[2024-01-24 14:19:45,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,628] [INFO] DQC Reference Directory: /var/lib/cwl/stga226df92-c06a-4f80-ad3f-a759de9d2c72/dqc_reference
[2024-01-24 14:19:47,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,008] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg08bd01c5-7e3d-4a37-a1c2-dfb33147fb28/GCF_024753245.1_ASM2475324v1_genomic.fna.gz | prodigal -d GCF_024753245.1_ASM2475324v1_genomic.fna/cds.fna -a GCF_024753245.1_ASM2475324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:04,894] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:04,895] [INFO] Task started: HMMsearch
[2024-01-24 14:20:04,895] [INFO] Running command: hmmsearch --tblout GCF_024753245.1_ASM2475324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga226df92-c06a-4f80-ad3f-a759de9d2c72/dqc_reference/reference_markers.hmm GCF_024753245.1_ASM2475324v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:05,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:05,320] [INFO] Found 6/6 markers.
[2024-01-24 14:20:05,407] [INFO] Query marker FASTA was written to GCF_024753245.1_ASM2475324v1_genomic.fna/markers.fasta
[2024-01-24 14:20:05,408] [INFO] Task started: Blastn
[2024-01-24 14:20:05,408] [INFO] Running command: blastn -query GCF_024753245.1_ASM2475324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga226df92-c06a-4f80-ad3f-a759de9d2c72/dqc_reference/reference_markers.fasta -out GCF_024753245.1_ASM2475324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:06,625] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:06,631] [INFO] Selected 9 target genomes.
[2024-01-24 14:20:06,632] [INFO] Target genome list was writen to GCF_024753245.1_ASM2475324v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:06,656] [INFO] Task started: fastANI
[2024-01-24 14:20:06,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg08bd01c5-7e3d-4a37-a1c2-dfb33147fb28/GCF_024753245.1_ASM2475324v1_genomic.fna.gz --refList GCF_024753245.1_ASM2475324v1_genomic.fna/target_genomes.txt --output GCF_024753245.1_ASM2475324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:23,282] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:23,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga226df92-c06a-4f80-ad3f-a759de9d2c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:23,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga226df92-c06a-4f80-ad3f-a759de9d2c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:23,292] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:23,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:23,292] [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 norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	100.0	1904	1906	95	conclusive
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	85.1877	1331	1906	95	below_threshold
Massilia putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	84.3915	1379	1906	95	below_threshold
Massilia rhizosphaerae	strain=NEAU-GH312	GCA_016093545.1	2784389	2784389	type	True	84.0	1301	1906	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	83.8008	1185	1906	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	83.7392	1202	1906	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	83.7185	1224	1906	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	83.3852	1227	1906	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	82.9973	1098	1906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:23,294] [INFO] DFAST Taxonomy check result was written to GCF_024753245.1_ASM2475324v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:23,294] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:23,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:23,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga226df92-c06a-4f80-ad3f-a759de9d2c72/dqc_reference/checkm_data
[2024-01-24 14:20:23,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:23,358] [INFO] Task started: CheckM
[2024-01-24 14:20:23,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024753245.1_ASM2475324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024753245.1_ASM2475324v1_genomic.fna/checkm_input GCF_024753245.1_ASM2475324v1_genomic.fna/checkm_result
[2024-01-24 14:21:14,104] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:14,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:14,125] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:14,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:14,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024753245.1_ASM2475324v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:14,127] [INFO] Task started: Blastn
[2024-01-24 14:21:14,127] [INFO] Running command: blastn -query GCF_024753245.1_ASM2475324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga226df92-c06a-4f80-ad3f-a759de9d2c72/dqc_reference/reference_markers_gtdb.fasta -out GCF_024753245.1_ASM2475324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:16,177] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:16,182] [INFO] Selected 14 target genomes.
[2024-01-24 14:21:16,182] [INFO] Target genome list was writen to GCF_024753245.1_ASM2475324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:16,209] [INFO] Task started: fastANI
[2024-01-24 14:21:16,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg08bd01c5-7e3d-4a37-a1c2-dfb33147fb28/GCF_024753245.1_ASM2475324v1_genomic.fna.gz --refList GCF_024753245.1_ASM2475324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024753245.1_ASM2475324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:37,400] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:37,418] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:21:37,418] [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_001412595.2	s__Massilia sp001412595	89.1201	1435	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_006715485.1	s__Massilia sp006715485	85.9179	1396	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745265.1	s__Massilia sp000745265	85.368	1293	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849555.1	s__Massilia sp012849555	85.1859	1331	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003484545.1	s__Massilia sp003484545	84.6519	743	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354135.1	s__Massilia sp002354135	84.2845	943	1906	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	84.2034	1352	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.62	99.38	0.97	0.95	3	-
GCF_900101265.1	s__Massilia sp900101265	84.105	1362	1906	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	84.0702	1348	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968015.1	s__Massilia phosphatilytica	83.8905	1336	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382345.1	s__Massilia niastensis	83.7996	1185	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018119395.1	s__Massilia sp018119395	83.759	1186	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_000427785.1	s__Massilia alkalitolerans	83.703	1208	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.93	95.88	0.90	0.87	5	-
GCF_902506415.1	s__Massilia sp902506415	83.5569	1213	1906	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 14:21:37,420] [INFO] GTDB search result was written to GCF_024753245.1_ASM2475324v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:37,421] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:37,425] [INFO] DFAST_QC result json was written to GCF_024753245.1_ASM2475324v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:37,425] [INFO] DFAST_QC completed!
[2024-01-24 14:21:37,425] [INFO] Total running time: 0h1m52s