[2024-01-24 13:13:07,615] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:07,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:07,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaa62d89-14f6-4287-b014-90a80513905e/dqc_reference
[2024-01-24 13:13:08,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:08,896] [INFO] Task started: Prodigal
[2024-01-24 13:13:08,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a811cf5-696a-48e1-a99b-431ac8a05ea9/GCF_003590855.1_ASM359085v1_genomic.fna.gz | prodigal -d GCF_003590855.1_ASM359085v1_genomic.fna/cds.fna -a GCF_003590855.1_ASM359085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:25,133] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:25,133] [INFO] Task started: HMMsearch
[2024-01-24 13:13:25,134] [INFO] Running command: hmmsearch --tblout GCF_003590855.1_ASM359085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaa62d89-14f6-4287-b014-90a80513905e/dqc_reference/reference_markers.hmm GCF_003590855.1_ASM359085v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:25,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:25,509] [INFO] Found 6/6 markers.
[2024-01-24 13:13:25,552] [INFO] Query marker FASTA was written to GCF_003590855.1_ASM359085v1_genomic.fna/markers.fasta
[2024-01-24 13:13:25,553] [INFO] Task started: Blastn
[2024-01-24 13:13:25,553] [INFO] Running command: blastn -query GCF_003590855.1_ASM359085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa62d89-14f6-4287-b014-90a80513905e/dqc_reference/reference_markers.fasta -out GCF_003590855.1_ASM359085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:26,671] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:26,674] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:26,674] [INFO] Target genome list was writen to GCF_003590855.1_ASM359085v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:26,749] [INFO] Task started: fastANI
[2024-01-24 13:13:26,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a811cf5-696a-48e1-a99b-431ac8a05ea9/GCF_003590855.1_ASM359085v1_genomic.fna.gz --refList GCF_003590855.1_ASM359085v1_genomic.fna/target_genomes.txt --output GCF_003590855.1_ASM359085v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:46,981] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:46,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaa62d89-14f6-4287-b014-90a80513905e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:46,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaa62d89-14f6-4287-b014-90a80513905e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:46,995] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:46,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:46,995] [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 cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	100.0	1693	1708	95	conclusive
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	85.8715	991	1708	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	85.1417	989	1708	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	82.8663	940	1708	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	82.7118	950	1708	95	below_threshold
Massilia frigida	strain=CCM 8695	GCA_011682175.1	2609281	2609281	type	True	82.4671	891	1708	95	below_threshold
Massilia mucilaginosa	strain=CCM 8733	GCA_011682145.1	2609282	2609282	type	True	82.4591	918	1708	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	82.3536	919	1708	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	82.1977	888	1708	95	below_threshold
Massilia yuzhufengensis	strain=CGMCC 1.12041	GCA_900112225.1	1164594	1164594	type	True	82.0883	897	1708	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	81.8923	856	1708	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	81.8774	878	1708	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	81.5898	778	1708	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.4135	787	1708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:46,997] [INFO] DFAST Taxonomy check result was written to GCF_003590855.1_ASM359085v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:46,998] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:46,998] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:46,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaa62d89-14f6-4287-b014-90a80513905e/dqc_reference/checkm_data
[2024-01-24 13:13:47,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:47,060] [INFO] Task started: CheckM
[2024-01-24 13:13:47,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003590855.1_ASM359085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003590855.1_ASM359085v1_genomic.fna/checkm_input GCF_003590855.1_ASM359085v1_genomic.fna/checkm_result
[2024-01-24 13:14:35,029] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:35,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:35,054] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:35,055] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:35,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003590855.1_ASM359085v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:35,056] [INFO] Task started: Blastn
[2024-01-24 13:14:35,056] [INFO] Running command: blastn -query GCF_003590855.1_ASM359085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaa62d89-14f6-4287-b014-90a80513905e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003590855.1_ASM359085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:37,185] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:37,190] [INFO] Selected 17 target genomes.
[2024-01-24 13:14:37,190] [INFO] Target genome list was writen to GCF_003590855.1_ASM359085v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:37,211] [INFO] Task started: fastANI
[2024-01-24 13:14:37,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a811cf5-696a-48e1-a99b-431ac8a05ea9/GCF_003590855.1_ASM359085v1_genomic.fna.gz --refList GCF_003590855.1_ASM359085v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003590855.1_ASM359085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:59,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:59,367] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:59,367] [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_003590855.1	s__Massilia sp003590855	100.0	1694	1708	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_012927275.1	s__Massilia sp012927275	85.8649	991	1708	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	82.8724	940	1708	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	82.7629	945	1708	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	82.4656	917	1708	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	82.4478	591	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011682175.1	s__Massilia frigida	82.438	894	1708	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	82.3513	844	1708	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	82.2022	889	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.93	95.88	0.90	0.87	5	-
GCF_011682065.1	s__Massilia rubra	82.162	922	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	96.47	95.98	0.89	0.89	3	-
GCA_015277795.1	s__Massilia sp015277795	82.1131	873	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740675.1	s__Massilia sp000740675	82.0852	842	1708	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	82.0391	897	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_003011895.2	s__Massilia glaciei	81.6278	844	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001191005.1	s__Pseudoduganella sp001191005	81.0056	765	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129765.1	s__Massilia sp900129765	80.9452	786	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013369485.1	s__Pseudoduganella sp013369485	80.8825	734	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:59,369] [INFO] GTDB search result was written to GCF_003590855.1_ASM359085v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:59,369] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:59,373] [INFO] DFAST_QC result json was written to GCF_003590855.1_ASM359085v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:59,373] [INFO] DFAST_QC completed!
[2024-01-24 13:14:59,373] [INFO] Total running time: 0h1m52s