[2024-01-25 20:15:50,347] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:50,349] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:50,349] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbf5f70d-b251-48bc-aae0-8dd1015fbac0/dqc_reference
[2024-01-25 20:15:51,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:51,520] [INFO] Task started: Prodigal
[2024-01-25 20:15:51,521] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ab72666-1d67-4abb-9309-a2793fadf918/GCF_024756225.1_ASM2475622v1_genomic.fna.gz | prodigal -d GCF_024756225.1_ASM2475622v1_genomic.fna/cds.fna -a GCF_024756225.1_ASM2475622v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:11,810] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:11,811] [INFO] Task started: HMMsearch
[2024-01-25 20:16:11,811] [INFO] Running command: hmmsearch --tblout GCF_024756225.1_ASM2475622v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbf5f70d-b251-48bc-aae0-8dd1015fbac0/dqc_reference/reference_markers.hmm GCF_024756225.1_ASM2475622v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:12,208] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:12,209] [INFO] Found 6/6 markers.
[2024-01-25 20:16:12,265] [INFO] Query marker FASTA was written to GCF_024756225.1_ASM2475622v1_genomic.fna/markers.fasta
[2024-01-25 20:16:12,266] [INFO] Task started: Blastn
[2024-01-25 20:16:12,266] [INFO] Running command: blastn -query GCF_024756225.1_ASM2475622v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbf5f70d-b251-48bc-aae0-8dd1015fbac0/dqc_reference/reference_markers.fasta -out GCF_024756225.1_ASM2475622v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:13,181] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:13,186] [INFO] Selected 8 target genomes.
[2024-01-25 20:16:13,186] [INFO] Target genome list was writen to GCF_024756225.1_ASM2475622v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:13,187] [INFO] Task started: fastANI
[2024-01-25 20:16:13,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ab72666-1d67-4abb-9309-a2793fadf918/GCF_024756225.1_ASM2475622v1_genomic.fna.gz --refList GCF_024756225.1_ASM2475622v1_genomic.fna/target_genomes.txt --output GCF_024756225.1_ASM2475622v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:26,404] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:26,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbf5f70d-b251-48bc-aae0-8dd1015fbac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:26,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbf5f70d-b251-48bc-aae0-8dd1015fbac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:26,411] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:16:26,411] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:16:26,411] [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 putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	90.0677	1821	2446	95	below_threshold
Massilia rhizosphaerae	strain=NEAU-GH312	GCA_016093545.1	2784389	2784389	type	True	89.3934	1787	2446	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	89.0763	1712	2446	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	83.9753	1366	2446	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	83.5876	1425	2446	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	82.2486	1211	2446	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.7547	1181	2446	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	81.6967	1089	2446	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:26,412] [INFO] DFAST Taxonomy check result was written to GCF_024756225.1_ASM2475622v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:26,412] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:26,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:26,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbf5f70d-b251-48bc-aae0-8dd1015fbac0/dqc_reference/checkm_data
[2024-01-25 20:16:26,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:26,478] [INFO] Task started: CheckM
[2024-01-25 20:16:26,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024756225.1_ASM2475622v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024756225.1_ASM2475622v1_genomic.fna/checkm_input GCF_024756225.1_ASM2475622v1_genomic.fna/checkm_result
[2024-01-25 20:17:30,046] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:30,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:30,066] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:30,067] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:30,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024756225.1_ASM2475622v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:30,068] [INFO] Task started: Blastn
[2024-01-25 20:17:30,068] [INFO] Running command: blastn -query GCF_024756225.1_ASM2475622v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbf5f70d-b251-48bc-aae0-8dd1015fbac0/dqc_reference/reference_markers_gtdb.fasta -out GCF_024756225.1_ASM2475622v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:31,873] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:31,876] [INFO] Selected 8 target genomes.
[2024-01-25 20:17:31,876] [INFO] Target genome list was writen to GCF_024756225.1_ASM2475622v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:31,877] [INFO] Task started: fastANI
[2024-01-25 20:17:31,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ab72666-1d67-4abb-9309-a2793fadf918/GCF_024756225.1_ASM2475622v1_genomic.fna.gz --refList GCF_024756225.1_ASM2475622v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024756225.1_ASM2475622v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:48,023] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:48,029] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:17:48,029] [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_000759615.1	s__Massilia sp000759615	93.3832	2027	2446	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	93.2804	1984	2446	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	93.0916	2038	2446	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	93.0168	2023	2446	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	90.0578	1822	2446	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	89.9351	1761	2446	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	89.3977	1787	2446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682055.1	s__Massilia sp011682055	88.9727	1779	2446	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 20:17:48,030] [INFO] GTDB search result was written to GCF_024756225.1_ASM2475622v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:48,031] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:48,035] [INFO] DFAST_QC result json was written to GCF_024756225.1_ASM2475622v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:48,035] [INFO] DFAST_QC completed!
[2024-01-25 20:17:48,035] [INFO] Total running time: 0h1m58s