[2023-06-30 10:22:10,075] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:22:10,085] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:22:10,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg45f6a8a3-fa24-4992-8a01-14f422ce2368/dqc_reference
[2023-06-30 10:22:11,394] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:22:11,395] [INFO] Task started: Prodigal
[2023-06-30 10:22:11,395] [INFO] Running command: gunzip -c /var/lib/cwl/stg0062d7ab-2dc5-4751-a3cc-e9775c51fff4/GCA_019455205.1_ASM1945520v1_genomic.fna.gz | prodigal -d GCA_019455205.1_ASM1945520v1_genomic.fna/cds.fna -a GCA_019455205.1_ASM1945520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:22:22,681] [INFO] Task succeeded: Prodigal
[2023-06-30 10:22:22,681] [INFO] Task started: HMMsearch
[2023-06-30 10:22:22,681] [INFO] Running command: hmmsearch --tblout GCA_019455205.1_ASM1945520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45f6a8a3-fa24-4992-8a01-14f422ce2368/dqc_reference/reference_markers.hmm GCA_019455205.1_ASM1945520v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:22:22,948] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:22:22,949] [INFO] Found 6/6 markers.
[2023-06-30 10:22:22,991] [INFO] Query marker FASTA was written to GCA_019455205.1_ASM1945520v1_genomic.fna/markers.fasta
[2023-06-30 10:22:22,992] [INFO] Task started: Blastn
[2023-06-30 10:22:22,992] [INFO] Running command: blastn -query GCA_019455205.1_ASM1945520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45f6a8a3-fa24-4992-8a01-14f422ce2368/dqc_reference/reference_markers.fasta -out GCA_019455205.1_ASM1945520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:22:23,627] [INFO] Task succeeded: Blastn
[2023-06-30 10:22:23,631] [INFO] Selected 27 target genomes.
[2023-06-30 10:22:23,631] [INFO] Target genome list was writen to GCA_019455205.1_ASM1945520v1_genomic.fna/target_genomes.txt
[2023-06-30 10:22:23,641] [INFO] Task started: fastANI
[2023-06-30 10:22:23,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg0062d7ab-2dc5-4751-a3cc-e9775c51fff4/GCA_019455205.1_ASM1945520v1_genomic.fna.gz --refList GCA_019455205.1_ASM1945520v1_genomic.fna/target_genomes.txt --output GCA_019455205.1_ASM1945520v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:22:39,028] [INFO] Task succeeded: fastANI
[2023-06-30 10:22:39,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45f6a8a3-fa24-4992-8a01-14f422ce2368/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:22:39,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45f6a8a3-fa24-4992-8a01-14f422ce2368/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:22:39,037] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:22:39,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:22:39,038] [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
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	76.4117	84	1043	95	below_threshold
Brumimicrobium salinarum	strain=LHR20	GCA_002844555.1	2058658	2058658	type	True	76.3027	96	1043	95	below_threshold
Brumimicrobium aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	76.1427	102	1043	95	below_threshold
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	75.8086	93	1043	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:22:39,040] [INFO] DFAST Taxonomy check result was written to GCA_019455205.1_ASM1945520v1_genomic.fna/tc_result.tsv
[2023-06-30 10:22:39,040] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:22:39,040] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:22:39,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45f6a8a3-fa24-4992-8a01-14f422ce2368/dqc_reference/checkm_data
[2023-06-30 10:22:39,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:22:39,103] [INFO] Task started: CheckM
[2023-06-30 10:22:39,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019455205.1_ASM1945520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019455205.1_ASM1945520v1_genomic.fna/checkm_input GCA_019455205.1_ASM1945520v1_genomic.fna/checkm_result
[2023-06-30 10:23:15,964] [INFO] Task succeeded: CheckM
[2023-06-30 10:23:15,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:23:16,000] [INFO] ===== Completeness check finished =====
[2023-06-30 10:23:16,000] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:23:16,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019455205.1_ASM1945520v1_genomic.fna/markers.fasta)
[2023-06-30 10:23:16,001] [INFO] Task started: Blastn
[2023-06-30 10:23:16,001] [INFO] Running command: blastn -query GCA_019455205.1_ASM1945520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45f6a8a3-fa24-4992-8a01-14f422ce2368/dqc_reference/reference_markers_gtdb.fasta -out GCA_019455205.1_ASM1945520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:23:16,800] [INFO] Task succeeded: Blastn
[2023-06-30 10:23:16,806] [INFO] Selected 26 target genomes.
[2023-06-30 10:23:16,806] [INFO] Target genome list was writen to GCA_019455205.1_ASM1945520v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:23:16,818] [INFO] Task started: fastANI
[2023-06-30 10:23:16,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg0062d7ab-2dc5-4751-a3cc-e9775c51fff4/GCA_019455205.1_ASM1945520v1_genomic.fna.gz --refList GCA_019455205.1_ASM1945520v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019455205.1_ASM1945520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:23:29,653] [INFO] Task succeeded: fastANI
[2023-06-30 10:23:29,666] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 10:23:29,666] [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_003025005.1	s__Brumimicrobium mesophilum	76.4117	84	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844555.1	s__Brumimicrobium salinarum	76.3027	96	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402975.1	s__Brumimicrobium aurantiacum	76.1601	101	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143775.1	s__Brumimicrobium sp003143775	76.1343	88	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117355.1	s__CSBr16-161 sp007117355	75.8941	53	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CSBr16-161	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152935.1	s__Brumimicrobium glaciale	75.8241	92	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178305.1	s__CAIUKX01 sp016178305	75.629	59	1043	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:23:29,668] [INFO] GTDB search result was written to GCA_019455205.1_ASM1945520v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:23:29,668] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:23:29,671] [INFO] DFAST_QC result json was written to GCA_019455205.1_ASM1945520v1_genomic.fna/dqc_result.json
[2023-06-30 10:23:29,671] [INFO] DFAST_QC completed!
[2023-06-30 10:23:29,672] [INFO] Total running time: 0h1m20s