[2024-01-24 14:05:34,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,132] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb4e8ff7-a5f1-41f1-b64a-05bec9beca63/dqc_reference
[2024-01-24 14:05:35,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,521] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg69e603ed-4693-47a0-ac2f-d54d7acbef77/GCF_003867075.1_ASM386707v1_genomic.fna.gz | prodigal -d GCF_003867075.1_ASM386707v1_genomic.fna/cds.fna -a GCF_003867075.1_ASM386707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:45,684] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:45,685] [INFO] Task started: HMMsearch
[2024-01-24 14:05:45,685] [INFO] Running command: hmmsearch --tblout GCF_003867075.1_ASM386707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb4e8ff7-a5f1-41f1-b64a-05bec9beca63/dqc_reference/reference_markers.hmm GCF_003867075.1_ASM386707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:45,958] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:45,959] [INFO] Found 6/6 markers.
[2024-01-24 14:05:45,990] [INFO] Query marker FASTA was written to GCF_003867075.1_ASM386707v1_genomic.fna/markers.fasta
[2024-01-24 14:05:45,991] [INFO] Task started: Blastn
[2024-01-24 14:05:45,991] [INFO] Running command: blastn -query GCF_003867075.1_ASM386707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb4e8ff7-a5f1-41f1-b64a-05bec9beca63/dqc_reference/reference_markers.fasta -out GCF_003867075.1_ASM386707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:46,670] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:46,673] [INFO] Selected 11 target genomes.
[2024-01-24 14:05:46,674] [INFO] Target genome list was writen to GCF_003867075.1_ASM386707v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:46,682] [INFO] Task started: fastANI
[2024-01-24 14:05:46,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg69e603ed-4693-47a0-ac2f-d54d7acbef77/GCF_003867075.1_ASM386707v1_genomic.fna.gz --refList GCF_003867075.1_ASM386707v1_genomic.fna/target_genomes.txt --output GCF_003867075.1_ASM386707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:55,804] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:55,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb4e8ff7-a5f1-41f1-b64a-05bec9beca63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:55,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb4e8ff7-a5f1-41f1-b64a-05bec9beca63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:55,815] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:05:55,815] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:55,816] [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
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	100.0	1108	1114	95	conclusive
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	100.0	1108	1114	95	conclusive
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	99.9958	1086	1114	95	conclusive
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	92.3995	876	1114	95	below_threshold
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	88.7876	881	1114	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	84.0742	756	1114	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	79.7248	513	1114	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	78.277	353	1114	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.1766	365	1114	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.7327	317	1114	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.7156	295	1114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:55,818] [INFO] DFAST Taxonomy check result was written to GCF_003867075.1_ASM386707v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:55,819] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:55,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:55,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb4e8ff7-a5f1-41f1-b64a-05bec9beca63/dqc_reference/checkm_data
[2024-01-24 14:05:55,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:55,871] [INFO] Task started: CheckM
[2024-01-24 14:05:55,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003867075.1_ASM386707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003867075.1_ASM386707v1_genomic.fna/checkm_input GCF_003867075.1_ASM386707v1_genomic.fna/checkm_result
[2024-01-24 14:06:29,876] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:29,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.94%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:29,903] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:29,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:29,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003867075.1_ASM386707v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:29,904] [INFO] Task started: Blastn
[2024-01-24 14:06:29,904] [INFO] Running command: blastn -query GCF_003867075.1_ASM386707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb4e8ff7-a5f1-41f1-b64a-05bec9beca63/dqc_reference/reference_markers_gtdb.fasta -out GCF_003867075.1_ASM386707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:30,868] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:30,871] [INFO] Selected 6 target genomes.
[2024-01-24 14:06:30,871] [INFO] Target genome list was writen to GCF_003867075.1_ASM386707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:30,881] [INFO] Task started: fastANI
[2024-01-24 14:06:30,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg69e603ed-4693-47a0-ac2f-d54d7acbef77/GCF_003867075.1_ASM386707v1_genomic.fna.gz --refList GCF_003867075.1_ASM386707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003867075.1_ASM386707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:36,046] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:36,052] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:36,052] [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_003867075.1	s__Tenacibaculum mesophilum	100.0	1108	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	conclusive
GCF_003867015.1	s__Tenacibaculum singaporense	92.3777	875	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_003664185.1	s__Tenacibaculum discolor	88.7716	882	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	-
GCF_003387615.1	s__Tenacibaculum gallaicum	88.6402	913	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610735.1	s__Tenacibaculum lutimaris	85.5408	749	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	84.0682	756	1114	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:36,054] [INFO] GTDB search result was written to GCF_003867075.1_ASM386707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:36,054] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:36,057] [INFO] DFAST_QC result json was written to GCF_003867075.1_ASM386707v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:36,058] [INFO] DFAST_QC completed!
[2024-01-24 14:06:36,058] [INFO] Total running time: 0h1m2s