[2024-01-24 13:49:33,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg0514148c-5e9a-483e-9261-dd28b05486e0/dqc_reference
[2024-01-24 13:49:35,250] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:35,251] [INFO] Task started: Prodigal
[2024-01-24 13:49:35,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg27da1e0b-2bd1-4682-8953-7de77e2fc07f/GCF_011682055.1_ASM1168205v1_genomic.fna.gz | prodigal -d GCF_011682055.1_ASM1168205v1_genomic.fna/cds.fna -a GCF_011682055.1_ASM1168205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:58,465] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:58,465] [INFO] Task started: HMMsearch
[2024-01-24 13:49:58,465] [INFO] Running command: hmmsearch --tblout GCF_011682055.1_ASM1168205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0514148c-5e9a-483e-9261-dd28b05486e0/dqc_reference/reference_markers.hmm GCF_011682055.1_ASM1168205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:58,877] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:58,879] [INFO] Found 6/6 markers.
[2024-01-24 13:49:58,934] [INFO] Query marker FASTA was written to GCF_011682055.1_ASM1168205v1_genomic.fna/markers.fasta
[2024-01-24 13:49:58,935] [INFO] Task started: Blastn
[2024-01-24 13:49:58,935] [INFO] Running command: blastn -query GCF_011682055.1_ASM1168205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0514148c-5e9a-483e-9261-dd28b05486e0/dqc_reference/reference_markers.fasta -out GCF_011682055.1_ASM1168205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:59,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:59,981] [INFO] Selected 7 target genomes.
[2024-01-24 13:49:59,982] [INFO] Target genome list was writen to GCF_011682055.1_ASM1168205v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:59,986] [INFO] Task started: fastANI
[2024-01-24 13:49:59,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg27da1e0b-2bd1-4682-8953-7de77e2fc07f/GCF_011682055.1_ASM1168205v1_genomic.fna.gz --refList GCF_011682055.1_ASM1168205v1_genomic.fna/target_genomes.txt --output GCF_011682055.1_ASM1168205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:12,187] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:12,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0514148c-5e9a-483e-9261-dd28b05486e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:12,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0514148c-5e9a-483e-9261-dd28b05486e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:12,195] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:12,195] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:12,196] [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
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	93.9909	1856	2328	95	below_threshold
Massilia putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	89.2882	1773	2328	95	below_threshold
Massilia rhizosphaerae	strain=NEAU-GH312	GCA_016093545.1	2784389	2784389	type	True	88.9281	1700	2328	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	83.6472	1274	2328	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	83.1122	1351	2328	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	81.5154	1036	2328	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.4404	1095	2328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:12,197] [INFO] DFAST Taxonomy check result was written to GCF_011682055.1_ASM1168205v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:12,198] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:12,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:12,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0514148c-5e9a-483e-9261-dd28b05486e0/dqc_reference/checkm_data
[2024-01-24 13:50:12,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:12,273] [INFO] Task started: CheckM
[2024-01-24 13:50:12,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011682055.1_ASM1168205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011682055.1_ASM1168205v1_genomic.fna/checkm_input GCF_011682055.1_ASM1168205v1_genomic.fna/checkm_result
[2024-01-24 13:51:19,005] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:19,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:19,026] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:19,026] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:19,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011682055.1_ASM1168205v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:19,027] [INFO] Task started: Blastn
[2024-01-24 13:51:19,027] [INFO] Running command: blastn -query GCF_011682055.1_ASM1168205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0514148c-5e9a-483e-9261-dd28b05486e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_011682055.1_ASM1168205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:20,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:20,929] [INFO] Selected 8 target genomes.
[2024-01-24 13:51:20,929] [INFO] Target genome list was writen to GCF_011682055.1_ASM1168205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:20,939] [INFO] Task started: fastANI
[2024-01-24 13:51:20,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg27da1e0b-2bd1-4682-8953-7de77e2fc07f/GCF_011682055.1_ASM1168205v1_genomic.fna.gz --refList GCF_011682055.1_ASM1168205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011682055.1_ASM1168205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:36,666] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:36,677] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:36,677] [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_011682055.1	s__Massilia sp011682055	100.0	2325	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001941825.1	s__Massilia putida	89.3017	1771	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101265.1	s__Massilia sp900101265	89.1329	1765	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425685.1	s__Massilia sp001425685	89.1309	1710	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759615.1	s__Massilia sp000759615	89.0555	1722	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426525.1	s__Massilia sp001426525	89.0299	1752	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.62	99.38	0.97	0.95	3	-
GCF_002968015.1	s__Massilia phosphatilytica	88.9908	1771	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016093545.1	s__Massilia sp016093545	88.9183	1701	2328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:36,679] [INFO] GTDB search result was written to GCF_011682055.1_ASM1168205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:36,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:36,683] [INFO] DFAST_QC result json was written to GCF_011682055.1_ASM1168205v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:36,683] [INFO] DFAST_QC completed!
[2024-01-24 13:51:36,684] [INFO] Total running time: 0h2m3s