[2024-01-24 10:57:09,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:09,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:09,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg5069ec9d-f10f-4afc-ba41-8ae6a7a5b18c/dqc_reference
[2024-01-24 10:57:10,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:10,646] [INFO] Task started: Prodigal
[2024-01-24 10:57:10,647] [INFO] Running command: gunzip -c /var/lib/cwl/stgde10baf2-39f5-48e7-84e2-bfdb8c8f0efa/GCF_005160065.1_ASM516006v1_genomic.fna.gz | prodigal -d GCF_005160065.1_ASM516006v1_genomic.fna/cds.fna -a GCF_005160065.1_ASM516006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:22,283] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:22,283] [INFO] Task started: HMMsearch
[2024-01-24 10:57:22,283] [INFO] Running command: hmmsearch --tblout GCF_005160065.1_ASM516006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5069ec9d-f10f-4afc-ba41-8ae6a7a5b18c/dqc_reference/reference_markers.hmm GCF_005160065.1_ASM516006v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:22,585] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:22,586] [INFO] Found 6/6 markers.
[2024-01-24 10:57:22,639] [INFO] Query marker FASTA was written to GCF_005160065.1_ASM516006v1_genomic.fna/markers.fasta
[2024-01-24 10:57:22,640] [INFO] Task started: Blastn
[2024-01-24 10:57:22,640] [INFO] Running command: blastn -query GCF_005160065.1_ASM516006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5069ec9d-f10f-4afc-ba41-8ae6a7a5b18c/dqc_reference/reference_markers.fasta -out GCF_005160065.1_ASM516006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:23,396] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:23,399] [INFO] Selected 11 target genomes.
[2024-01-24 10:57:23,399] [INFO] Target genome list was writen to GCF_005160065.1_ASM516006v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:23,404] [INFO] Task started: fastANI
[2024-01-24 10:57:23,404] [INFO] Running command: fastANI --query /var/lib/cwl/stgde10baf2-39f5-48e7-84e2-bfdb8c8f0efa/GCF_005160065.1_ASM516006v1_genomic.fna.gz --refList GCF_005160065.1_ASM516006v1_genomic.fna/target_genomes.txt --output GCF_005160065.1_ASM516006v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:34,308] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:34,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5069ec9d-f10f-4afc-ba41-8ae6a7a5b18c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:34,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5069ec9d-f10f-4afc-ba41-8ae6a7a5b18c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:34,316] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:34,316] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:34,316] [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
Geobacillus kaustophilus	strain=NBRC 102445	GCA_005160065.1	1462	1462	type	True	100.0	1223	1223	95	conclusive
Geobacillus kaustophilus	strain=NBRC 102445	GCA_000739955.1	1462	1462	type	True	99.8944	1085	1223	95	conclusive
Geobacillus jurassicus	strain=NBRC 107829	GCA_001544315.1	235932	235932	type	True	91.2766	919	1223	95	below_threshold
Geobacillus stearothermophilus	strain=ATCC 12980	GCA_001277805.1	1422	1422	type	True	90.8021	732	1223	95	below_threshold
Geobacillus subterraneus	strain=KCTC 3922	GCA_001618685.1	129338	129338	type	True	87.349	888	1223	95	below_threshold
Geobacillus icigianus	strain=G1w1	GCA_000750005.1	1430331	1430331	type	True	85.8841	837	1223	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:34,319] [INFO] DFAST Taxonomy check result was written to GCF_005160065.1_ASM516006v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:34,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:34,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:34,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5069ec9d-f10f-4afc-ba41-8ae6a7a5b18c/dqc_reference/checkm_data
[2024-01-24 10:57:34,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:34,373] [INFO] Task started: CheckM
[2024-01-24 10:57:34,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005160065.1_ASM516006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005160065.1_ASM516006v1_genomic.fna/checkm_input GCF_005160065.1_ASM516006v1_genomic.fna/checkm_result
[2024-01-24 10:58:13,092] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:13,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:13,111] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:13,112] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:13,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005160065.1_ASM516006v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:13,113] [INFO] Task started: Blastn
[2024-01-24 10:58:13,113] [INFO] Running command: blastn -query GCF_005160065.1_ASM516006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5069ec9d-f10f-4afc-ba41-8ae6a7a5b18c/dqc_reference/reference_markers_gtdb.fasta -out GCF_005160065.1_ASM516006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:14,273] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:14,275] [INFO] Selected 9 target genomes.
[2024-01-24 10:58:14,276] [INFO] Target genome list was writen to GCF_005160065.1_ASM516006v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:14,292] [INFO] Task started: fastANI
[2024-01-24 10:58:14,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgde10baf2-39f5-48e7-84e2-bfdb8c8f0efa/GCF_005160065.1_ASM516006v1_genomic.fna.gz --refList GCF_005160065.1_ASM516006v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005160065.1_ASM516006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:23,951] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:23,963] [INFO] Found 9 fastANI hits (3 hits with ANI > circumscription radius)
[2024-01-24 10:58:23,964] [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
GCA_001610955.1	s__Geobacillus thermoleovorans	98.0327	1019	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	98.02	96.77	0.87	0.82	28	inconclusive
GCF_001544135.1	s__Geobacillus zalihae	95.9752	939	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	97.99	97.08	0.88	0.86	9	inconclusive
GCF_001908025.1	s__Geobacillus proteiniphilus	95.9213	951	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9151	98.36	98.36	0.87	0.87	2	inconclusive
GCF_002217655.1	s__Geobacillus thermocatenulatus	94.4303	987	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.1122	99.55	99.04	0.96	0.93	6	-
GCF_000948285.1	s__Geobacillus thermoleovorans_A	93.3513	987	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	97.57	95.98	0.88	0.86	3	-
GCF_000733845.1	s__Geobacillus vulcani	91.4675	944	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	99.16	99.16	0.91	0.91	2	-
GCF_002809955.1	s__Geobacillus sp002809955	90.9342	874	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.916	97.67	97.25	0.87	0.84	4	-
GCA_900450595.1	s__Geobacillus thermophilus	90.893	915	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.9743	97.77	97.20	0.86	0.80	4	-
GCF_001277805.1	s__Geobacillus stearothermophilus	90.7859	733	1223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.9983	98.75	97.28	0.90	0.86	19	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:23,965] [INFO] GTDB search result was written to GCF_005160065.1_ASM516006v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:23,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:23,969] [INFO] DFAST_QC result json was written to GCF_005160065.1_ASM516006v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:23,969] [INFO] DFAST_QC completed!
[2024-01-24 10:58:23,969] [INFO] Total running time: 0h1m15s