[2024-01-24 13:17:27,110] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:27,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:27,112] [INFO] DQC Reference Directory: /var/lib/cwl/stgc30f8f90-badf-41b3-a69c-8faf00c28193/dqc_reference
[2024-01-24 13:17:28,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,361] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,361] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0105ee8-21e8-4bec-8d26-eed022e3e7d1/GCF_009856445.1_ASM985644v1_genomic.fna.gz | prodigal -d GCF_009856445.1_ASM985644v1_genomic.fna/cds.fna -a GCF_009856445.1_ASM985644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:38,255] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:38,256] [INFO] Task started: HMMsearch
[2024-01-24 13:17:38,256] [INFO] Running command: hmmsearch --tblout GCF_009856445.1_ASM985644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc30f8f90-badf-41b3-a69c-8faf00c28193/dqc_reference/reference_markers.hmm GCF_009856445.1_ASM985644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:38,536] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:38,538] [INFO] Found 6/6 markers.
[2024-01-24 13:17:38,578] [INFO] Query marker FASTA was written to GCF_009856445.1_ASM985644v1_genomic.fna/markers.fasta
[2024-01-24 13:17:38,578] [INFO] Task started: Blastn
[2024-01-24 13:17:38,579] [INFO] Running command: blastn -query GCF_009856445.1_ASM985644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc30f8f90-badf-41b3-a69c-8faf00c28193/dqc_reference/reference_markers.fasta -out GCF_009856445.1_ASM985644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:39,171] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:39,175] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:39,176] [INFO] Target genome list was writen to GCF_009856445.1_ASM985644v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:39,180] [INFO] Task started: fastANI
[2024-01-24 13:17:39,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0105ee8-21e8-4bec-8d26-eed022e3e7d1/GCF_009856445.1_ASM985644v1_genomic.fna.gz --refList GCF_009856445.1_ASM985644v1_genomic.fna/target_genomes.txt --output GCF_009856445.1_ASM985644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:49,846] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:49,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc30f8f90-badf-41b3-a69c-8faf00c28193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:49,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc30f8f90-badf-41b3-a69c-8faf00c28193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:49,856] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:49,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:49,856] [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 litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	100.0	1314	1316	95	conclusive
Halobacillus trueperi	strain=KCTC 3686	GCA_003386945.1	156205	156205	type	True	88.0267	1094	1316	95	below_threshold
Halobacillus aidingensis	strain=CGMCC 1.3703	GCA_900104185.1	240303	240303	type	True	87.9895	1107	1316	95	below_threshold
Halobacillus faecis	strain=NBRC 103569	GCA_007991335.1	360184	360184	type	True	87.0483	1075	1316	95	below_threshold
Halobacillus karajensis	strain=DSM 14948	GCA_900108515.1	195088	195088	type	True	80.5204	596	1316	95	below_threshold
Halobacillus dabanensis	strain=CGMCC 1.3704	GCA_900114165.1	240302	240302	type	True	80.2837	563	1316	95	below_threshold
Halobacillus alkaliphilus	strain=FP5	GCA_900113125.1	396056	396056	type	True	78.3056	262	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:49,858] [INFO] DFAST Taxonomy check result was written to GCF_009856445.1_ASM985644v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:49,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:49,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:49,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc30f8f90-badf-41b3-a69c-8faf00c28193/dqc_reference/checkm_data
[2024-01-24 13:17:49,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:49,904] [INFO] Task started: CheckM
[2024-01-24 13:17:49,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009856445.1_ASM985644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009856445.1_ASM985644v1_genomic.fna/checkm_input GCF_009856445.1_ASM985644v1_genomic.fna/checkm_result
[2024-01-24 13:18:24,728] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:24,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:24,746] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:24,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:24,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009856445.1_ASM985644v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:24,747] [INFO] Task started: Blastn
[2024-01-24 13:18:24,748] [INFO] Running command: blastn -query GCF_009856445.1_ASM985644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc30f8f90-badf-41b3-a69c-8faf00c28193/dqc_reference/reference_markers_gtdb.fasta -out GCF_009856445.1_ASM985644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:25,567] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:25,571] [INFO] Selected 8 target genomes.
[2024-01-24 13:18:25,571] [INFO] Target genome list was writen to GCF_009856445.1_ASM985644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:25,591] [INFO] Task started: fastANI
[2024-01-24 13:18:25,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0105ee8-21e8-4bec-8d26-eed022e3e7d1/GCF_009856445.1_ASM985644v1_genomic.fna.gz --refList GCF_009856445.1_ASM985644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009856445.1_ASM985644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:35,974] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:35,982] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:35,982] [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_009856445.1	s__Halobacillus litoralis	100.0	1314	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	95.88	95.88	0.90	0.90	2	conclusive
GCF_009856415.1	s__Halobacillus litoralis_C	88.0572	1103	1316	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_900104185.1	s__Halobacillus aidingensis	87.9895	1107	1316	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_007991335.1	s__Halobacillus faecis	87.0549	1074	1316	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_900108515.1	s__Halobacillus karajensis	80.5229	596	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.38	99.37	0.93	0.93	4	-
GCF_900114165.1	s__Halobacillus dabanensis	80.2994	561	1316	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_009856355.1	s__Halobacillus litoralis_B	79.1487	365	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.99	98.95	0.95	0.95	3	-
GCA_004078665.1	s__Halobacillus sp004078665	78.6823	275	1316	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 13:18:35,984] [INFO] GTDB search result was written to GCF_009856445.1_ASM985644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:35,984] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:35,987] [INFO] DFAST_QC result json was written to GCF_009856445.1_ASM985644v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:35,987] [INFO] DFAST_QC completed!
[2024-01-24 13:18:35,987] [INFO] Total running time: 0h1m9s