[2024-01-24 11:05:03,928] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,930] [INFO] DQC Reference Directory: /var/lib/cwl/stgafc4aabe-6c3c-4928-a786-516d250d2375/dqc_reference
[2024-01-24 11:05:05,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,765] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg0efe8b46-ce22-4e6e-b47f-b918b161a1f1/GCF_002217655.1_ASM221765v1_genomic.fna.gz | prodigal -d GCF_002217655.1_ASM221765v1_genomic.fna/cds.fna -a GCF_002217655.1_ASM221765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:15,786] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:15,787] [INFO] Task started: HMMsearch
[2024-01-24 11:05:15,787] [INFO] Running command: hmmsearch --tblout GCF_002217655.1_ASM221765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafc4aabe-6c3c-4928-a786-516d250d2375/dqc_reference/reference_markers.hmm GCF_002217655.1_ASM221765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:16,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:16,102] [INFO] Found 6/6 markers.
[2024-01-24 11:05:16,137] [INFO] Query marker FASTA was written to GCF_002217655.1_ASM221765v1_genomic.fna/markers.fasta
[2024-01-24 11:05:16,137] [INFO] Task started: Blastn
[2024-01-24 11:05:16,137] [INFO] Running command: blastn -query GCF_002217655.1_ASM221765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafc4aabe-6c3c-4928-a786-516d250d2375/dqc_reference/reference_markers.fasta -out GCF_002217655.1_ASM221765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:16,708] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:16,710] [INFO] Selected 11 target genomes.
[2024-01-24 11:05:16,711] [INFO] Target genome list was writen to GCF_002217655.1_ASM221765v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:16,717] [INFO] Task started: fastANI
[2024-01-24 11:05:16,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg0efe8b46-ce22-4e6e-b47f-b918b161a1f1/GCF_002217655.1_ASM221765v1_genomic.fna.gz --refList GCF_002217655.1_ASM221765v1_genomic.fna/target_genomes.txt --output GCF_002217655.1_ASM221765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:26,265] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:26,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafc4aabe-6c3c-4928-a786-516d250d2375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:26,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafc4aabe-6c3c-4928-a786-516d250d2375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:26,271] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:26,271] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:26,271] [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	94.4357	973	1187	95	below_threshold
Geobacillus kaustophilus	strain=NBRC 102445	GCA_005160065.1	1462	1462	type	True	94.3454	995	1187	95	below_threshold
Geobacillus jurassicus	strain=NBRC 107829	GCA_001544315.1	235932	235932	type	True	90.4139	904	1187	95	below_threshold
Geobacillus stearothermophilus	strain=ATCC 12980	GCA_001277805.1	1422	1422	type	True	90.2229	743	1187	95	below_threshold
Geobacillus subterraneus	strain=KCTC 3922	GCA_001618685.1	129338	129338	type	True	85.8805	882	1187	95	below_threshold
Geobacillus icigianus	strain=G1w1	GCA_000750005.1	1430331	1430331	type	True	85.1602	842	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:26,272] [INFO] DFAST Taxonomy check result was written to GCF_002217655.1_ASM221765v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:26,273] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:26,273] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:26,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafc4aabe-6c3c-4928-a786-516d250d2375/dqc_reference/checkm_data
[2024-01-24 11:05:26,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:26,310] [INFO] Task started: CheckM
[2024-01-24 11:05:26,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217655.1_ASM221765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217655.1_ASM221765v1_genomic.fna/checkm_input GCF_002217655.1_ASM221765v1_genomic.fna/checkm_result
[2024-01-24 11:05:57,803] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:57,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:57,816] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:57,816] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:57,816] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217655.1_ASM221765v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:57,816] [INFO] Task started: Blastn
[2024-01-24 11:05:57,816] [INFO] Running command: blastn -query GCF_002217655.1_ASM221765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafc4aabe-6c3c-4928-a786-516d250d2375/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217655.1_ASM221765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:58,609] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:58,612] [INFO] Selected 9 target genomes.
[2024-01-24 11:05:58,612] [INFO] Target genome list was writen to GCF_002217655.1_ASM221765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:58,617] [INFO] Task started: fastANI
[2024-01-24 11:05:58,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg0efe8b46-ce22-4e6e-b47f-b918b161a1f1/GCF_002217655.1_ASM221765v1_genomic.fna.gz --refList GCF_002217655.1_ASM221765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217655.1_ASM221765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:08,261] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:08,268] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:08,268] [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_002217655.1	s__Geobacillus thermocatenulatus	100.0	1187	1187	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.1122	99.55	99.04	0.96	0.93	6	conclusive
GCF_001544135.1	s__Geobacillus zalihae	95.0272	932	1187	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	94.4615	987	1187	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9751	98.02	96.77	0.87	0.82	28	-
GCF_001908025.1	s__Geobacillus proteiniphilus	93.3136	939	1187	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.9151	98.36	98.36	0.87	0.87	2	-
GCF_000948285.1	s__Geobacillus thermoleovorans_A	92.1826	990	1187	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	97.57	95.98	0.88	0.86	3	-
GCA_002243605.1	s__Geobacillus lituanicus	90.5299	920	1187	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.9983	97.54	97.16	0.84	0.82	3	-
GCF_001277805.1	s__Geobacillus stearothermophilus	90.276	740	1187	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.9983	98.75	97.28	0.90	0.86	19	-
GCF_000733845.1	s__Geobacillus vulcani	90.1052	940	1187	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	99.16	99.16	0.91	0.91	2	-
GCA_900450595.1	s__Geobacillus thermophilus	90.0367	928	1187	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	96.9743	97.77	97.20	0.86	0.80	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:08,270] [INFO] GTDB search result was written to GCF_002217655.1_ASM221765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:08,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:08,273] [INFO] DFAST_QC result json was written to GCF_002217655.1_ASM221765v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:08,273] [INFO] DFAST_QC completed!
[2024-01-24 11:06:08,273] [INFO] Total running time: 0h1m4s