[2024-01-24 11:05:49,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,404] [INFO] DQC Reference Directory: /var/lib/cwl/stge2301f57-ce4a-4245-891d-65c1257f41eb/dqc_reference
[2024-01-24 11:05:51,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,279] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,280] [INFO] Running command: gunzip -c /var/lib/cwl/stg22dc3133-7158-4bb3-a7c6-8adc69e4a207/GCF_003289955.1_ASM328995v1_genomic.fna.gz | prodigal -d GCF_003289955.1_ASM328995v1_genomic.fna/cds.fna -a GCF_003289955.1_ASM328995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:00,552] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:00,553] [INFO] Task started: HMMsearch
[2024-01-24 11:06:00,553] [INFO] Running command: hmmsearch --tblout GCF_003289955.1_ASM328995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2301f57-ce4a-4245-891d-65c1257f41eb/dqc_reference/reference_markers.hmm GCF_003289955.1_ASM328995v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:00,766] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:00,767] [INFO] Found 6/6 markers.
[2024-01-24 11:06:00,794] [INFO] Query marker FASTA was written to GCF_003289955.1_ASM328995v1_genomic.fna/markers.fasta
[2024-01-24 11:06:00,794] [INFO] Task started: Blastn
[2024-01-24 11:06:00,794] [INFO] Running command: blastn -query GCF_003289955.1_ASM328995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2301f57-ce4a-4245-891d-65c1257f41eb/dqc_reference/reference_markers.fasta -out GCF_003289955.1_ASM328995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:01,376] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:01,380] [INFO] Selected 17 target genomes.
[2024-01-24 11:06:01,380] [INFO] Target genome list was writen to GCF_003289955.1_ASM328995v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:01,419] [INFO] Task started: fastANI
[2024-01-24 11:06:01,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg22dc3133-7158-4bb3-a7c6-8adc69e4a207/GCF_003289955.1_ASM328995v1_genomic.fna.gz --refList GCF_003289955.1_ASM328995v1_genomic.fna/target_genomes.txt --output GCF_003289955.1_ASM328995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:11,917] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:11,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2301f57-ce4a-4245-891d-65c1257f41eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:11,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2301f57-ce4a-4245-891d-65c1257f41eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:11,929] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:11,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:11,929] [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=DSM 23820	GCA_001856085.1	622695	622695	type	True	82.8572	209	1198	95	below_threshold
Planococcus salinarum	strain=KCTC 13584	GCA_007004625.1	622695	622695	type	True	82.6354	750	1198	95	below_threshold
Planococcus salinarum	strain=ISL-16	GCA_003428865.1	622695	622695	type	True	82.5952	741	1198	95	below_threshold
Planococcus donghaensis	strain=DSM 22276	GCA_001687665.2	414778	414778	type	True	79.1855	250	1198	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	79.0476	362	1198	95	below_threshold
Planococcus glaciei	strain=CGMCC 1.6846	GCA_900099655.1	459472	459472	type	True	79.0387	358	1198	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	78.912	361	1198	95	below_threshold
Planococcus salinus	strain=LCB217	GCA_003719725.1	1848460	1848460	type	True	78.898	333	1198	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_001687565.2	161360	161360	type	True	78.886	284	1198	95	below_threshold
Planococcus massiliensis	strain=ES2	GCA_000821325.2	1499687	1499687	type	True	78.8414	370	1198	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	78.8399	359	1198	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	78.7646	344	1198	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	78.6752	277	1198	95	below_threshold
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	78.5465	357	1198	95	below_threshold
Planococcus rifietoensis	strain=M8	GCA_001465795.2	200991	200991	type	True	78.2901	295	1198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:11,931] [INFO] DFAST Taxonomy check result was written to GCF_003289955.1_ASM328995v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:11,932] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:11,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:11,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2301f57-ce4a-4245-891d-65c1257f41eb/dqc_reference/checkm_data
[2024-01-24 11:06:11,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:11,967] [INFO] Task started: CheckM
[2024-01-24 11:06:11,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003289955.1_ASM328995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003289955.1_ASM328995v1_genomic.fna/checkm_input GCF_003289955.1_ASM328995v1_genomic.fna/checkm_result
[2024-01-24 11:06:43,229] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:43,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:43,246] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:43,246] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:43,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003289955.1_ASM328995v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:43,247] [INFO] Task started: Blastn
[2024-01-24 11:06:43,247] [INFO] Running command: blastn -query GCF_003289955.1_ASM328995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2301f57-ce4a-4245-891d-65c1257f41eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003289955.1_ASM328995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:44,004] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:44,007] [INFO] Selected 6 target genomes.
[2024-01-24 11:06:44,007] [INFO] Target genome list was writen to GCF_003289955.1_ASM328995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:44,011] [INFO] Task started: fastANI
[2024-01-24 11:06:44,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg22dc3133-7158-4bb3-a7c6-8adc69e4a207/GCF_003289955.1_ASM328995v1_genomic.fna.gz --refList GCF_003289955.1_ASM328995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003289955.1_ASM328995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:49,999] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:50,005] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:50,005] [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_003289955.1	s__Planococcus halotolerans	100.0	1197	1198	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.14	99.14	0.94	0.94	2	conclusive
GCF_003668635.1	s__Planococcus sp003668635	94.6158	1067	1198	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	86.6968	876	1198	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_017873465.1	s__Planococcus mcmeekinii	82.7109	735	1198	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	82.6764	746	1198	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_000775575.1	s__Planococcus sp000775575	81.684	604	1198	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 11:06:50,007] [INFO] GTDB search result was written to GCF_003289955.1_ASM328995v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:50,008] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:50,010] [INFO] DFAST_QC result json was written to GCF_003289955.1_ASM328995v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:50,011] [INFO] DFAST_QC completed!
[2024-01-24 11:06:50,011] [INFO] Total running time: 0h1m1s