[2024-01-25 19:57:05,522] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:05,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:05,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg387694ad-5140-4451-9e53-591556054112/dqc_reference
[2024-01-25 19:57:06,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:06,704] [INFO] Task started: Prodigal
[2024-01-25 19:57:06,704] [INFO] Running command: gunzip -c /var/lib/cwl/stga2de92ec-a1bf-48a3-8d8c-e737de697f60/GCF_002763455.1_ASM276345v1_genomic.fna.gz | prodigal -d GCF_002763455.1_ASM276345v1_genomic.fna/cds.fna -a GCF_002763455.1_ASM276345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:15,092] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:15,092] [INFO] Task started: HMMsearch
[2024-01-25 19:57:15,092] [INFO] Running command: hmmsearch --tblout GCF_002763455.1_ASM276345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg387694ad-5140-4451-9e53-591556054112/dqc_reference/reference_markers.hmm GCF_002763455.1_ASM276345v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:15,308] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:15,309] [INFO] Found 6/6 markers.
[2024-01-25 19:57:15,341] [INFO] Query marker FASTA was written to GCF_002763455.1_ASM276345v1_genomic.fna/markers.fasta
[2024-01-25 19:57:15,341] [INFO] Task started: Blastn
[2024-01-25 19:57:15,341] [INFO] Running command: blastn -query GCF_002763455.1_ASM276345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg387694ad-5140-4451-9e53-591556054112/dqc_reference/reference_markers.fasta -out GCF_002763455.1_ASM276345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:15,877] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:15,880] [INFO] Selected 22 target genomes.
[2024-01-25 19:57:15,880] [INFO] Target genome list was writen to GCF_002763455.1_ASM276345v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:15,897] [INFO] Task started: fastANI
[2024-01-25 19:57:15,898] [INFO] Running command: fastANI --query /var/lib/cwl/stga2de92ec-a1bf-48a3-8d8c-e737de697f60/GCF_002763455.1_ASM276345v1_genomic.fna.gz --refList GCF_002763455.1_ASM276345v1_genomic.fna/target_genomes.txt --output GCF_002763455.1_ASM276345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:33,611] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:33,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg387694ad-5140-4451-9e53-591556054112/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:33,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg387694ad-5140-4451-9e53-591556054112/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:33,620] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:33,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:33,620] [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
Lentibacillus sediminis	strain=0W14	GCA_002763455.1	1940529	1940529	type	True	100.0	1196	1197	95	conclusive
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	77.3318	70	1197	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_018075365.1	1473	1473	type	True	77.1754	73	1197	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.1726	149	1197	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.1704	96	1197	95	below_threshold
Virgibacillus ihumii	strain=Marseille-Q1233	GCA_902726655.1	2686091	2686091	type	True	77.1645	102	1197	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.0597	150	1197	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	77.0249	73	1197	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	76.9726	102	1197	95	below_threshold
Lentibacillus cibarius	strain=NKC220-2	GCA_005887555.1	2583219	2583219	type	True	76.5653	89	1197	95	below_threshold
Oceanobacillus timonensis	strain=Marseille-P3532	GCA_900166635.1	1926285	1926285	type	True	76.4098	83	1197	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.3139	66	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:33,623] [INFO] DFAST Taxonomy check result was written to GCF_002763455.1_ASM276345v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:33,627] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:33,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:33,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg387694ad-5140-4451-9e53-591556054112/dqc_reference/checkm_data
[2024-01-25 19:57:33,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:33,665] [INFO] Task started: CheckM
[2024-01-25 19:57:33,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002763455.1_ASM276345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002763455.1_ASM276345v1_genomic.fna/checkm_input GCF_002763455.1_ASM276345v1_genomic.fna/checkm_result
[2024-01-25 19:58:01,894] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:01,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:01,911] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:01,911] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:01,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002763455.1_ASM276345v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:01,912] [INFO] Task started: Blastn
[2024-01-25 19:58:01,912] [INFO] Running command: blastn -query GCF_002763455.1_ASM276345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg387694ad-5140-4451-9e53-591556054112/dqc_reference/reference_markers_gtdb.fasta -out GCF_002763455.1_ASM276345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:02,684] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:02,686] [INFO] Selected 27 target genomes.
[2024-01-25 19:58:02,687] [INFO] Target genome list was writen to GCF_002763455.1_ASM276345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:02,711] [INFO] Task started: fastANI
[2024-01-25 19:58:02,711] [INFO] Running command: fastANI --query /var/lib/cwl/stga2de92ec-a1bf-48a3-8d8c-e737de697f60/GCF_002763455.1_ASM276345v1_genomic.fna.gz --refList GCF_002763455.1_ASM276345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002763455.1_ASM276345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:20,946] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:20,955] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:20,955] [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_002763455.1	s__Lentibacillus_A sediminis	100.0	1196	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004565465.1	s__Lentibacillus salicampi	77.2747	129	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002266285.1	s__Virgibacillus_G indicus	77.1814	148	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902726655.1	s__Lentibacillus ihumii	77.1664	101	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638995.1	s__Virgibacillus_E oceani	77.1485	96	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018075365.1	s__Virgibacillus pantothenticus	77.14	73	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.44	97.53	0.92	0.86	18	-
GCF_900162615.1	s__Virgibacillus proomii_A	77.1215	75	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018916875.1	s__Virgibacillus proomii_B	77.0882	64	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287375.1	s__Virgibacillus_G profundi	77.0445	151	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010994035.1	s__Virgibacillus sp010994035	76.6253	119	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887555.1	s__Lentibacillus cibarius	76.6149	89	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.44	97.49	0.90	0.85	3	-
GCF_900166635.1	s__Oceanobacillus timonensis	76.4098	83	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000821065.1	s__Oceanobacillus oncorhynchi	76.1085	87	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.79	98.49	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:20,957] [INFO] GTDB search result was written to GCF_002763455.1_ASM276345v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:20,957] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:20,960] [INFO] DFAST_QC result json was written to GCF_002763455.1_ASM276345v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:20,960] [INFO] DFAST_QC completed!
[2024-01-25 19:58:20,960] [INFO] Total running time: 0h1m15s