[2024-01-24 14:15:29,300] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:29,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:29,301] [INFO] DQC Reference Directory: /var/lib/cwl/stga500d096-9190-4094-85cf-bbd9b1caf0f9/dqc_reference
[2024-01-24 14:15:30,544] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:30,545] [INFO] Task started: Prodigal
[2024-01-24 14:15:30,545] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc3b1a37-3e54-4b47-ada1-0d4750c5fe2b/GCF_002884495.1_ASM288449v1_genomic.fna.gz | prodigal -d GCF_002884495.1_ASM288449v1_genomic.fna/cds.fna -a GCF_002884495.1_ASM288449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:37,944] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:37,945] [INFO] Task started: HMMsearch
[2024-01-24 14:15:37,945] [INFO] Running command: hmmsearch --tblout GCF_002884495.1_ASM288449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga500d096-9190-4094-85cf-bbd9b1caf0f9/dqc_reference/reference_markers.hmm GCF_002884495.1_ASM288449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:38,168] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:38,169] [INFO] Found 6/6 markers.
[2024-01-24 14:15:38,200] [INFO] Query marker FASTA was written to GCF_002884495.1_ASM288449v1_genomic.fna/markers.fasta
[2024-01-24 14:15:38,201] [INFO] Task started: Blastn
[2024-01-24 14:15:38,201] [INFO] Running command: blastn -query GCF_002884495.1_ASM288449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga500d096-9190-4094-85cf-bbd9b1caf0f9/dqc_reference/reference_markers.fasta -out GCF_002884495.1_ASM288449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:38,797] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:38,801] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:38,801] [INFO] Target genome list was writen to GCF_002884495.1_ASM288449v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:38,820] [INFO] Task started: fastANI
[2024-01-24 14:15:38,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3b1a37-3e54-4b47-ada1-0d4750c5fe2b/GCF_002884495.1_ASM288449v1_genomic.fna.gz --refList GCF_002884495.1_ASM288449v1_genomic.fna/target_genomes.txt --output GCF_002884495.1_ASM288449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:50,342] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:50,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga500d096-9190-4094-85cf-bbd9b1caf0f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:50,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga500d096-9190-4094-85cf-bbd9b1caf0f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:50,354] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:50,354] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:50,354] [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
Rummeliibacillus pycnus	strain=DSM 15030	GCA_002884495.1	101070	101070	type	True	100.0	1277	1283	95	conclusive
Rummeliibacillus suwonensis	strain=G20	GCA_007896435.1	1306154	1306154	type	True	81.0382	625	1283	95	below_threshold
Rummeliibacillus stabekisii	strain=DSM 25578	GCA_014202625.1	241244	241244	type	True	79.3061	316	1283	95	below_threshold
Rummeliibacillus stabekisii	strain=NBRC 104870	GCA_007988965.1	241244	241244	type	True	79.281	305	1283	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	79.067	76	1283	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	78.5404	321	1283	95	below_threshold
Viridibacillus arvi	strain=DSM 16317	GCA_001274945.1	263475	263475	type	True	78.518	346	1283	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	78.3022	155	1283	95	below_threshold
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	78.2484	217	1283	95	below_threshold
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	78.2401	208	1283	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	77.7213	141	1283	95	below_threshold
Lysinibacillus parviboronicapiens	strain=BAM-582	GCA_003049575.1	436516	436516	type	True	77.6862	178	1283	95	below_threshold
Caryophanon latum	strain=DSM 14151	GCA_001700325.1	33977	33977	type	True	77.6844	91	1283	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	77.4545	142	1283	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	77.2124	124	1283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:50,355] [INFO] DFAST Taxonomy check result was written to GCF_002884495.1_ASM288449v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:50,356] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:50,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:50,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga500d096-9190-4094-85cf-bbd9b1caf0f9/dqc_reference/checkm_data
[2024-01-24 14:15:50,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:50,401] [INFO] Task started: CheckM
[2024-01-24 14:15:50,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002884495.1_ASM288449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002884495.1_ASM288449v1_genomic.fna/checkm_input GCF_002884495.1_ASM288449v1_genomic.fna/checkm_result
[2024-01-24 14:16:17,469] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:17,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:17,497] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:17,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:17,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002884495.1_ASM288449v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:17,498] [INFO] Task started: Blastn
[2024-01-24 14:16:17,498] [INFO] Running command: blastn -query GCF_002884495.1_ASM288449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga500d096-9190-4094-85cf-bbd9b1caf0f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002884495.1_ASM288449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:18,278] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:18,284] [INFO] Selected 11 target genomes.
[2024-01-24 14:16:18,284] [INFO] Target genome list was writen to GCF_002884495.1_ASM288449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:18,295] [INFO] Task started: fastANI
[2024-01-24 14:16:18,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc3b1a37-3e54-4b47-ada1-0d4750c5fe2b/GCF_002884495.1_ASM288449v1_genomic.fna.gz --refList GCF_002884495.1_ASM288449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002884495.1_ASM288449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:27,863] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:27,873] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:27,873] [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_002884495.1	s__Rummeliibacillus pycnus	100.0	1278	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003576525.1	s__Rummeliibacillus sp003576525	81.6877	648	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.66	98.66	0.89	0.89	2	-
GCF_007896435.1	s__Rummeliibacillus suwonensis	81.0404	624	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.15	97.53	0.89	0.86	3	-
GCF_007988965.1	s__Rummeliibacillus stabekisii	79.265	306	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.11	96.96	0.93	0.90	5	-
GCF_002813185.1	s__Viridibacillus sp002813185	79.0927	345	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	98.00	98.00	0.85	0.85	2	-
GCF_003073375.1	s__Solibacillus sp003073375	79.0898	174	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001955655.1	s__Viridibacillus arenosi	78.7358	315	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	99.71	99.53	0.97	0.96	4	-
GCF_001274945.1	s__Viridibacillus arvi	78.5342	346	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	95.96	95.96	0.91	0.91	2	-
GCA_018065935.1	s__Kurthia sp018065935	78.0058	203	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002973635.1	s__Lysinibacillus sp002973635	77.8154	192	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111345.1	s__Psychrobacillus sp900111345	77.3745	132	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:27,875] [INFO] GTDB search result was written to GCF_002884495.1_ASM288449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:27,876] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:27,879] [INFO] DFAST_QC result json was written to GCF_002884495.1_ASM288449v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:27,879] [INFO] DFAST_QC completed!
[2024-01-24 14:16:27,879] [INFO] Total running time: 0h0m59s