[2024-01-24 13:55:57,327] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:57,329] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:57,329] [INFO] DQC Reference Directory: /var/lib/cwl/stg689e9d70-8871-4e48-81e4-8eeb6da14395/dqc_reference
[2024-01-24 13:55:58,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:58,571] [INFO] Task started: Prodigal
[2024-01-24 13:55:58,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg0108ba19-d0b4-4138-8323-066fd74a2c41/GCF_000264415.1_ASM26441v1_genomic.fna.gz | prodigal -d GCF_000264415.1_ASM26441v1_genomic.fna/cds.fna -a GCF_000264415.1_ASM26441v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:07,643] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:07,644] [INFO] Task started: HMMsearch
[2024-01-24 13:56:07,644] [INFO] Running command: hmmsearch --tblout GCF_000264415.1_ASM26441v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg689e9d70-8871-4e48-81e4-8eeb6da14395/dqc_reference/reference_markers.hmm GCF_000264415.1_ASM26441v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:07,902] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:07,904] [INFO] Found 6/6 markers.
[2024-01-24 13:56:07,936] [INFO] Query marker FASTA was written to GCF_000264415.1_ASM26441v1_genomic.fna/markers.fasta
[2024-01-24 13:56:07,936] [INFO] Task started: Blastn
[2024-01-24 13:56:07,936] [INFO] Running command: blastn -query GCF_000264415.1_ASM26441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg689e9d70-8871-4e48-81e4-8eeb6da14395/dqc_reference/reference_markers.fasta -out GCF_000264415.1_ASM26441v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:08,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:08,542] [INFO] Selected 13 target genomes.
[2024-01-24 13:56:08,543] [INFO] Target genome list was writen to GCF_000264415.1_ASM26441v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:08,628] [INFO] Task started: fastANI
[2024-01-24 13:56:08,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg0108ba19-d0b4-4138-8323-066fd74a2c41/GCF_000264415.1_ASM26441v1_genomic.fna.gz --refList GCF_000264415.1_ASM26441v1_genomic.fna/target_genomes.txt --output GCF_000264415.1_ASM26441v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:18,536] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:18,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg689e9d70-8871-4e48-81e4-8eeb6da14395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:18,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg689e9d70-8871-4e48-81e4-8eeb6da14395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:18,555] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:18,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:18,555] [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 antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	100.0	1187	1193	95	conclusive
Planococcus antarcticus	strain=DSM 14505	GCA_001687565.2	161360	161360	type	True	99.3667	1133	1193	95	conclusive
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	83.6151	878	1193	95	below_threshold
Planococcus faecalis	strain=CECT 8759	GCA_001856115.1	1598147	1598147	suspected-type	True	82.5312	714	1193	95	below_threshold
Planococcus faecalis	strain=AJ003	GCA_002009235.1	1598147	1598147	suspected-type	True	82.5258	726	1193	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	81.7463	748	1193	95	below_threshold
Planococcus versutus	strain=L10.15	GCA_001186155.3	1302659	1302659	type	True	81.4776	606	1193	95	below_threshold
Planococcus halocryophilus	strain=Or1	GCA_000342445.1	1215089	1215089	type	True	81.2783	648	1193	95	below_threshold
Planococcus halocryophilus	strain=DSM 24743	GCA_001687585.2	1215089	1215089	type	True	81.2661	657	1193	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	78.5973	315	1193	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:18,557] [INFO] DFAST Taxonomy check result was written to GCF_000264415.1_ASM26441v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:18,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:18,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:18,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg689e9d70-8871-4e48-81e4-8eeb6da14395/dqc_reference/checkm_data
[2024-01-24 13:56:18,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:18,595] [INFO] Task started: CheckM
[2024-01-24 13:56:18,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000264415.1_ASM26441v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000264415.1_ASM26441v1_genomic.fna/checkm_input GCF_000264415.1_ASM26441v1_genomic.fna/checkm_result
[2024-01-24 13:56:50,540] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:50,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:50,562] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:50,562] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:50,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000264415.1_ASM26441v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:50,563] [INFO] Task started: Blastn
[2024-01-24 13:56:50,563] [INFO] Running command: blastn -query GCF_000264415.1_ASM26441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg689e9d70-8871-4e48-81e4-8eeb6da14395/dqc_reference/reference_markers_gtdb.fasta -out GCF_000264415.1_ASM26441v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:51,290] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:51,294] [INFO] Selected 10 target genomes.
[2024-01-24 13:56:51,294] [INFO] Target genome list was writen to GCF_000264415.1_ASM26441v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:51,306] [INFO] Task started: fastANI
[2024-01-24 13:56:51,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg0108ba19-d0b4-4138-8323-066fd74a2c41/GCF_000264415.1_ASM26441v1_genomic.fna.gz --refList GCF_000264415.1_ASM26441v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000264415.1_ASM26441v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:00,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:00,014] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:00,014] [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_001687565.2	s__Planococcus antarcticus	99.3708	1133	1193	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.42	99.42	0.95	0.95	2	conclusive
GCF_018613575.1	s__Planococcus sp018613575	84.5303	886	1193	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	83.6151	878	1193	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_001465835.2	s__Planococcus kocurii	82.5749	754	1193	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_007859295.1	s__Planococcus sp007859295	82.4376	792	1193	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_014836985.1	s__Planococcus sp014836985	81.7429	748	1193	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_000189395.1	s__Planococcus donghaensis_B	81.3423	598	1193	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	81.2962	592	1193	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	81.2622	658	1193	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	81.1923	616	1193	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 13:57:00,016] [INFO] GTDB search result was written to GCF_000264415.1_ASM26441v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:00,016] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:00,019] [INFO] DFAST_QC result json was written to GCF_000264415.1_ASM26441v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:00,019] [INFO] DFAST_QC completed!
[2024-01-24 13:57:00,019] [INFO] Total running time: 0h1m3s