[2024-01-24 13:49:17,514] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:17,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:17,519] [INFO] DQC Reference Directory: /var/lib/cwl/stgad44612b-7d4f-43f9-8698-11702c09246b/dqc_reference
[2024-01-24 13:49:18,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:18,805] [INFO] Task started: Prodigal
[2024-01-24 13:49:18,806] [INFO] Running command: gunzip -c /var/lib/cwl/stgd627c44c-25a6-47a1-b9f9-00e6fcc13370/GCF_002441655.1_ASM244165v1_genomic.fna.gz | prodigal -d GCF_002441655.1_ASM244165v1_genomic.fna/cds.fna -a GCF_002441655.1_ASM244165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:23,536] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:23,537] [INFO] Task started: HMMsearch
[2024-01-24 13:49:23,537] [INFO] Running command: hmmsearch --tblout GCF_002441655.1_ASM244165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad44612b-7d4f-43f9-8698-11702c09246b/dqc_reference/reference_markers.hmm GCF_002441655.1_ASM244165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:23,838] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:23,840] [INFO] Found 6/6 markers.
[2024-01-24 13:49:23,867] [INFO] Query marker FASTA was written to GCF_002441655.1_ASM244165v1_genomic.fna/markers.fasta
[2024-01-24 13:49:23,868] [INFO] Task started: Blastn
[2024-01-24 13:49:23,868] [INFO] Running command: blastn -query GCF_002441655.1_ASM244165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad44612b-7d4f-43f9-8698-11702c09246b/dqc_reference/reference_markers.fasta -out GCF_002441655.1_ASM244165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:24,465] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:24,468] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:24,469] [INFO] Target genome list was writen to GCF_002441655.1_ASM244165v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:24,526] [INFO] Task started: fastANI
[2024-01-24 13:49:24,526] [INFO] Running command: fastANI --query /var/lib/cwl/stgd627c44c-25a6-47a1-b9f9-00e6fcc13370/GCF_002441655.1_ASM244165v1_genomic.fna.gz --refList GCF_002441655.1_ASM244165v1_genomic.fna/target_genomes.txt --output GCF_002441655.1_ASM244165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:31,817] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:31,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad44612b-7d4f-43f9-8698-11702c09246b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:31,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad44612b-7d4f-43f9-8698-11702c09246b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:31,833] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:31,833] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:31,833] [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
Lactococcus fujiensis	strain=JCM 16395	GCA_002441655.1	610251	610251	type	True	100.0	662	663	95	conclusive
Lactococcus fujiensis	strain=JCM 16395	GCA_001311235.1	610251	610251	type	True	99.8435	654	663	95	conclusive
Lactococcus hircilactis	strain=DSM 28960	GCA_009601015.1	1494462	1494462	type	True	78.8314	221	663	95	below_threshold
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_001456385.1	1360	1358	type	True	78.523	161	663	95	below_threshold
Lactococcus lactis subsp. lactis	strain=ATCC 19435	GCA_004354485.1	1360	1358	type	True	78.3525	164	663	95	below_threshold
Lactococcus lactis	strain=ATCC 19435	GCA_900099625.1	1358	1358	type	True	78.3471	167	663	95	below_threshold
Lactococcus taiwanensis	strain=NBRC 109049	GCA_014905395.1	1151742	1151742	type	True	78.2849	123	663	95	below_threshold
Lactococcus nasutitermitis	strain=NBRC 111537	GCA_018403765.1	1652957	1652957	type	True	78.2416	115	663	95	below_threshold
Lactococcus protaetiae	strain=KACC 19320	GCA_006965445.1	2592653	2592653	type	True	77.927	133	663	95	below_threshold
Lactococcus allomyrinae	strain=1JSPR-7	GCA_003627095.1	2419773	2419773	type	True	77.6346	123	663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:31,845] [INFO] DFAST Taxonomy check result was written to GCF_002441655.1_ASM244165v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:31,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:31,847] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:31,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad44612b-7d4f-43f9-8698-11702c09246b/dqc_reference/checkm_data
[2024-01-24 13:49:31,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:31,872] [INFO] Task started: CheckM
[2024-01-24 13:49:31,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002441655.1_ASM244165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002441655.1_ASM244165v1_genomic.fna/checkm_input GCF_002441655.1_ASM244165v1_genomic.fna/checkm_result
[2024-01-24 13:49:53,670] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:53,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:53,688] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:53,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:53,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002441655.1_ASM244165v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:53,688] [INFO] Task started: Blastn
[2024-01-24 13:49:53,689] [INFO] Running command: blastn -query GCF_002441655.1_ASM244165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad44612b-7d4f-43f9-8698-11702c09246b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002441655.1_ASM244165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:54,582] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:54,656] [INFO] Selected 23 target genomes.
[2024-01-24 13:49:54,657] [INFO] Target genome list was writen to GCF_002441655.1_ASM244165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:54,690] [INFO] Task started: fastANI
[2024-01-24 13:49:54,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgd627c44c-25a6-47a1-b9f9-00e6fcc13370/GCF_002441655.1_ASM244165v1_genomic.fna.gz --refList GCF_002441655.1_ASM244165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002441655.1_ASM244165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:03,274] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:03,286] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:03,286] [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_002441655.1	s__Lactococcus fujiensis	100.0	662	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	99.84	99.84	0.99	0.99	2	conclusive
GCF_009601055.1	s__Lactococcus sp009601055	79.739	276	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	100.00	99.99	0.99	0.98	3	-
GCF_009601015.1	s__Lactococcus hircilactis	78.8314	221	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099625.1	s__Lactococcus lactis	78.358	166	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.37	97.03	0.87	0.82	223	-
GCF_001591705.1	s__Lactococcus cremoris	78.3096	147	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.76	97.45	0.91	0.82	70	-
GCF_014905395.1	s__Lactococcus taiwanensis	78.2849	123	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.39	0.94	0.93	6	-
GCF_018403765.1	s__Lactococcus nasutitermitis	78.2416	115	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004210295.1	s__Lactococcus sp004210295	78.1384	136	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006965445.1	s__Lactococcus sp006965445	77.927	133	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.72	98.72	0.90	0.90	2	-
GCF_016027715.1	s__Lactococcus garvieae_A	77.8032	97	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	98.53	98.50	0.90	0.89	3	-
GCF_003627095.1	s__Lactococcus allomyrinae	77.6346	123	663	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:03,288] [INFO] GTDB search result was written to GCF_002441655.1_ASM244165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:03,288] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:03,292] [INFO] DFAST_QC result json was written to GCF_002441655.1_ASM244165v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:03,293] [INFO] DFAST_QC completed!
[2024-01-24 13:50:03,293] [INFO] Total running time: 0h0m46s