[2024-01-25 19:52:20,446] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:52:20,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:52:20,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg983cd219-f451-4ecd-835a-c0a536136b68/dqc_reference
[2024-01-25 19:52:21,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:52:21,645] [INFO] Task started: Prodigal
[2024-01-25 19:52:21,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg729861ae-b912-49e5-9a5f-a11eee26caf5/GCF_000739955.1_ASM73995v1_genomic.fna.gz | prodigal -d GCF_000739955.1_ASM73995v1_genomic.fna/cds.fna -a GCF_000739955.1_ASM73995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:52:30,787] [INFO] Task succeeded: Prodigal
[2024-01-25 19:52:30,787] [INFO] Task started: HMMsearch
[2024-01-25 19:52:30,787] [INFO] Running command: hmmsearch --tblout GCF_000739955.1_ASM73995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg983cd219-f451-4ecd-835a-c0a536136b68/dqc_reference/reference_markers.hmm GCF_000739955.1_ASM73995v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:52:31,034] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:52:31,035] [INFO] Found 6/6 markers.
[2024-01-25 19:52:31,063] [INFO] Query marker FASTA was written to GCF_000739955.1_ASM73995v1_genomic.fna/markers.fasta
[2024-01-25 19:52:31,063] [INFO] Task started: Blastn
[2024-01-25 19:52:31,063] [INFO] Running command: blastn -query GCF_000739955.1_ASM73995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg983cd219-f451-4ecd-835a-c0a536136b68/dqc_reference/reference_markers.fasta -out GCF_000739955.1_ASM73995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:31,679] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:31,682] [INFO] Selected 11 target genomes.
[2024-01-25 19:52:31,682] [INFO] Target genome list was writen to GCF_000739955.1_ASM73995v1_genomic.fna/target_genomes.txt
[2024-01-25 19:52:31,691] [INFO] Task started: fastANI
[2024-01-25 19:52:31,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg729861ae-b912-49e5-9a5f-a11eee26caf5/GCF_000739955.1_ASM73995v1_genomic.fna.gz --refList GCF_000739955.1_ASM73995v1_genomic.fna/target_genomes.txt --output GCF_000739955.1_ASM73995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:40,774] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:40,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg983cd219-f451-4ecd-835a-c0a536136b68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:40,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg983cd219-f451-4ecd-835a-c0a536136b68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:40,780] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:52:40,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:40,780] [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_000739955.1	1462	1462	type	True	100.0	1089	1093	95	conclusive
Geobacillus kaustophilus	strain=NBRC 102445	GCA_005160065.1	1462	1462	type	True	99.9617	1088	1093	95	conclusive
Geobacillus jurassicus	strain=NBRC 107829	GCA_001544315.1	235932	235932	type	True	91.4869	885	1093	95	below_threshold
Geobacillus stearothermophilus	strain=ATCC 12980	GCA_001277805.1	1422	1422	type	True	90.721	729	1093	95	below_threshold
Geobacillus subterraneus	strain=KCTC 3922	GCA_001618685.1	129338	129338	type	True	86.9489	871	1093	95	below_threshold
Geobacillus icigianus	strain=G1w1	GCA_000750005.1	1430331	1430331	type	True	86.0109	811	1093	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:40,782] [INFO] DFAST Taxonomy check result was written to GCF_000739955.1_ASM73995v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:40,782] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:40,782] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:40,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg983cd219-f451-4ecd-835a-c0a536136b68/dqc_reference/checkm_data
[2024-01-25 19:52:40,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:40,819] [INFO] Task started: CheckM
[2024-01-25 19:52:40,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000739955.1_ASM73995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000739955.1_ASM73995v1_genomic.fna/checkm_input GCF_000739955.1_ASM73995v1_genomic.fna/checkm_result
[2024-01-25 19:53:10,239] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:10,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:10,261] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:10,261] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:10,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000739955.1_ASM73995v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:10,262] [INFO] Task started: Blastn
[2024-01-25 19:53:10,262] [INFO] Running command: blastn -query GCF_000739955.1_ASM73995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg983cd219-f451-4ecd-835a-c0a536136b68/dqc_reference/reference_markers_gtdb.fasta -out GCF_000739955.1_ASM73995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:11,346] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:11,351] [INFO] Selected 9 target genomes.
[2024-01-25 19:53:11,351] [INFO] Target genome list was writen to GCF_000739955.1_ASM73995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:11,362] [INFO] Task started: fastANI
[2024-01-25 19:53:11,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg729861ae-b912-49e5-9a5f-a11eee26caf5/GCF_000739955.1_ASM73995v1_genomic.fna.gz --refList GCF_000739955.1_ASM73995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000739955.1_ASM73995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:19,478] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:19,485] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:19,485] [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	98.1941	961	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	98.02	96.77	0.87	0.82	28	conclusive
GCF_001908025.1	s__Geobacillus proteiniphilus	95.9117	930	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9151	98.36	98.36	0.87	0.87	2	-
GCF_001544135.1	s__Geobacillus zalihae	95.8676	918	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	97.99	97.08	0.88	0.86	9	-
GCF_002217655.1	s__Geobacillus thermocatenulatus	94.4804	967	1093	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	93.4378	935	1093	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	91.482	893	1093	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	90.997	846	1093	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	90.8359	859	1093	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	90.7206	729	1093	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.9983	98.75	97.28	0.90	0.86	19	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:19,486] [INFO] GTDB search result was written to GCF_000739955.1_ASM73995v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:19,487] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:19,489] [INFO] DFAST_QC result json was written to GCF_000739955.1_ASM73995v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:19,489] [INFO] DFAST_QC completed!
[2024-01-25 19:53:19,489] [INFO] Total running time: 0h0m59s