[2024-01-24 10:47:06,553] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg367af851-82af-4207-a851-b38bd70214ed/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg97af35e3-1ea7-4ba8-900d-103be551ca92/GCF_011682145.1_ASM1168214v1_genomic.fna.gz | prodigal -d GCF_011682145.1_ASM1168214v1_genomic.fna/cds.fna -a GCF_011682145.1_ASM1168214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:36,456] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:36,456] [INFO] Task started: HMMsearch
[2024-01-24 10:47:36,456] [INFO] Running command: hmmsearch --tblout GCF_011682145.1_ASM1168214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg367af851-82af-4207-a851-b38bd70214ed/dqc_reference/reference_markers.hmm GCF_011682145.1_ASM1168214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:36,865] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:36,866] [INFO] Found 6/6 markers.
[2024-01-24 10:47:36,925] [INFO] Query marker FASTA was written to GCF_011682145.1_ASM1168214v1_genomic.fna/markers.fasta
[2024-01-24 10:47:36,926] [INFO] Task started: Blastn
[2024-01-24 10:47:36,926] [INFO] Running command: blastn -query GCF_011682145.1_ASM1168214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg367af851-82af-4207-a851-b38bd70214ed/dqc_reference/reference_markers.fasta -out GCF_011682145.1_ASM1168214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:37,850] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:37,854] [INFO] Selected 10 target genomes.
[2024-01-24 10:47:37,854] [INFO] Target genome list was writen to GCF_011682145.1_ASM1168214v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:37,856] [INFO] Task started: fastANI
[2024-01-24 10:47:37,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg97af35e3-1ea7-4ba8-900d-103be551ca92/GCF_011682145.1_ASM1168214v1_genomic.fna.gz --refList GCF_011682145.1_ASM1168214v1_genomic.fna/target_genomes.txt --output GCF_011682145.1_ASM1168214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:55,518] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:55,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg367af851-82af-4207-a851-b38bd70214ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:55,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg367af851-82af-4207-a851-b38bd70214ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:55,529] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:55,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:55,530] [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 mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	100.0	2441	2448	95	conclusive
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	92.4948	2086	2448	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	91.0857	1975	2448	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	89.5374	1908	2448	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	89.5011	1870	2448	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	82.409	921	2448	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	82.3161	1020	2448	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	80.9468	1077	2448	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.697	1007	2448	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.6624	1015	2448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:55,541] [INFO] DFAST Taxonomy check result was written to GCF_011682145.1_ASM1168214v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:55,542] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:55,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:55,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg367af851-82af-4207-a851-b38bd70214ed/dqc_reference/checkm_data
[2024-01-24 10:47:55,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:55,638] [INFO] Task started: CheckM
[2024-01-24 10:47:55,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011682145.1_ASM1168214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011682145.1_ASM1168214v1_genomic.fna/checkm_input GCF_011682145.1_ASM1168214v1_genomic.fna/checkm_result
[2024-01-24 10:49:04,553] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:04,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:04,574] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:04,574] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:04,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011682145.1_ASM1168214v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:04,574] [INFO] Task started: Blastn
[2024-01-24 10:49:04,575] [INFO] Running command: blastn -query GCF_011682145.1_ASM1168214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg367af851-82af-4207-a851-b38bd70214ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_011682145.1_ASM1168214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:06,182] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:06,185] [INFO] Selected 10 target genomes.
[2024-01-24 10:49:06,185] [INFO] Target genome list was writen to GCF_011682145.1_ASM1168214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:06,189] [INFO] Task started: fastANI
[2024-01-24 10:49:06,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg97af35e3-1ea7-4ba8-900d-103be551ca92/GCF_011682145.1_ASM1168214v1_genomic.fna.gz --refList GCF_011682145.1_ASM1168214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011682145.1_ASM1168214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:22,770] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:22,779] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:22,780] [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_011682145.1	s__Massilia mucilaginosa	100.0	2441	2448	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_011682045.1	s__Massilia aquatica	93.557	2045	2448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682065.1	s__Massilia rubra	92.4996	2085	2448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_003953935.1	s__Massilia atriviolacea	91.0942	1974	2448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682175.1	s__Massilia frigida	89.5362	1908	2448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752675.1	s__Massilia violaceinigra	89.4662	1874	2448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689335.1	s__Massilia sp001485665	89.2436	1903	2448	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	97.10	97.10	0.90	0.90	3	-
GCA_009835395.1	s__VXNF01 sp009835395	74.7239	68	2448	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__VXNF01	95.0	99.94	99.92	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:22,781] [INFO] GTDB search result was written to GCF_011682145.1_ASM1168214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:22,782] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:22,785] [INFO] DFAST_QC result json was written to GCF_011682145.1_ASM1168214v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:22,785] [INFO] DFAST_QC completed!
[2024-01-24 10:49:22,785] [INFO] Total running time: 0h2m16s