[2024-01-24 12:13:40,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:40,402] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:40,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a8dfa1b-dfb3-4ee7-8b26-11507d76067c/dqc_reference
[2024-01-24 12:13:41,672] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:41,673] [INFO] Task started: Prodigal
[2024-01-24 12:13:41,673] [INFO] Running command: gunzip -c /var/lib/cwl/stg63e96f8e-b328-47cc-ad69-24941c536114/GCF_002760655.1_ASM276065v1_genomic.fna.gz | prodigal -d GCF_002760655.1_ASM276065v1_genomic.fna/cds.fna -a GCF_002760655.1_ASM276065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:00,665] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:00,665] [INFO] Task started: HMMsearch
[2024-01-24 12:14:00,665] [INFO] Running command: hmmsearch --tblout GCF_002760655.1_ASM276065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a8dfa1b-dfb3-4ee7-8b26-11507d76067c/dqc_reference/reference_markers.hmm GCF_002760655.1_ASM276065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:01,082] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:01,083] [INFO] Found 6/6 markers.
[2024-01-24 12:14:01,161] [INFO] Query marker FASTA was written to GCF_002760655.1_ASM276065v1_genomic.fna/markers.fasta
[2024-01-24 12:14:01,162] [INFO] Task started: Blastn
[2024-01-24 12:14:01,162] [INFO] Running command: blastn -query GCF_002760655.1_ASM276065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a8dfa1b-dfb3-4ee7-8b26-11507d76067c/dqc_reference/reference_markers.fasta -out GCF_002760655.1_ASM276065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:02,355] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:02,359] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:02,359] [INFO] Target genome list was writen to GCF_002760655.1_ASM276065v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:02,370] [INFO] Task started: fastANI
[2024-01-24 12:14:02,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e96f8e-b328-47cc-ad69-24941c536114/GCF_002760655.1_ASM276065v1_genomic.fna.gz --refList GCF_002760655.1_ASM276065v1_genomic.fna/target_genomes.txt --output GCF_002760655.1_ASM276065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:25,461] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:25,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a8dfa1b-dfb3-4ee7-8b26-11507d76067c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:25,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a8dfa1b-dfb3-4ee7-8b26-11507d76067c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:25,475] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:25,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:25,476] [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 eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	100.0	1933	1936	95	conclusive
Massilia psychrophila	strain=JCM 30813	GCA_002760665.1	1603353	1603353	type	True	84.9678	1101	1936	95	below_threshold
Massilia psychrophila	strain=CGMCC 1.15196	GCA_014641415.1	1603353	1603353	type	True	84.8654	1119	1936	95	below_threshold
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	82.7081	984	1936	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	82.6863	932	1936	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	82.6652	1125	1936	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	82.4766	1120	1936	95	below_threshold
Massilia rubra	strain=CCM 8692	GCA_011682065.1	2607910	2607910	type	True	82.3858	1090	1936	95	below_threshold
Massilia glaciei	strain=B448-2	GCA_003011895.2	1524097	1524097	type	True	82.3682	1014	1936	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	82.3208	1072	1936	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	81.6291	951	1936	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	81.5449	1011	1936	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	81.3563	985	1936	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.0237	990	1936	95	below_threshold
Massilia aurea	strain=JCM 13879	GCA_024753205.1	373040	373040	type	True	80.5975	883	1936	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:25,486] [INFO] DFAST Taxonomy check result was written to GCF_002760655.1_ASM276065v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:25,487] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:25,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:25,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a8dfa1b-dfb3-4ee7-8b26-11507d76067c/dqc_reference/checkm_data
[2024-01-24 12:14:25,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:25,548] [INFO] Task started: CheckM
[2024-01-24 12:14:25,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002760655.1_ASM276065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002760655.1_ASM276065v1_genomic.fna/checkm_input GCF_002760655.1_ASM276065v1_genomic.fna/checkm_result
[2024-01-24 12:15:19,430] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:19,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:19,459] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:19,460] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:19,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002760655.1_ASM276065v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:19,461] [INFO] Task started: Blastn
[2024-01-24 12:15:19,461] [INFO] Running command: blastn -query GCF_002760655.1_ASM276065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a8dfa1b-dfb3-4ee7-8b26-11507d76067c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002760655.1_ASM276065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:21,679] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:21,684] [INFO] Selected 15 target genomes.
[2024-01-24 12:15:21,684] [INFO] Target genome list was writen to GCF_002760655.1_ASM276065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:21,695] [INFO] Task started: fastANI
[2024-01-24 12:15:21,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg63e96f8e-b328-47cc-ad69-24941c536114/GCF_002760655.1_ASM276065v1_genomic.fna.gz --refList GCF_002760655.1_ASM276065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002760655.1_ASM276065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:43,253] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:43,270] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:43,271] [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_002760655.1	s__Massilia eurypsychrophila	100.0	1933	1936	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_002760665.1	s__Massilia psychrophila	84.949	1103	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012927275.1	s__Massilia sp012927275	82.6956	986	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003953935.1	s__Massilia atriviolacea	82.6867	1122	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590855.1	s__Massilia sp003590855	82.6703	933	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682145.1	s__Massilia mucilaginosa	82.4699	1121	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428015.1	s__Massilia sp002428015	82.4229	977	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682045.1	s__Massilia aquatica	82.4168	1085	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011895.2	s__Massilia glaciei	82.3497	1017	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752675.1	s__Massilia violaceinigra	82.3394	1071	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682065.1	s__Massilia rubra	82.3319	1098	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCF_016461825.1	s__Rugamonas sp016461825	81.9702	982	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382345.1	s__Massilia niastensis	81.9255	1011	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379395.1	s__Janthinobacterium sp014379395	81.8828	509	1936	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018119405.1	s__Massilia sp018119405	81.5477	965	1936	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 12:15:43,272] [INFO] GTDB search result was written to GCF_002760655.1_ASM276065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:43,273] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:43,277] [INFO] DFAST_QC result json was written to GCF_002760655.1_ASM276065v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:43,277] [INFO] DFAST_QC completed!
[2024-01-24 12:15:43,277] [INFO] Total running time: 0h2m3s