[2024-01-24 12:44:09,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:09,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:09,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg590b541f-673b-4194-8d3d-b9e92c94e579/dqc_reference
[2024-01-24 12:44:10,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:10,991] [INFO] Task started: Prodigal
[2024-01-24 12:44:10,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cd1d6c2-c10d-4534-81ee-09e186302bb7/GCF_003953935.1_ASM395393v1_genomic.fna.gz | prodigal -d GCF_003953935.1_ASM395393v1_genomic.fna/cds.fna -a GCF_003953935.1_ASM395393v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:35,725] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:35,725] [INFO] Task started: HMMsearch
[2024-01-24 12:44:35,725] [INFO] Running command: hmmsearch --tblout GCF_003953935.1_ASM395393v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg590b541f-673b-4194-8d3d-b9e92c94e579/dqc_reference/reference_markers.hmm GCF_003953935.1_ASM395393v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:36,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:36,181] [INFO] Found 6/6 markers.
[2024-01-24 12:44:36,238] [INFO] Query marker FASTA was written to GCF_003953935.1_ASM395393v1_genomic.fna/markers.fasta
[2024-01-24 12:44:36,238] [INFO] Task started: Blastn
[2024-01-24 12:44:36,239] [INFO] Running command: blastn -query GCF_003953935.1_ASM395393v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg590b541f-673b-4194-8d3d-b9e92c94e579/dqc_reference/reference_markers.fasta -out GCF_003953935.1_ASM395393v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:37,395] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:37,399] [INFO] Selected 10 target genomes.
[2024-01-24 12:44:37,399] [INFO] Target genome list was writen to GCF_003953935.1_ASM395393v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:37,409] [INFO] Task started: fastANI
[2024-01-24 12:44:37,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cd1d6c2-c10d-4534-81ee-09e186302bb7/GCF_003953935.1_ASM395393v1_genomic.fna.gz --refList GCF_003953935.1_ASM395393v1_genomic.fna/target_genomes.txt --output GCF_003953935.1_ASM395393v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:55,263] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:55,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg590b541f-673b-4194-8d3d-b9e92c94e579/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:55,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg590b541f-673b-4194-8d3d-b9e92c94e579/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:55,280] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:55,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:55,281] [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 atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	100.0	2412	2414	95	conclusive
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	91.1314	1949	2414	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	90.5553	1947	2414	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	89.3423	1863	2414	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	89.2255	1860	2414	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	82.7427	955	2414	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	82.6147	1022	2414	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.374	991	2414	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	81.1813	1147	2414	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.0422	1067	2414	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:55,284] [INFO] DFAST Taxonomy check result was written to GCF_003953935.1_ASM395393v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:55,285] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:55,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:55,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg590b541f-673b-4194-8d3d-b9e92c94e579/dqc_reference/checkm_data
[2024-01-24 12:44:55,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:55,358] [INFO] Task started: CheckM
[2024-01-24 12:44:55,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003953935.1_ASM395393v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003953935.1_ASM395393v1_genomic.fna/checkm_input GCF_003953935.1_ASM395393v1_genomic.fna/checkm_result
[2024-01-24 12:46:05,333] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:05,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:05,362] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:05,363] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:05,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003953935.1_ASM395393v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:05,363] [INFO] Task started: Blastn
[2024-01-24 12:46:05,364] [INFO] Running command: blastn -query GCF_003953935.1_ASM395393v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg590b541f-673b-4194-8d3d-b9e92c94e579/dqc_reference/reference_markers_gtdb.fasta -out GCF_003953935.1_ASM395393v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:07,457] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:07,462] [INFO] Selected 7 target genomes.
[2024-01-24 12:46:07,462] [INFO] Target genome list was writen to GCF_003953935.1_ASM395393v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:07,471] [INFO] Task started: fastANI
[2024-01-24 12:46:07,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cd1d6c2-c10d-4534-81ee-09e186302bb7/GCF_003953935.1_ASM395393v1_genomic.fna.gz --refList GCF_003953935.1_ASM395393v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003953935.1_ASM395393v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:22,553] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:22,565] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:22,566] [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_003953935.1	s__Massilia atriviolacea	100.0	2412	2414	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_011682145.1	s__Massilia mucilaginosa	91.1379	1948	2414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682045.1	s__Massilia aquatica	90.6505	1948	2414	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	90.5541	1947	2414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_002752675.1	s__Massilia violaceinigra	89.3305	1864	2414	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	89.217	1861	2414	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	89.0631	1861	2414	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	97.10	97.10	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:22,568] [INFO] GTDB search result was written to GCF_003953935.1_ASM395393v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:22,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:22,572] [INFO] DFAST_QC result json was written to GCF_003953935.1_ASM395393v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:22,573] [INFO] DFAST_QC completed!
[2024-01-24 12:46:22,573] [INFO] Total running time: 0h2m13s