[2024-01-25 20:02:05,728] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:05,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:05,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg90a5b917-62db-485f-821c-4312a9e3d175/dqc_reference
[2024-01-25 20:02:06,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:06,938] [INFO] Task started: Prodigal
[2024-01-25 20:02:06,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg6abc7dd5-8b7c-47ad-a5d7-1a55ebe06592/GCF_001593005.1_ASM159300v1_genomic.fna.gz | prodigal -d GCF_001593005.1_ASM159300v1_genomic.fna/cds.fna -a GCF_001593005.1_ASM159300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:21,681] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:21,681] [INFO] Task started: HMMsearch
[2024-01-25 20:02:21,681] [INFO] Running command: hmmsearch --tblout GCF_001593005.1_ASM159300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90a5b917-62db-485f-821c-4312a9e3d175/dqc_reference/reference_markers.hmm GCF_001593005.1_ASM159300v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:21,962] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:21,963] [INFO] Found 6/6 markers.
[2024-01-25 20:02:22,000] [INFO] Query marker FASTA was written to GCF_001593005.1_ASM159300v1_genomic.fna/markers.fasta
[2024-01-25 20:02:22,000] [INFO] Task started: Blastn
[2024-01-25 20:02:22,000] [INFO] Running command: blastn -query GCF_001593005.1_ASM159300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90a5b917-62db-485f-821c-4312a9e3d175/dqc_reference/reference_markers.fasta -out GCF_001593005.1_ASM159300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:22,551] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:22,554] [INFO] Selected 10 target genomes.
[2024-01-25 20:02:22,554] [INFO] Target genome list was writen to GCF_001593005.1_ASM159300v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:22,570] [INFO] Task started: fastANI
[2024-01-25 20:02:22,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg6abc7dd5-8b7c-47ad-a5d7-1a55ebe06592/GCF_001593005.1_ASM159300v1_genomic.fna.gz --refList GCF_001593005.1_ASM159300v1_genomic.fna/target_genomes.txt --output GCF_001593005.1_ASM159300v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:30,033] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:30,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90a5b917-62db-485f-821c-4312a9e3d175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:30,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90a5b917-62db-485f-821c-4312a9e3d175/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:30,038] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:02:30,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:30,038] [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
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	100.0	1399	1401	95	conclusive
Roseivirga ehrenbergii	strain=DSM 102268	GCA_004340805.1	279360	279360	type	True	99.997	1400	1401	95	conclusive
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	93.1706	1171	1401	95	below_threshold
Roseivirga seohaensis	strain=SW-152	GCA_001592945.1	1914963	1914963	type	True	93.0262	1181	1401	95	below_threshold
Roseivirga echinicomitans	strain=KMM 6058	GCA_001592935.1	296218	296218	type	True	86.0209	1050	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:30,040] [INFO] DFAST Taxonomy check result was written to GCF_001593005.1_ASM159300v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:30,040] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:30,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:30,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90a5b917-62db-485f-821c-4312a9e3d175/dqc_reference/checkm_data
[2024-01-25 20:02:30,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:30,082] [INFO] Task started: CheckM
[2024-01-25 20:02:30,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001593005.1_ASM159300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001593005.1_ASM159300v1_genomic.fna/checkm_input GCF_001593005.1_ASM159300v1_genomic.fna/checkm_result
[2024-01-25 20:03:13,470] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:13,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:13,486] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:13,486] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:13,486] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001593005.1_ASM159300v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:13,487] [INFO] Task started: Blastn
[2024-01-25 20:03:13,487] [INFO] Running command: blastn -query GCF_001593005.1_ASM159300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90a5b917-62db-485f-821c-4312a9e3d175/dqc_reference/reference_markers_gtdb.fasta -out GCF_001593005.1_ASM159300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:14,266] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:14,268] [INFO] Selected 12 target genomes.
[2024-01-25 20:03:14,269] [INFO] Target genome list was writen to GCF_001593005.1_ASM159300v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:14,288] [INFO] Task started: fastANI
[2024-01-25 20:03:14,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg6abc7dd5-8b7c-47ad-a5d7-1a55ebe06592/GCF_001593005.1_ASM159300v1_genomic.fna.gz --refList GCF_001593005.1_ASM159300v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001593005.1_ASM159300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:23,577] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:23,584] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:23,584] [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_001593005.1	s__Roseivirga ehrenbergii	100.0	1399	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001592945.1	s__Roseivirga seohaensis	93.0262	1181	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	97.29	97.29	0.91	0.91	2	-
GCF_001592935.1	s__Roseivirga echinicomitans	86.0209	1050	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786855.1	s__Roseivirga sp002786855	77.9482	355	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	99.94	99.94	0.97	0.97	2	-
GCF_001592965.1	s__Fabibacter spongicola	77.1845	154	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
GCF_001747105.1	s__Fabibacter misakiensis	77.0845	94	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427755.1	s__Fabibacter sp002427755	77.0362	91	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111145.1	s__Fabibacter pacificus	76.9352	145	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014653175.1	s__Fabibacter thermotolerans	76.9316	109	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	98.67	98.61	0.92	0.91	4	-
GCF_017592825.1	s__Fabibacter sp017592825	76.7187	113	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:23,586] [INFO] GTDB search result was written to GCF_001593005.1_ASM159300v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:23,588] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:23,593] [INFO] DFAST_QC result json was written to GCF_001593005.1_ASM159300v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:23,593] [INFO] DFAST_QC completed!
[2024-01-25 20:03:23,593] [INFO] Total running time: 0h1m18s