[2024-01-24 10:47:08,352] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:08,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:08,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d534101-37d7-43ce-9c59-7488ccf61924/dqc_reference
[2024-01-24 10:47:11,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,933] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg333e8734-a4cf-4636-a886-11201d5dd221/GCF_017052555.1_ASM1705255v1_genomic.fna.gz | prodigal -d GCF_017052555.1_ASM1705255v1_genomic.fna/cds.fna -a GCF_017052555.1_ASM1705255v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,299] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,299] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,299] [INFO] Running command: hmmsearch --tblout GCF_017052555.1_ASM1705255v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d534101-37d7-43ce-9c59-7488ccf61924/dqc_reference/reference_markers.hmm GCF_017052555.1_ASM1705255v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:21,591] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:21,593] [INFO] Found 6/6 markers.
[2024-01-24 10:47:21,629] [INFO] Query marker FASTA was written to GCF_017052555.1_ASM1705255v1_genomic.fna/markers.fasta
[2024-01-24 10:47:21,630] [INFO] Task started: Blastn
[2024-01-24 10:47:21,630] [INFO] Running command: blastn -query GCF_017052555.1_ASM1705255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d534101-37d7-43ce-9c59-7488ccf61924/dqc_reference/reference_markers.fasta -out GCF_017052555.1_ASM1705255v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,244] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,249] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:22,249] [INFO] Target genome list was writen to GCF_017052555.1_ASM1705255v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:22,666] [INFO] Task started: fastANI
[2024-01-24 10:47:22,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg333e8734-a4cf-4636-a886-11201d5dd221/GCF_017052555.1_ASM1705255v1_genomic.fna.gz --refList GCF_017052555.1_ASM1705255v1_genomic.fna/target_genomes.txt --output GCF_017052555.1_ASM1705255v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:32,704] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:32,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d534101-37d7-43ce-9c59-7488ccf61924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:32,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d534101-37d7-43ce-9c59-7488ccf61924/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:32,712] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:32,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:32,712] [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
Fictibacillus barbaricus	strain=DSM 14730	GCA_017052555.1	182136	182136	type	True	100.0	1427	1429	95	conclusive
Fictibacillus barbaricus	strain=CCM 4982	GCA_014635025.1	182136	182136	type	True	99.9838	1422	1429	95	conclusive
Fictibacillus halophilus	strain=KCTC 33758	GCA_016401385.1	1610490	1610490	type	True	82.0888	768	1429	95	below_threshold
Fictibacillus norfolkensis	strain=Sa2CUA10	GCA_014836645.1	2762233	2762233	type	True	81.8286	762	1429	95	below_threshold
Fictibacillus arsenicus	strain=Con a/3	GCA_001999465.1	255247	255247	type	True	81.3565	734	1429	95	below_threshold
Fictibacillus aquaticus	strain=GDSW-R2A3	GCA_002245695.1	2021314	2021314	type	True	78.1866	168	1429	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.671	63	1429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:32,714] [INFO] DFAST Taxonomy check result was written to GCF_017052555.1_ASM1705255v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:32,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:32,716] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:32,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d534101-37d7-43ce-9c59-7488ccf61924/dqc_reference/checkm_data
[2024-01-24 10:47:32,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:32,776] [INFO] Task started: CheckM
[2024-01-24 10:47:32,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017052555.1_ASM1705255v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017052555.1_ASM1705255v1_genomic.fna/checkm_input GCF_017052555.1_ASM1705255v1_genomic.fna/checkm_result
[2024-01-24 10:48:05,892] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:05,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:05,918] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:05,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:05,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017052555.1_ASM1705255v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:05,919] [INFO] Task started: Blastn
[2024-01-24 10:48:05,919] [INFO] Running command: blastn -query GCF_017052555.1_ASM1705255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d534101-37d7-43ce-9c59-7488ccf61924/dqc_reference/reference_markers_gtdb.fasta -out GCF_017052555.1_ASM1705255v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:06,686] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:06,689] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:06,690] [INFO] Target genome list was writen to GCF_017052555.1_ASM1705255v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:06,711] [INFO] Task started: fastANI
[2024-01-24 10:48:06,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg333e8734-a4cf-4636-a886-11201d5dd221/GCF_017052555.1_ASM1705255v1_genomic.fna.gz --refList GCF_017052555.1_ASM1705255v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017052555.1_ASM1705255v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:16,764] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:16,778] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:16,778] [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_014635025.1	s__Fictibacillus barbaricus	99.9838	1422	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001619875.1	s__Fictibacillus phosphorivorans_B	82.7497	840	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016401385.1	s__Fictibacillus halophilus	82.0888	768	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503015.1	s__Fictibacillus sp005503015	82.0546	740	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017052515.1	s__Fictibacillus nanhaiensis_B	81.9014	743	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836645.1	s__Fictibacillus sp014836645	81.8286	762	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007673525.1	s__Fictibacillus phosphorivorans_C	81.7921	778	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	98.18	98.18	0.90	0.90	2	-
GCA_016401345.1	s__Fictibacillus nanhaiensis_A	81.7578	811	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	97.66	97.26	0.91	0.88	5	-
GCF_001999465.1	s__Fictibacillus arsenicus	81.3493	735	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216955.1	s__Fictibacillus sp004216955	81.1001	752	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426085.1	s__URHB0009 sp000426085	76.6956	65	1429	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__URHB0009	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,780] [INFO] GTDB search result was written to GCF_017052555.1_ASM1705255v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:16,780] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:16,784] [INFO] DFAST_QC result json was written to GCF_017052555.1_ASM1705255v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:16,784] [INFO] DFAST_QC completed!
[2024-01-24 10:48:16,784] [INFO] Total running time: 0h1m8s