[2024-01-24 13:37:13,767] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:13,769] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:13,769] [INFO] DQC Reference Directory: /var/lib/cwl/stgd920617d-d39b-4c19-a81d-cc3b7a9b492b/dqc_reference
[2024-01-24 13:37:15,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:15,015] [INFO] Task started: Prodigal
[2024-01-24 13:37:15,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg91950f74-f8cf-4ef8-a6e9-8fd7cc1c86f9/GCF_000425705.1_ASM42570v1_genomic.fna.gz | prodigal -d GCF_000425705.1_ASM42570v1_genomic.fna/cds.fna -a GCF_000425705.1_ASM42570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:24,905] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:24,906] [INFO] Task started: HMMsearch
[2024-01-24 13:37:24,906] [INFO] Running command: hmmsearch --tblout GCF_000425705.1_ASM42570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd920617d-d39b-4c19-a81d-cc3b7a9b492b/dqc_reference/reference_markers.hmm GCF_000425705.1_ASM42570v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:25,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:25,200] [INFO] Found 6/6 markers.
[2024-01-24 13:37:25,241] [INFO] Query marker FASTA was written to GCF_000425705.1_ASM42570v1_genomic.fna/markers.fasta
[2024-01-24 13:37:25,242] [INFO] Task started: Blastn
[2024-01-24 13:37:25,242] [INFO] Running command: blastn -query GCF_000425705.1_ASM42570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd920617d-d39b-4c19-a81d-cc3b7a9b492b/dqc_reference/reference_markers.fasta -out GCF_000425705.1_ASM42570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:25,862] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:25,868] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:25,869] [INFO] Target genome list was writen to GCF_000425705.1_ASM42570v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:25,889] [INFO] Task started: fastANI
[2024-01-24 13:37:25,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg91950f74-f8cf-4ef8-a6e9-8fd7cc1c86f9/GCF_000425705.1_ASM42570v1_genomic.fna.gz --refList GCF_000425705.1_ASM42570v1_genomic.fna/target_genomes.txt --output GCF_000425705.1_ASM42570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:39,195] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:39,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd920617d-d39b-4c19-a81d-cc3b7a9b492b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:39,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd920617d-d39b-4c19-a81d-cc3b7a9b492b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:39,206] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:39,206] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:39,206] [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
Halobacillus kuroshimensis	strain=DSM 18393	GCA_000425705.1	302481	302481	type	True	100.0	1273	1274	95	conclusive
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	79.3358	371	1274	95	below_threshold
Halobacillus aidingensis	strain=CGMCC 1.3703	GCA_900104185.1	240303	240303	type	True	79.2045	363	1274	95	below_threshold
Halobacillus faecis	strain=NBRC 103569	GCA_007991335.1	360184	360184	type	True	79.1277	355	1274	95	below_threshold
Halobacillus litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	78.9686	369	1274	95	below_threshold
Halobacillus karajensis	strain=DSM 14948	GCA_900108515.1	195088	195088	type	True	78.7947	304	1274	95	below_threshold
Halobacillus locisalis	strain=KCTC 3788	GCA_013694105.1	220753	220753	type	True	78.2259	229	1274	95	below_threshold
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	77.8833	144	1274	95	below_threshold
Halobacillus andaensis	strain=CGMCC 1.12153	GCA_014636475.1	1176239	1176239	type	True	77.8482	143	1274	95	below_threshold
Thalassobacillus devorans	strain=CCM 7282	GCA_014635125.1	279813	279813	type	True	77.3572	100	1274	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:39,209] [INFO] DFAST Taxonomy check result was written to GCF_000425705.1_ASM42570v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:39,210] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:39,210] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:39,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd920617d-d39b-4c19-a81d-cc3b7a9b492b/dqc_reference/checkm_data
[2024-01-24 13:37:39,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:39,253] [INFO] Task started: CheckM
[2024-01-24 13:37:39,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425705.1_ASM42570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425705.1_ASM42570v1_genomic.fna/checkm_input GCF_000425705.1_ASM42570v1_genomic.fna/checkm_result
[2024-01-24 13:38:15,181] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:15,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:15,204] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:15,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:15,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425705.1_ASM42570v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:15,205] [INFO] Task started: Blastn
[2024-01-24 13:38:15,206] [INFO] Running command: blastn -query GCF_000425705.1_ASM42570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd920617d-d39b-4c19-a81d-cc3b7a9b492b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425705.1_ASM42570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:16,023] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:16,027] [INFO] Selected 12 target genomes.
[2024-01-24 13:38:16,027] [INFO] Target genome list was writen to GCF_000425705.1_ASM42570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:16,039] [INFO] Task started: fastANI
[2024-01-24 13:38:16,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg91950f74-f8cf-4ef8-a6e9-8fd7cc1c86f9/GCF_000425705.1_ASM42570v1_genomic.fna.gz --refList GCF_000425705.1_ASM42570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425705.1_ASM42570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:25,670] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:25,683] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:25,684] [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_000425705.1	s__Halobacillus kuroshimensis	100.0	1273	1274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.79	98.79	0.92	0.92	2	conclusive
GCF_009856355.1	s__Halobacillus litoralis_B	87.9542	1067	1274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.99	98.95	0.95	0.95	3	-
GCF_900104185.1	s__Halobacillus aidingensis	79.1933	362	1274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	96.52	96.52	0.91	0.91	2	-
GCF_009856415.1	s__Halobacillus litoralis_C	79.143	381	1274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991335.1	s__Halobacillus faecis	79.1277	355	1274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856445.1	s__Halobacillus litoralis	78.9941	368	1274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	95.88	95.88	0.90	0.90	2	-
GCF_000469135.2	s__Halobacillus sp001592845	78.5834	293	1274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.23	99.19	0.95	0.95	3	-
GCF_002097535.1	s__Halobacillus mangrovi	78.2797	251	1274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004078665.1	s__Halobacillus sp004078665	78.276	251	1274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:25,685] [INFO] GTDB search result was written to GCF_000425705.1_ASM42570v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:25,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:25,689] [INFO] DFAST_QC result json was written to GCF_000425705.1_ASM42570v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:25,689] [INFO] DFAST_QC completed!
[2024-01-24 13:38:25,689] [INFO] Total running time: 0h1m12s