[2024-01-25 19:09:20,529] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:20,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:20,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg85bdb35b-ddf6-47e2-8d99-90e81d9d46bd/dqc_reference
[2024-01-25 19:09:21,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:21,664] [INFO] Task started: Prodigal
[2024-01-25 19:09:21,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg1577f501-150f-4587-b1d5-7bcf04265459/GCF_014635125.1_ASM1463512v1_genomic.fna.gz | prodigal -d GCF_014635125.1_ASM1463512v1_genomic.fna/cds.fna -a GCF_014635125.1_ASM1463512v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:30,223] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:30,224] [INFO] Task started: HMMsearch
[2024-01-25 19:09:30,224] [INFO] Running command: hmmsearch --tblout GCF_014635125.1_ASM1463512v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85bdb35b-ddf6-47e2-8d99-90e81d9d46bd/dqc_reference/reference_markers.hmm GCF_014635125.1_ASM1463512v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:30,492] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:30,493] [INFO] Found 6/6 markers.
[2024-01-25 19:09:30,525] [INFO] Query marker FASTA was written to GCF_014635125.1_ASM1463512v1_genomic.fna/markers.fasta
[2024-01-25 19:09:30,526] [INFO] Task started: Blastn
[2024-01-25 19:09:30,526] [INFO] Running command: blastn -query GCF_014635125.1_ASM1463512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85bdb35b-ddf6-47e2-8d99-90e81d9d46bd/dqc_reference/reference_markers.fasta -out GCF_014635125.1_ASM1463512v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:31,081] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:31,084] [INFO] Selected 19 target genomes.
[2024-01-25 19:09:31,084] [INFO] Target genome list was writen to GCF_014635125.1_ASM1463512v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:31,104] [INFO] Task started: fastANI
[2024-01-25 19:09:31,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg1577f501-150f-4587-b1d5-7bcf04265459/GCF_014635125.1_ASM1463512v1_genomic.fna.gz --refList GCF_014635125.1_ASM1463512v1_genomic.fna/target_genomes.txt --output GCF_014635125.1_ASM1463512v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:45,047] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:45,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85bdb35b-ddf6-47e2-8d99-90e81d9d46bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:45,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85bdb35b-ddf6-47e2-8d99-90e81d9d46bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:45,055] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:09:45,055] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:45,056] [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
Thalassobacillus devorans	strain=CCM 7282	GCA_014635125.1	279813	279813	type	True	100.0	1341	1342	95	conclusive
Thalassobacillus devorans	strain=CECT 7046	GCA_011761345.1	279813	279813	type	True	99.9996	1334	1342	95	conclusive
Thalassobacillus cyri	strain=CCM7597	GCA_900107755.1	571932	571932	type	True	81.8167	752	1342	95	below_threshold
Thalassobacillus pellis	strain=DSM 22784	GCA_016908295.1	748008	748008	type	True	78.4579	288	1342	95	below_threshold
Halobacillus dabanensis	strain=CGMCC 1.3704	GCA_900114165.1	240302	240302	type	True	78.1038	142	1342	95	below_threshold
Halobacillus locisalis	strain=KCTC 3788	GCA_013694105.1	220753	220753	type	True	77.728	94	1342	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	77.4998	65	1342	95	below_threshold
Halobacillus massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	77.1527	117	1342	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:45,057] [INFO] DFAST Taxonomy check result was written to GCF_014635125.1_ASM1463512v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:45,058] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:45,058] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:45,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85bdb35b-ddf6-47e2-8d99-90e81d9d46bd/dqc_reference/checkm_data
[2024-01-25 19:09:45,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:45,100] [INFO] Task started: CheckM
[2024-01-25 19:09:45,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635125.1_ASM1463512v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635125.1_ASM1463512v1_genomic.fna/checkm_input GCF_014635125.1_ASM1463512v1_genomic.fna/checkm_result
[2024-01-25 19:10:13,958] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:13,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:13,978] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:13,979] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:13,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635125.1_ASM1463512v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:13,980] [INFO] Task started: Blastn
[2024-01-25 19:10:13,980] [INFO] Running command: blastn -query GCF_014635125.1_ASM1463512v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85bdb35b-ddf6-47e2-8d99-90e81d9d46bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635125.1_ASM1463512v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:14,775] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:14,778] [INFO] Selected 13 target genomes.
[2024-01-25 19:10:14,778] [INFO] Target genome list was writen to GCF_014635125.1_ASM1463512v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:14,798] [INFO] Task started: fastANI
[2024-01-25 19:10:14,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg1577f501-150f-4587-b1d5-7bcf04265459/GCF_014635125.1_ASM1463512v1_genomic.fna.gz --refList GCF_014635125.1_ASM1463512v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635125.1_ASM1463512v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:25,501] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:25,506] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:25,507] [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_011761345.1	s__Thalassobacillus devorans	99.9996	1334	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_900176565.1	s__Thalassobacillus devorans_A	92.9384	1123	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107755.1	s__Thalassobacillus cyri	81.7935	757	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496835.1	s__Thalassobacillus devorans_B	81.6331	758	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908295.1	s__Thalassobacillus pellis	78.4795	287	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Thalassobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870085.1	s__BH258 sp005870085	77.3583	65	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015905325.1	s__Halobacillus sp015905325	77.1853	114	1342	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_000469135.2	s__Halobacillus sp001592845	77.1622	113	1342	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.23	99.19	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:25,508] [INFO] GTDB search result was written to GCF_014635125.1_ASM1463512v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:25,508] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:25,510] [INFO] DFAST_QC result json was written to GCF_014635125.1_ASM1463512v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:25,511] [INFO] DFAST_QC completed!
[2024-01-25 19:10:25,511] [INFO] Total running time: 0h1m5s