[2024-01-24 12:53:36,768] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg86344ebd-1367-4c6a-ad5a-3d96748011a4/dqc_reference
[2024-01-24 12:53:37,970] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:37,971] [INFO] Task started: Prodigal
[2024-01-24 12:53:37,971] [INFO] Running command: gunzip -c /var/lib/cwl/stgad4d7a4d-ec85-4c30-80d6-8fafb9d25686/GCF_003428875.1_ASM342887v1_genomic.fna.gz | prodigal -d GCF_003428875.1_ASM342887v1_genomic.fna/cds.fna -a GCF_003428875.1_ASM342887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:46,789] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:46,790] [INFO] Task started: HMMsearch
[2024-01-24 12:53:46,790] [INFO] Running command: hmmsearch --tblout GCF_003428875.1_ASM342887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86344ebd-1367-4c6a-ad5a-3d96748011a4/dqc_reference/reference_markers.hmm GCF_003428875.1_ASM342887v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:47,043] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:47,044] [INFO] Found 6/6 markers.
[2024-01-24 12:53:47,075] [INFO] Query marker FASTA was written to GCF_003428875.1_ASM342887v1_genomic.fna/markers.fasta
[2024-01-24 12:53:47,075] [INFO] Task started: Blastn
[2024-01-24 12:53:47,075] [INFO] Running command: blastn -query GCF_003428875.1_ASM342887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86344ebd-1367-4c6a-ad5a-3d96748011a4/dqc_reference/reference_markers.fasta -out GCF_003428875.1_ASM342887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:47,659] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:47,663] [INFO] Selected 14 target genomes.
[2024-01-24 12:53:47,664] [INFO] Target genome list was writen to GCF_003428875.1_ASM342887v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:47,674] [INFO] Task started: fastANI
[2024-01-24 12:53:47,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgad4d7a4d-ec85-4c30-80d6-8fafb9d25686/GCF_003428875.1_ASM342887v1_genomic.fna.gz --refList GCF_003428875.1_ASM342887v1_genomic.fna/target_genomes.txt --output GCF_003428875.1_ASM342887v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:55,925] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:55,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86344ebd-1367-4c6a-ad5a-3d96748011a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:55,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86344ebd-1367-4c6a-ad5a-3d96748011a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:55,946] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:53:55,947] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:53:55,947] [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 salinarum	strain=KCTC 13584	GCA_007004625.1	622695	622695	type	True	82.5123	690	1089	95	below_threshold
Planococcus salinarum	strain=ISL-16	GCA_003428865.1	622695	622695	type	True	82.4547	688	1089	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	79.3067	335	1089	95	below_threshold
Planococcus glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	79.1604	361	1089	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	79.0978	350	1089	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	79.0968	350	1089	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	78.9642	341	1089	95	below_threshold
Planococcus massiliensis	strain=ES2	GCA_000821325.2	1499687	1499687	type	True	78.912	353	1089	95	below_threshold
Planococcus salinus	strain=LCB217	GCA_003719725.1	1848460	1848460	type	True	78.8454	311	1089	95	below_threshold
Planococcus maitriensis	strain=S1	GCA_003289925.1	221799	221799	type	True	78.8178	294	1089	95	below_threshold
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	78.7736	322	1089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:55,949] [INFO] DFAST Taxonomy check result was written to GCF_003428875.1_ASM342887v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:55,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:55,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:55,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86344ebd-1367-4c6a-ad5a-3d96748011a4/dqc_reference/checkm_data
[2024-01-24 12:53:55,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:55,984] [INFO] Task started: CheckM
[2024-01-24 12:53:55,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003428875.1_ASM342887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003428875.1_ASM342887v1_genomic.fna/checkm_input GCF_003428875.1_ASM342887v1_genomic.fna/checkm_result
[2024-01-24 12:54:27,347] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:27,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:27,371] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:27,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:27,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003428875.1_ASM342887v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:27,372] [INFO] Task started: Blastn
[2024-01-24 12:54:27,372] [INFO] Running command: blastn -query GCF_003428875.1_ASM342887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86344ebd-1367-4c6a-ad5a-3d96748011a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003428875.1_ASM342887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:28,136] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:28,140] [INFO] Selected 6 target genomes.
[2024-01-24 12:54:28,140] [INFO] Target genome list was writen to GCF_003428875.1_ASM342887v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:28,145] [INFO] Task started: fastANI
[2024-01-24 12:54:28,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgad4d7a4d-ec85-4c30-80d6-8fafb9d25686/GCF_003428875.1_ASM342887v1_genomic.fna.gz --refList GCF_003428875.1_ASM342887v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003428875.1_ASM342887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:33,985] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:33,991] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:33,991] [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_003428875.1	s__Planococcus okeanokoites	100.0	1089	1089	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.50	97.25	0.88	0.87	3	conclusive
GCF_003289955.1	s__Planococcus halotolerans	86.668	889	1089	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.14	99.14	0.94	0.94	2	-
GCF_003668635.1	s__Planococcus sp003668635	86.5412	914	1089	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_007004625.1	s__Planococcus salinarum	82.5094	690	1089	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017873465.1	s__Planococcus mcmeekinii	82.4054	726	1089	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	81.7268	564	1089	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 12:54:33,993] [INFO] GTDB search result was written to GCF_003428875.1_ASM342887v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:33,994] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:33,996] [INFO] DFAST_QC result json was written to GCF_003428875.1_ASM342887v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:33,997] [INFO] DFAST_QC completed!
[2024-01-24 12:54:33,997] [INFO] Total running time: 0h0m57s