[2024-01-24 12:53:49,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:49,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:49,414] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e4e02f4-1d12-46e2-b248-ebe7ecd2926f/dqc_reference
[2024-01-24 12:53:51,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:51,732] [INFO] Task started: Prodigal
[2024-01-24 12:53:51,733] [INFO] Running command: gunzip -c /var/lib/cwl/stga95ae3d5-2016-4b22-b502-898f8d764031/GCF_024753255.1_ASM2475325v1_genomic.fna.gz | prodigal -d GCF_024753255.1_ASM2475325v1_genomic.fna/cds.fna -a GCF_024753255.1_ASM2475325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:07,922] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:07,923] [INFO] Task started: HMMsearch
[2024-01-24 12:54:07,923] [INFO] Running command: hmmsearch --tblout GCF_024753255.1_ASM2475325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e4e02f4-1d12-46e2-b248-ebe7ecd2926f/dqc_reference/reference_markers.hmm GCF_024753255.1_ASM2475325v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:08,239] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:08,240] [INFO] Found 6/6 markers.
[2024-01-24 12:54:08,288] [INFO] Query marker FASTA was written to GCF_024753255.1_ASM2475325v1_genomic.fna/markers.fasta
[2024-01-24 12:54:08,289] [INFO] Task started: Blastn
[2024-01-24 12:54:08,289] [INFO] Running command: blastn -query GCF_024753255.1_ASM2475325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e4e02f4-1d12-46e2-b248-ebe7ecd2926f/dqc_reference/reference_markers.fasta -out GCF_024753255.1_ASM2475325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:09,273] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:09,277] [INFO] Selected 10 target genomes.
[2024-01-24 12:54:09,277] [INFO] Target genome list was writen to GCF_024753255.1_ASM2475325v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:09,284] [INFO] Task started: fastANI
[2024-01-24 12:54:09,285] [INFO] Running command: fastANI --query /var/lib/cwl/stga95ae3d5-2016-4b22-b502-898f8d764031/GCF_024753255.1_ASM2475325v1_genomic.fna.gz --refList GCF_024753255.1_ASM2475325v1_genomic.fna/target_genomes.txt --output GCF_024753255.1_ASM2475325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:24,982] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:24,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e4e02f4-1d12-46e2-b248-ebe7ecd2926f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:24,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e4e02f4-1d12-46e2-b248-ebe7ecd2926f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:25,002] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:25,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:25,003] [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 agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	100.0	1809	1810	95	conclusive
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	87.6997	1440	1810	95	below_threshold
Massilia yuzhufengensis	strain=CGMCC 1.12041	GCA_900112225.1	1164594	1164594	type	True	86.8097	1358	1810	95	below_threshold
Massilia aromaticivorans	strain=ML15P13	GCA_013003915.1	2725995	2725995	type	True	86.1601	1335	1810	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	85.2064	1279	1810	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	84.4759	1253	1810	95	below_threshold
Massilia arenae	strain=GEM5	GCA_008014745.1	2603288	2603288	type	True	84.0899	1254	1810	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	83.4283	1201	1810	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	82.6939	1164	1810	95	below_threshold
Massilia putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	81.8015	1141	1810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:25,005] [INFO] DFAST Taxonomy check result was written to GCF_024753255.1_ASM2475325v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:25,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:25,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:25,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e4e02f4-1d12-46e2-b248-ebe7ecd2926f/dqc_reference/checkm_data
[2024-01-24 12:54:25,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:25,058] [INFO] Task started: CheckM
[2024-01-24 12:54:25,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024753255.1_ASM2475325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024753255.1_ASM2475325v1_genomic.fna/checkm_input GCF_024753255.1_ASM2475325v1_genomic.fna/checkm_result
[2024-01-24 12:55:13,269] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:13,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:13,291] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:13,291] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:13,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024753255.1_ASM2475325v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:13,292] [INFO] Task started: Blastn
[2024-01-24 12:55:13,292] [INFO] Running command: blastn -query GCF_024753255.1_ASM2475325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e4e02f4-1d12-46e2-b248-ebe7ecd2926f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024753255.1_ASM2475325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:15,303] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:15,307] [INFO] Selected 10 target genomes.
[2024-01-24 12:55:15,307] [INFO] Target genome list was writen to GCF_024753255.1_ASM2475325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:15,315] [INFO] Task started: fastANI
[2024-01-24 12:55:15,315] [INFO] Running command: fastANI --query /var/lib/cwl/stga95ae3d5-2016-4b22-b502-898f8d764031/GCF_024753255.1_ASM2475325v1_genomic.fna.gz --refList GCF_024753255.1_ASM2475325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024753255.1_ASM2475325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:29,976] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:29,990] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:55:29,991] [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_902506415.1	s__Massilia sp902506415	87.7724	1437	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427785.1	s__Massilia alkalitolerans	87.7077	1439	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.93	95.88	0.90	0.87	5	-
GCF_000740675.1	s__Massilia sp000740675	87.4089	1356	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015277795.1	s__Massilia sp015277795	87.3434	1367	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112225.1	s__Massilia yuzhufengensis	86.817	1357	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018119405.1	s__Massilia sp018119405	85.8823	1275	1810	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	85.8802	1279	1810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCF_002007115.1	s__Massilia sp002007115	85.5562	1335	1810	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	85.2263	1276	1810	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	84.7711	933	1810	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 12:55:29,993] [INFO] GTDB search result was written to GCF_024753255.1_ASM2475325v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:29,994] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:29,997] [INFO] DFAST_QC result json was written to GCF_024753255.1_ASM2475325v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:29,998] [INFO] DFAST_QC completed!
[2024-01-24 12:55:29,998] [INFO] Total running time: 0h1m41s