[2024-01-25 17:51:50,897] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:50,899] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:50,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d1ebcf9-8c23-4faf-a26f-0b8bc416493f/dqc_reference
[2024-01-25 17:51:52,092] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:52,093] [INFO] Task started: Prodigal
[2024-01-25 17:51:52,093] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c0d257c-2ac5-4a3f-8767-3d1e696ff266/GCF_024753145.1_ASM2475314v1_genomic.fna.gz | prodigal -d GCF_024753145.1_ASM2475314v1_genomic.fna/cds.fna -a GCF_024753145.1_ASM2475314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:08,311] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:08,312] [INFO] Task started: HMMsearch
[2024-01-25 17:52:08,312] [INFO] Running command: hmmsearch --tblout GCF_024753145.1_ASM2475314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d1ebcf9-8c23-4faf-a26f-0b8bc416493f/dqc_reference/reference_markers.hmm GCF_024753145.1_ASM2475314v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:08,581] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:08,582] [INFO] Found 6/6 markers.
[2024-01-25 17:52:08,627] [INFO] Query marker FASTA was written to GCF_024753145.1_ASM2475314v1_genomic.fna/markers.fasta
[2024-01-25 17:52:08,627] [INFO] Task started: Blastn
[2024-01-25 17:52:08,627] [INFO] Running command: blastn -query GCF_024753145.1_ASM2475314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d1ebcf9-8c23-4faf-a26f-0b8bc416493f/dqc_reference/reference_markers.fasta -out GCF_024753145.1_ASM2475314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:09,648] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:09,650] [INFO] Selected 11 target genomes.
[2024-01-25 17:52:09,651] [INFO] Target genome list was writen to GCF_024753145.1_ASM2475314v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:09,683] [INFO] Task started: fastANI
[2024-01-25 17:52:09,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c0d257c-2ac5-4a3f-8767-3d1e696ff266/GCF_024753145.1_ASM2475314v1_genomic.fna.gz --refList GCF_024753145.1_ASM2475314v1_genomic.fna/target_genomes.txt --output GCF_024753145.1_ASM2475314v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:24,756] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:24,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d1ebcf9-8c23-4faf-a26f-0b8bc416493f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:24,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d1ebcf9-8c23-4faf-a26f-0b8bc416493f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:24,765] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:24,765] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:24,766] [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 terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	100.0	1845	1845	95	conclusive
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	85.459	1226	1845	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	85.3696	1227	1845	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	83.31	1067	1845	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	83.0715	1086	1845	95	below_threshold
Massilia horti	strain=ONC3	GCA_004614195.1	2562153	2562153	type	True	83.0512	1032	1845	95	below_threshold
Massilia forsythiae	strain=GN2-R2	GCA_012849555.1	2728020	2728020	type	True	82.7208	1129	1845	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	82.7078	1098	1845	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	82.6138	1054	1845	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	82.054	875	1845	95	below_threshold
Massilia arenosa	strain=MC02	GCA_004614185.1	2561931	2561931	type	True	81.4187	877	1845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:24,767] [INFO] DFAST Taxonomy check result was written to GCF_024753145.1_ASM2475314v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:24,767] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:24,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:24,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d1ebcf9-8c23-4faf-a26f-0b8bc416493f/dqc_reference/checkm_data
[2024-01-25 17:52:24,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:24,821] [INFO] Task started: CheckM
[2024-01-25 17:52:24,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024753145.1_ASM2475314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024753145.1_ASM2475314v1_genomic.fna/checkm_input GCF_024753145.1_ASM2475314v1_genomic.fna/checkm_result
[2024-01-25 17:53:12,814] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:12,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:12,836] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:12,837] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:12,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024753145.1_ASM2475314v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:12,837] [INFO] Task started: Blastn
[2024-01-25 17:53:12,837] [INFO] Running command: blastn -query GCF_024753145.1_ASM2475314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d1ebcf9-8c23-4faf-a26f-0b8bc416493f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024753145.1_ASM2475314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:15,046] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:15,058] [INFO] Selected 18 target genomes.
[2024-01-25 17:53:15,058] [INFO] Target genome list was writen to GCF_024753145.1_ASM2475314v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:15,082] [INFO] Task started: fastANI
[2024-01-25 17:53:15,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c0d257c-2ac5-4a3f-8767-3d1e696ff266/GCF_024753145.1_ASM2475314v1_genomic.fna.gz --refList GCF_024753145.1_ASM2475314v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024753145.1_ASM2475314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:38,825] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:38,837] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:53:38,837] [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_000382345.1	s__Massilia niastensis	83.3245	1065	1845	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	83.3178	1037	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.25	99.25	0.95	0.95	2	-
GCA_003484545.1	s__Massilia sp003484545	83.2823	681	1845	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	83.2741	1157	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_018119405.1	s__Massilia sp018119405	83.1508	1037	1845	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	83.0681	830	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614195.1	s__Massilia horti	83.037	1033	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007115.1	s__Massilia sp002007115	82.8605	1076	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506415.1	s__Massilia sp902506415	82.8056	1089	1845	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	82.7621	1070	1845	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	82.7525	1091	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.93	95.88	0.90	0.87	5	-
GCF_012849555.1	s__Massilia sp012849555	82.7267	1128	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715485.1	s__Massilia sp006715485	82.6846	1125	1845	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	82.5839	1052	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017582745.1	s__Massilia oculi	82.096	1049	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.07	95.07	0.86	0.86	2	-
GCF_003590855.1	s__Massilia sp003590855	82.0241	879	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339265.1	s__Massilia sp002339265	81.7059	848	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004614185.1	s__Massilia arenosa	81.4382	873	1845	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 17:53:38,838] [INFO] GTDB search result was written to GCF_024753145.1_ASM2475314v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:38,839] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:38,842] [INFO] DFAST_QC result json was written to GCF_024753145.1_ASM2475314v1_genomic.fna/dqc_result.json
[2024-01-25 17:53:38,842] [INFO] DFAST_QC completed!
[2024-01-25 17:53:38,842] [INFO] Total running time: 0h1m48s