[2024-01-25 19:38:35,648] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:35,650] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:35,650] [INFO] DQC Reference Directory: /var/lib/cwl/stgf99795e5-3151-43cc-9452-ab576b36b737/dqc_reference
[2024-01-25 19:38:36,799] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:36,800] [INFO] Task started: Prodigal
[2024-01-25 19:38:36,800] [INFO] Running command: gunzip -c /var/lib/cwl/stg99ed92eb-2cd6-4c43-956a-635845905e67/GCF_024753285.1_ASM2475328v1_genomic.fna.gz | prodigal -d GCF_024753285.1_ASM2475328v1_genomic.fna/cds.fna -a GCF_024753285.1_ASM2475328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:54,717] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:54,717] [INFO] Task started: HMMsearch
[2024-01-25 19:38:54,717] [INFO] Running command: hmmsearch --tblout GCF_024753285.1_ASM2475328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf99795e5-3151-43cc-9452-ab576b36b737/dqc_reference/reference_markers.hmm GCF_024753285.1_ASM2475328v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:55,066] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:55,067] [INFO] Found 6/6 markers.
[2024-01-25 19:38:55,122] [INFO] Query marker FASTA was written to GCF_024753285.1_ASM2475328v1_genomic.fna/markers.fasta
[2024-01-25 19:38:55,122] [INFO] Task started: Blastn
[2024-01-25 19:38:55,122] [INFO] Running command: blastn -query GCF_024753285.1_ASM2475328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf99795e5-3151-43cc-9452-ab576b36b737/dqc_reference/reference_markers.fasta -out GCF_024753285.1_ASM2475328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:56,056] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:56,059] [INFO] Selected 9 target genomes.
[2024-01-25 19:38:56,059] [INFO] Target genome list was writen to GCF_024753285.1_ASM2475328v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:56,077] [INFO] Task started: fastANI
[2024-01-25 19:38:56,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ed92eb-2cd6-4c43-956a-635845905e67/GCF_024753285.1_ASM2475328v1_genomic.fna.gz --refList GCF_024753285.1_ASM2475328v1_genomic.fna/target_genomes.txt --output GCF_024753285.1_ASM2475328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:10,228] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:10,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf99795e5-3151-43cc-9452-ab576b36b737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:10,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf99795e5-3151-43cc-9452-ab576b36b737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:10,236] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:39:10,237] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:10,237] [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	100.0	2139	2140	95	conclusive
Massilia putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	89.2858	1679	2140	95	below_threshold
Massilia rhizosphaerae	strain=NEAU-GH312	GCA_016093545.1	2784389	2784389	type	True	89.0244	1662	2140	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	83.6369	1233	2140	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	83.2415	1305	2140	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	81.8434	1101	2140	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	81.643	1011	2140	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	81.599	1084	2140	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.5959	1055	2140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:10,238] [INFO] DFAST Taxonomy check result was written to GCF_024753285.1_ASM2475328v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:10,239] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:10,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:10,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf99795e5-3151-43cc-9452-ab576b36b737/dqc_reference/checkm_data
[2024-01-25 19:39:10,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:10,302] [INFO] Task started: CheckM
[2024-01-25 19:39:10,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024753285.1_ASM2475328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024753285.1_ASM2475328v1_genomic.fna/checkm_input GCF_024753285.1_ASM2475328v1_genomic.fna/checkm_result
[2024-01-25 19:40:07,364] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:07,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:07,384] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:07,384] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:07,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024753285.1_ASM2475328v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:07,386] [INFO] Task started: Blastn
[2024-01-25 19:40:07,386] [INFO] Running command: blastn -query GCF_024753285.1_ASM2475328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf99795e5-3151-43cc-9452-ab576b36b737/dqc_reference/reference_markers_gtdb.fasta -out GCF_024753285.1_ASM2475328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:09,241] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:09,243] [INFO] Selected 8 target genomes.
[2024-01-25 19:40:09,244] [INFO] Target genome list was writen to GCF_024753285.1_ASM2475328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:09,250] [INFO] Task started: fastANI
[2024-01-25 19:40:09,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg99ed92eb-2cd6-4c43-956a-635845905e67/GCF_024753285.1_ASM2475328v1_genomic.fna.gz --refList GCF_024753285.1_ASM2475328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024753285.1_ASM2475328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:25,311] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:25,319] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:40:25,320] [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	93.9853	1870	2140	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	89.3035	1678	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941825.1	s__Massilia putida	89.2779	1680	2140	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	89.1816	1671	2140	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	89.1419	1697	2140	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	89.1102	1721	2140	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	89.0346	1675	2140	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	89.0082	1664	2140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:25,322] [INFO] GTDB search result was written to GCF_024753285.1_ASM2475328v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:25,322] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:25,325] [INFO] DFAST_QC result json was written to GCF_024753285.1_ASM2475328v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:25,326] [INFO] DFAST_QC completed!
[2024-01-25 19:40:25,326] [INFO] Total running time: 0h1m50s