[2024-01-25 19:37:06,053] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:06,054] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:06,055] [INFO] DQC Reference Directory: /var/lib/cwl/stge2a38f2a-f8e5-407c-b9f2-6c6a5e06763a/dqc_reference
[2024-01-25 19:37:07,181] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:07,182] [INFO] Task started: Prodigal
[2024-01-25 19:37:07,182] [INFO] Running command: gunzip -c /var/lib/cwl/stg5af96ac7-6cf1-4ece-9e68-2b5f5c085235/GCF_030369615.1_ASM3036961v1_genomic.fna.gz | prodigal -d GCF_030369615.1_ASM3036961v1_genomic.fna/cds.fna -a GCF_030369615.1_ASM3036961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:15,243] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:15,243] [INFO] Task started: HMMsearch
[2024-01-25 19:37:15,243] [INFO] Running command: hmmsearch --tblout GCF_030369615.1_ASM3036961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2a38f2a-f8e5-407c-b9f2-6c6a5e06763a/dqc_reference/reference_markers.hmm GCF_030369615.1_ASM3036961v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:15,526] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:15,527] [INFO] Found 6/6 markers.
[2024-01-25 19:37:15,553] [INFO] Query marker FASTA was written to GCF_030369615.1_ASM3036961v1_genomic.fna/markers.fasta
[2024-01-25 19:37:15,553] [INFO] Task started: Blastn
[2024-01-25 19:37:15,553] [INFO] Running command: blastn -query GCF_030369615.1_ASM3036961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a38f2a-f8e5-407c-b9f2-6c6a5e06763a/dqc_reference/reference_markers.fasta -out GCF_030369615.1_ASM3036961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:16,130] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:16,134] [INFO] Selected 12 target genomes.
[2024-01-25 19:37:16,134] [INFO] Target genome list was writen to GCF_030369615.1_ASM3036961v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:16,162] [INFO] Task started: fastANI
[2024-01-25 19:37:16,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af96ac7-6cf1-4ece-9e68-2b5f5c085235/GCF_030369615.1_ASM3036961v1_genomic.fna.gz --refList GCF_030369615.1_ASM3036961v1_genomic.fna/target_genomes.txt --output GCF_030369615.1_ASM3036961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:26,821] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:26,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2a38f2a-f8e5-407c-b9f2-6c6a5e06763a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:26,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2a38f2a-f8e5-407c-b9f2-6c6a5e06763a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:26,827] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:37:26,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:26,828] [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 stearothermophilus	strain=ATCC 12980	GCA_001277805.1	1422	1422	type	True	99.8566	812	952	95	conclusive
Geobacillus kaustophilus	strain=NBRC 102445	GCA_005160065.1	1462	1462	type	True	91.1822	786	952	95	below_threshold
Geobacillus kaustophilus	strain=NBRC 102445	GCA_000739955.1	1462	1462	type	True	90.9878	752	952	95	below_threshold
Geobacillus jurassicus	strain=NBRC 107829	GCA_001544315.1	235932	235932	type	True	87.612	744	952	95	below_threshold
Geobacillus subterraneus	strain=KCTC 3922	GCA_001618685.1	129338	129338	type	True	87.1914	767	952	95	below_threshold
Geobacillus icigianus	strain=G1w1	GCA_000750005.1	1430331	1430331	type	True	84.3736	701	952	95	below_threshold
Geobacillus thermodenitrificans subsp. thermodenitrificans	strain=DSM 465	GCA_000496575.1	1511749	33940	type	True	83.0804	693	952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:26,829] [INFO] DFAST Taxonomy check result was written to GCF_030369615.1_ASM3036961v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:26,829] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:26,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:26,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2a38f2a-f8e5-407c-b9f2-6c6a5e06763a/dqc_reference/checkm_data
[2024-01-25 19:37:26,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:26,859] [INFO] Task started: CheckM
[2024-01-25 19:37:26,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030369615.1_ASM3036961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030369615.1_ASM3036961v1_genomic.fna/checkm_input GCF_030369615.1_ASM3036961v1_genomic.fna/checkm_result
[2024-01-25 19:37:53,545] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:53,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:53,566] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:53,566] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:53,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030369615.1_ASM3036961v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:53,567] [INFO] Task started: Blastn
[2024-01-25 19:37:53,567] [INFO] Running command: blastn -query GCF_030369615.1_ASM3036961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2a38f2a-f8e5-407c-b9f2-6c6a5e06763a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030369615.1_ASM3036961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:54,365] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:54,368] [INFO] Selected 9 target genomes.
[2024-01-25 19:37:54,368] [INFO] Target genome list was writen to GCF_030369615.1_ASM3036961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:54,384] [INFO] Task started: fastANI
[2024-01-25 19:37:54,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af96ac7-6cf1-4ece-9e68-2b5f5c085235/GCF_030369615.1_ASM3036961v1_genomic.fna.gz --refList GCF_030369615.1_ASM3036961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030369615.1_ASM3036961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:03,756] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:03,773] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:03,773] [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_001277805.1	s__Geobacillus stearothermophilus	99.8566	812	952	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.9983	98.75	97.28	0.90	0.86	19	conclusive
GCA_002243605.1	s__Geobacillus lituanicus	96.9422	811	952	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.9983	97.54	97.16	0.84	0.82	3	-
GCA_900450595.1	s__Geobacillus thermophilus	96.2327	816	952	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.9743	97.77	97.20	0.86	0.80	4	-
GCF_002809955.1	s__Geobacillus sp002809955	96.0848	780	952	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.916	97.67	97.25	0.87	0.84	4	-
GCF_001544135.1	s__Geobacillus zalihae	91.7553	767	952	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	97.99	97.08	0.88	0.86	9	-
GCA_001610955.1	s__Geobacillus thermoleovorans	91.1109	794	952	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	98.02	96.77	0.87	0.82	28	-
GCF_002217655.1	s__Geobacillus thermocatenulatus	90.4048	788	952	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.1122	99.55	99.04	0.96	0.93	6	-
GCF_000445995.2	s__Geobacillus sp000445995	87.2918	774	952	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014679505.1	s__Geobacillus sp002077765	85.7184	776	952	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	98.81	97.63	0.94	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:03,774] [INFO] GTDB search result was written to GCF_030369615.1_ASM3036961v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:03,775] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:03,777] [INFO] DFAST_QC result json was written to GCF_030369615.1_ASM3036961v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:03,778] [INFO] DFAST_QC completed!
[2024-01-25 19:38:03,778] [INFO] Total running time: 0h0m58s