was writen to GCF_004761975.1_ASM476197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:12,582] [INFO] Task started: fastANI
[2024-01-24 14:23:12,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9e6d94-6abc-4eac-9987-0c71d0901600/GCF_004761975.1_ASM476197v1_genomic.fna.gz --refList GCF_004761975.1_ASM476197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004761975.1_ASM476197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:25,275] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:25,288] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:25,288] [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_004761975.1	s__Planococcus koreensis	100.0	1096	1102	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_016908095.1	s__Planococcus chinensis	80.9532	631	1102	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_900099655.1	s__Planococcus glaciei	79.9286	506	1102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.05	96.92	0.90	0.89	5	-
GCF_000821325.1	s__Planococcus massiliensis	79.8353	407	1102	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_014836985.1	s__Planococcus sp014836985	79.2873	378	1102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.16	97.16	0.91	0.91	2	-
GCF_007859395.1	s__Planococcus sp007859395	79.155	363	1102	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_017873465.1	s__Planococcus mcmeekinii	79.1287	337	1102	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	79.0819	338	1102	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_001465795.2	s__Planococcus rifietoensis	78.9668	338	1102	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	78.9095	239	1102	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_003668635.1	s__Planococcus sp003668635	78.8797	319	1102	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	78.8105	323	1102	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_018283455.1	s__Planococcus sp018283455	78.807	350	1102	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	78.7575	288	1102	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_003719725.1	s__Planococcus salinus	78.4143	292	1102	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 14:23:25,290] [INFO] GTDB search result was written to GCF_004761975.1_ASM476197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:25,290] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:25,294] [INFO] DFAST_QC result json was written to GCF_004761975.1_ASM476197v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:25,294] [INFO] DFAST_QC completed!
[2024-01-24 14:23:25,294] [INFO] Total running time: 0h1m10s