[2024-01-24 13:37:15,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:15,356] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:15,356] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe01828c-3b08-4410-a44f-e32e291aa0a0/dqc_reference
[2024-01-24 13:37:18,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:18,468] [INFO] Task started: Prodigal
[2024-01-24 13:37:18,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg241d0f6b-4d8f-4d76-8869-aded5baf6344/GCF_014637175.1_ASM1463717v1_genomic.fna.gz | prodigal -d GCF_014637175.1_ASM1463717v1_genomic.fna/cds.fna -a GCF_014637175.1_ASM1463717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:25,962] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:25,962] [INFO] Task started: HMMsearch
[2024-01-24 13:37:25,963] [INFO] Running command: hmmsearch --tblout GCF_014637175.1_ASM1463717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe01828c-3b08-4410-a44f-e32e291aa0a0/dqc_reference/reference_markers.hmm GCF_014637175.1_ASM1463717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:26,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:26,313] [INFO] Found 6/6 markers.
[2024-01-24 13:37:26,358] [INFO] Query marker FASTA was written to GCF_014637175.1_ASM1463717v1_genomic.fna/markers.fasta
[2024-01-24 13:37:26,358] [INFO] Task started: Blastn
[2024-01-24 13:37:26,358] [INFO] Running command: blastn -query GCF_014637175.1_ASM1463717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe01828c-3b08-4410-a44f-e32e291aa0a0/dqc_reference/reference_markers.fasta -out GCF_014637175.1_ASM1463717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:26,995] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:26,999] [INFO] Selected 21 target genomes.
[2024-01-24 13:37:27,000] [INFO] Target genome list was writen to GCF_014637175.1_ASM1463717v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:27,012] [INFO] Task started: fastANI
[2024-01-24 13:37:27,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg241d0f6b-4d8f-4d76-8869-aded5baf6344/GCF_014637175.1_ASM1463717v1_genomic.fna.gz --refList GCF_014637175.1_ASM1463717v1_genomic.fna/target_genomes.txt --output GCF_014637175.1_ASM1463717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:41,865] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:41,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe01828c-3b08-4410-a44f-e32e291aa0a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:41,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe01828c-3b08-4410-a44f-e32e291aa0a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:41,885] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:41,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:41,886] [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
Compostibacillus humi	strain=CGMCC 1.12360	GCA_014637175.1	1245525	1245525	type	True	100.0	1039	1047	95	conclusive
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	77.4277	67	1047	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.9129	102	1047	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	76.8506	54	1047	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	76.6704	69	1047	95	below_threshold
Oceanobacillus massiliensis	strain=Ndiop	GCA_000285495.1	1465765	1465765	type	True	76.5606	67	1047	95	below_threshold
Oceanobacillus timonensis	strain=Marseille-P3532	GCA_900166635.1	1926285	1926285	type	True	76.4258	61	1047	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	76.3302	54	1047	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.2319	50	1047	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.2032	57	1047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:41,888] [INFO] DFAST Taxonomy check result was written to GCF_014637175.1_ASM1463717v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:41,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:41,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:41,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe01828c-3b08-4410-a44f-e32e291aa0a0/dqc_reference/checkm_data
[2024-01-24 13:37:41,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:41,933] [INFO] Task started: CheckM
[2024-01-24 13:37:41,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014637175.1_ASM1463717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014637175.1_ASM1463717v1_genomic.fna/checkm_input GCF_014637175.1_ASM1463717v1_genomic.fna/checkm_result
[2024-01-24 13:38:10,541] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:10,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:10,566] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:10,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:10,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014637175.1_ASM1463717v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:10,568] [INFO] Task started: Blastn
[2024-01-24 13:38:10,568] [INFO] Running command: blastn -query GCF_014637175.1_ASM1463717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe01828c-3b08-4410-a44f-e32e291aa0a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014637175.1_ASM1463717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:11,390] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:11,394] [INFO] Selected 27 target genomes.
[2024-01-24 13:38:11,395] [INFO] Target genome list was writen to GCF_014637175.1_ASM1463717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:11,425] [INFO] Task started: fastANI
[2024-01-24 13:38:11,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg241d0f6b-4d8f-4d76-8869-aded5baf6344/GCF_014637175.1_ASM1463717v1_genomic.fna.gz --refList GCF_014637175.1_ASM1463717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014637175.1_ASM1463717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:29,576] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:29,591] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:29,591] [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_014637175.1	s__Oceanobacillus humi	100.0	1039	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001659985.1	s__Oceanobacillus sp001659985	77.6871	78	1047	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_009733865.1	s__Oceanobacillus salinisoli	76.8915	103	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014642895.1	s__Virgibacillus_E populi	76.8778	64	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	98.98	98.88	0.86	0.85	5	-
GCF_001618145.1	s__Oceanobacillus damuensis	76.8506	54	1047	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_900162695.1	s__Lentibacillus siamensis	76.7829	53	1047	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	76.6704	69	1047	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_000285495.1	s__Oceanobacillus massiliensis	76.5974	68	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	76.5888	62	1047	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_018333215.1	s__Oceanobacillus sp018333215	76.4352	65	1047	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_900166635.1	s__Oceanobacillus timonensis	76.4258	61	1047	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_900110695.1	s__Lentibacillus subterraneus	76.2319	50	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:29,593] [INFO] GTDB search result was written to GCF_014637175.1_ASM1463717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:29,594] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:29,598] [INFO] DFAST_QC result json was written to GCF_014637175.1_ASM1463717v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:29,598] [INFO] DFAST_QC completed!
[2024-01-24 13:38:29,598] [INFO] Total running time: 0h1m14s