[2024-01-25 18:13:05,636] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:05,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:05,639] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9dc17ea-5ff1-427b-8069-9c4fd9ae4714/dqc_reference
[2024-01-25 18:13:06,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:06,801] [INFO] Task started: Prodigal
[2024-01-25 18:13:06,801] [INFO] Running command: gunzip -c /var/lib/cwl/stg0002d21b-7541-4eb1-b56b-a8a095650d09/GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/cds.fna -a GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:13,655] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:13,655] [INFO] Task started: HMMsearch
[2024-01-25 18:13:13,655] [INFO] Running command: hmmsearch --tblout GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9dc17ea-5ff1-427b-8069-9c4fd9ae4714/dqc_reference/reference_markers.hmm GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:13,898] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:13,899] [INFO] Found 6/6 markers.
[2024-01-25 18:13:13,929] [INFO] Query marker FASTA was written to GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:13:13,929] [INFO] Task started: Blastn
[2024-01-25 18:13:13,929] [INFO] Running command: blastn -query GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9dc17ea-5ff1-427b-8069-9c4fd9ae4714/dqc_reference/reference_markers.fasta -out GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:14,487] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:14,490] [INFO] Selected 21 target genomes.
[2024-01-25 18:13:14,491] [INFO] Target genome list was writen to GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:13:14,495] [INFO] Task started: fastANI
[2024-01-25 18:13:14,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg0002d21b-7541-4eb1-b56b-a8a095650d09/GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna.gz --refList GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:27,082] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:27,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9dc17ea-5ff1-427b-8069-9c4fd9ae4714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:27,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9dc17ea-5ff1-427b-8069-9c4fd9ae4714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:27,092] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:13:27,092] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:13:27,092] [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
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	78.1576	258	1280	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	77.8084	185	1280	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	77.5886	180	1280	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.5547	150	1280	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	77.5522	172	1280	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.344	187	1280	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.2864	196	1280	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	77.2793	144	1280	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	77.1582	148	1280	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	77.1424	111	1280	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	77.1412	92	1280	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_014905475.1	1462526	1462526	suspected-type	True	77.1033	150	1280	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	76.9356	68	1280	95	below_threshold
Virgibacillus chiguensis	strain=CGMCC 1.6496	GCA_900129865.1	411959	411959	type	True	76.9169	126	1280	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.1086	63	1280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:27,094] [INFO] DFAST Taxonomy check result was written to GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:13:27,094] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:27,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:27,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9dc17ea-5ff1-427b-8069-9c4fd9ae4714/dqc_reference/checkm_data
[2024-01-25 18:13:27,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:27,134] [INFO] Task started: CheckM
[2024-01-25 18:13:27,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/checkm_input GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:13:52,401] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:52,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:52,421] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:52,422] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:52,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:13:52,422] [INFO] Task started: Blastn
[2024-01-25 18:13:52,422] [INFO] Running command: blastn -query GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9dc17ea-5ff1-427b-8069-9c4fd9ae4714/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:53,214] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:53,216] [INFO] Selected 19 target genomes.
[2024-01-25 18:13:53,217] [INFO] Target genome list was writen to GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:53,224] [INFO] Task started: fastANI
[2024-01-25 18:13:53,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg0002d21b-7541-4eb1-b56b-a8a095650d09/GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna.gz --refList GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:06,495] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:06,507] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:06,507] [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_900111445.1	s__Ornithinibacillus limi	100.0	1273	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009728145.1	s__Ornithinibacillus caprae	79.2885	462	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129485.1	s__Ornithinibacillus halophilus	78.1464	256	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038425.2	s__Ornithinibacillus contaminans	77.7286	187	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637405.1	s__Ornithinibacillus halotolerans	77.5763	180	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190475.1	s__Ornithinibacillus scapharcae	77.5345	173	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919725.1	s__Virgibacillus sp016919725	77.3441	156	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_003628445.1	s__Oceanobacillus bengalensis	77.2963	154	1280	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_900187325.1	s__Virgibacillus_E ndiopensis	77.2721	197	1280	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_016908155.1	s__Oceanobacillus caeni	77.2385	130	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_900166595.1	s__Virgibacillus dokdonensis	77.2335	120	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.95	98.88	0.93	0.90	3	-
GCF_014905415.1	s__Virgibacillus salexigens	77.1691	152	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.53	99.42	0.93	0.91	9	-
GCF_003730295.1	s__LJ137 sp003730295	77.1424	111	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__LJ137	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184735.1	s__Ornithinibacillus globulus_B	77.1421	210	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482485.1	s__Ornithinibacillus globulus	77.0839	197	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083865.1	s__Paraliobacillus salinarum	76.9356	68	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918075.1	s__MSJ-26 sp018918075	76.4942	104	1280	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__MSJ-26	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:06,509] [INFO] GTDB search result was written to GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:06,509] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:06,513] [INFO] DFAST_QC result json was written to GCF_900111445.1_IMG-taxon_2654587897_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:14:06,513] [INFO] DFAST_QC completed!
[2024-01-25 18:14:06,513] [INFO] Total running time: 0h1m1s