[2024-01-25 20:00:50,784] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:50,786] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:50,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d6f356e-140d-4820-9987-f7eb30db9103/dqc_reference
[2024-01-25 20:00:51,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:51,904] [INFO] Task started: Prodigal
[2024-01-25 20:00:51,904] [INFO] Running command: gunzip -c /var/lib/cwl/stga761a8a4-6956-469f-aadf-04cf460ae65d/GCF_012849555.1_ASM1284955v1_genomic.fna.gz | prodigal -d GCF_012849555.1_ASM1284955v1_genomic.fna/cds.fna -a GCF_012849555.1_ASM1284955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:09,911] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:09,911] [INFO] Task started: HMMsearch
[2024-01-25 20:01:09,912] [INFO] Running command: hmmsearch --tblout GCF_012849555.1_ASM1284955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d6f356e-140d-4820-9987-f7eb30db9103/dqc_reference/reference_markers.hmm GCF_012849555.1_ASM1284955v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:10,194] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:10,195] [INFO] Found 6/6 markers.
[2024-01-25 20:01:10,241] [INFO] Query marker FASTA was written to GCF_012849555.1_ASM1284955v1_genomic.fna/markers.fasta
[2024-01-25 20:01:10,241] [INFO] Task started: Blastn
[2024-01-25 20:01:10,241] [INFO] Running command: blastn -query GCF_012849555.1_ASM1284955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d6f356e-140d-4820-9987-f7eb30db9103/dqc_reference/reference_markers.fasta -out GCF_012849555.1_ASM1284955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:11,300] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:11,303] [INFO] Selected 10 target genomes.
[2024-01-25 20:01:11,303] [INFO] Target genome list was writen to GCF_012849555.1_ASM1284955v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:11,315] [INFO] Task started: fastANI
[2024-01-25 20:01:11,315] [INFO] Running command: fastANI --query /var/lib/cwl/stga761a8a4-6956-469f-aadf-04cf460ae65d/GCF_012849555.1_ASM1284955v1_genomic.fna.gz --refList GCF_012849555.1_ASM1284955v1_genomic.fna/target_genomes.txt --output GCF_012849555.1_ASM1284955v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:28,847] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:28,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d6f356e-140d-4820-9987-f7eb30db9103/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:28,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d6f356e-140d-4820-9987-f7eb30db9103/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:28,856] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:01:28,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:28,856] [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 forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	100.0	2121	2121	95	conclusive
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	85.0363	1349	2121	95	below_threshold
Massilia putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	83.8524	1378	2121	95	below_threshold
Massilia rhizosphaerae	strain=NEAU-GH312	GCA_016093545.1	2784389	2784389	type	True	83.6449	1351	2121	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	83.5265	1187	2121	95	below_threshold
Massilia timonae	strain=CCUG 45783	GCA_000315425.1	47229	47229	type	True	83.1523	1217	2121	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	83.0988	1301	2121	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	83.0812	1223	2121	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	82.8604	1152	2121	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	82.761	1121	2121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:28,858] [INFO] DFAST Taxonomy check result was written to GCF_012849555.1_ASM1284955v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:28,858] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:28,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:28,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d6f356e-140d-4820-9987-f7eb30db9103/dqc_reference/checkm_data
[2024-01-25 20:01:28,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:28,922] [INFO] Task started: CheckM
[2024-01-25 20:01:28,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012849555.1_ASM1284955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012849555.1_ASM1284955v1_genomic.fna/checkm_input GCF_012849555.1_ASM1284955v1_genomic.fna/checkm_result
[2024-01-25 20:02:31,593] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:31,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:31,611] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:31,611] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:31,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012849555.1_ASM1284955v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:31,612] [INFO] Task started: Blastn
[2024-01-25 20:02:31,613] [INFO] Running command: blastn -query GCF_012849555.1_ASM1284955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d6f356e-140d-4820-9987-f7eb30db9103/dqc_reference/reference_markers_gtdb.fasta -out GCF_012849555.1_ASM1284955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:33,890] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:33,894] [INFO] Selected 13 target genomes.
[2024-01-25 20:02:33,895] [INFO] Target genome list was writen to GCF_012849555.1_ASM1284955v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:33,906] [INFO] Task started: fastANI
[2024-01-25 20:02:33,906] [INFO] Running command: fastANI --query /var/lib/cwl/stga761a8a4-6956-469f-aadf-04cf460ae65d/GCF_012849555.1_ASM1284955v1_genomic.fna.gz --refList GCF_012849555.1_ASM1284955v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012849555.1_ASM1284955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:57,578] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:57,588] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:57,589] [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_012849555.1	s__Massilia sp012849555	100.0	2121	2121	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_006715485.1	s__Massilia sp006715485	86.2458	1503	2121	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412595.2	s__Massilia sp001412595	85.2511	1342	2121	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000745265.1	s__Massilia sp000745265	85.1958	1344	2121	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	84.2349	701	2121	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	83.9185	1386	2121	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	83.8523	1375	2121	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	83.5659	1182	2121	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	83.5645	1403	2121	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	83.4587	1396	2121	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	83.1387	1342	2121	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	83.0564	1227	2121	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.93	95.88	0.90	0.87	5	-
GCA_002339265.1	s__Massilia sp002339265	82.2165	1036	2121	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 20:02:57,590] [INFO] GTDB search result was written to GCF_012849555.1_ASM1284955v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:57,594] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:57,597] [INFO] DFAST_QC result json was written to GCF_012849555.1_ASM1284955v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:57,597] [INFO] DFAST_QC completed!
[2024-01-25 20:02:57,597] [INFO] Total running time: 0h2m7s