[2023-03-15 21:16:33,628] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:16:33,628] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:16:33,628] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaeb5f72-36e1-43e7-aff2-eb297255bf2d/dqc_reference
[2023-03-15 21:16:35,470] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:16:35,471] [INFO] Task started: Prodigal
[2023-03-15 21:16:35,471] [INFO] Running command: cat /var/lib/cwl/stgf54aafa4-053b-4be6-b34d-afc8c5122140/OceanDNA-b35333.fa | prodigal -d OceanDNA-b35333/cds.fna -a OceanDNA-b35333/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:16:42,279] [INFO] Task succeeded: Prodigal
[2023-03-15 21:16:42,279] [INFO] Task started: HMMsearch
[2023-03-15 21:16:42,279] [INFO] Running command: hmmsearch --tblout OceanDNA-b35333/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaeb5f72-36e1-43e7-aff2-eb297255bf2d/dqc_reference/reference_markers.hmm OceanDNA-b35333/protein.faa > /dev/null
[2023-03-15 21:16:42,444] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:16:42,445] [INFO] Found 6/6 markers.
[2023-03-15 21:16:42,456] [INFO] Query marker FASTA was written to OceanDNA-b35333/markers.fasta
[2023-03-15 21:16:42,456] [INFO] Task started: Blastn
[2023-03-15 21:16:42,456] [INFO] Running command: blastn -query OceanDNA-b35333/markers.fasta -db /var/lib/cwl/stgeaeb5f72-36e1-43e7-aff2-eb297255bf2d/dqc_reference/reference_markers.fasta -out OceanDNA-b35333/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:16:43,461] [INFO] Task succeeded: Blastn
[2023-03-15 21:16:43,462] [INFO] Selected 18 target genomes.
[2023-03-15 21:16:43,463] [INFO] Target genome list was writen to OceanDNA-b35333/target_genomes.txt
[2023-03-15 21:16:43,474] [INFO] Task started: fastANI
[2023-03-15 21:16:43,474] [INFO] Running command: fastANI --query /var/lib/cwl/stgf54aafa4-053b-4be6-b34d-afc8c5122140/OceanDNA-b35333.fa --refList OceanDNA-b35333/target_genomes.txt --output OceanDNA-b35333/fastani_result.tsv --threads 1
[2023-03-15 21:16:50,726] [INFO] Task succeeded: fastANI
[2023-03-15 21:16:50,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaeb5f72-36e1-43e7-aff2-eb297255bf2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:16:50,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaeb5f72-36e1-43e7-aff2-eb297255bf2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:16:50,735] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:16:50,736] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:16:50,736] [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
Francisella adeliensis	strain=FDC440	GCA_003290445.1	2007306	2007306	type	True	79.9856	216	440	95	below_threshold
Francisella noatunensis subsp. noatunensis	strain=2005/50/F292-6	GCA_009823375.1	360196	657445	type	True	78.1405	120	440	95	below_threshold
Francisella philomiragia	strain=O#319L	GCA_000833455.1	28110	28110	type	True	78.0152	141	440	95	below_threshold
Francisella philomiragia	strain=ATCC 25015	GCA_000156715.1	28110	28110	type	True	77.9806	141	440	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001885235.1	622488	622488	type	True	77.7049	148	440	95	below_threshold
Allofrancisella inopinata	strain=SYSU YG23	GCA_012222965.1	1085647	1085647	type	True	77.6846	130	440	95	below_threshold
Francisella salina	strain=TX07-7308	GCA_000219045.1	573569	573569	type	True	77.6704	149	440	95	below_threshold
Francisella uliginis	strain=TX07-7310	GCA_001895265.1	573570	573570	type	True	77.6666	158	440	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	77.6384	145	440	95	below_threshold
Allofrancisella inopinata	strain=DSM 101834	GCA_004365555.1	1085647	1085647	type	True	77.58	134	440	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	77.4498	141	440	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000833375.1	264	263	type	True	77.4018	146	440	95	below_threshold
Allofrancisella frigidaquae	strain=SYSU 10HL1970	GCA_012222825.1	1085644	1085644	type	True	77.3518	114	440	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:16:50,736] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35333/tc_result.tsv
[2023-03-15 21:16:50,736] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:16:50,736] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:16:50,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaeb5f72-36e1-43e7-aff2-eb297255bf2d/dqc_reference/checkm_data
[2023-03-15 21:16:50,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:16:50,769] [INFO] Task started: CheckM
[2023-03-15 21:16:50,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35333/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35333/checkm_input OceanDNA-b35333/checkm_result
[2023-03-15 21:17:13,072] [INFO] Task succeeded: CheckM
[2023-03-15 21:17:13,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.90%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:17:13,074] [INFO] ===== Completeness check finished =====
[2023-03-15 21:17:13,075] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:17:13,075] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35333/markers.fasta)
[2023-03-15 21:17:13,075] [INFO] Task started: Blastn
[2023-03-15 21:17:13,075] [INFO] Running command: blastn -query OceanDNA-b35333/markers.fasta -db /var/lib/cwl/stgeaeb5f72-36e1-43e7-aff2-eb297255bf2d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35333/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:17:13,941] [INFO] Task succeeded: Blastn
[2023-03-15 21:17:13,942] [INFO] Selected 17 target genomes.
[2023-03-15 21:17:13,942] [INFO] Target genome list was writen to OceanDNA-b35333/target_genomes_gtdb.txt
[2023-03-15 21:17:14,077] [INFO] Task started: fastANI
[2023-03-15 21:17:14,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgf54aafa4-053b-4be6-b34d-afc8c5122140/OceanDNA-b35333.fa --refList OceanDNA-b35333/target_genomes_gtdb.txt --output OceanDNA-b35333/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:17:20,399] [INFO] Task succeeded: fastANI
[2023-03-15 21:17:20,408] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:17:20,408] [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_003290445.1	s__Francisella_A adeliensis	79.9856	216	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella_A	95.0	98.86	95.45	0.98	0.93	5	-
GCF_000764555.1	s__Francisella sp000764555	78.3152	170	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014844275.1	s__Francisella noatunensis	78.1338	124	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.88	99.78	0.95	0.94	24	-
GCF_000156715.1	s__Francisella philomiragia	77.9806	141	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	97.81	97.38	0.91	0.88	49	-
GCF_001885235.1	s__Francisella hispaniensis	77.7049	148	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.55	97.74	0.95	0.92	4	-
GCF_012222965.1	s__Allofrancisella inopinata	77.6977	130	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007923265.1	s__Francisella salimarina	77.6827	143	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.26	97.77	0.94	0.91	8	-
GCF_001895265.1	s__Francisella uliginis	77.6666	158	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711465.1	s__Francisella sp008711465	77.6513	151	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001042525.2	s__Francisella orientalis	77.6161	134	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.91	95.40	0.99	0.93	54	-
GCF_003347135.1	s__Francisella opportunistica	77.5048	131	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.87	99.85	1.00	0.99	4	-
GCF_000815225.1	s__Allofrancisella guangzhouensis	77.3747	112	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	99.92	99.90	0.98	0.96	4	-
GCF_000008985.1	s__Francisella tularensis	77.3729	148	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.28	97.47	0.99	0.89	860	-
GCF_012222825.1	s__Allofrancisella frigidaquae	77.3518	114	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Allofrancisella	95.0	98.33	98.33	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:17:20,408] [INFO] GTDB search result was written to OceanDNA-b35333/result_gtdb.tsv
[2023-03-15 21:17:20,408] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:17:20,410] [INFO] DFAST_QC result json was written to OceanDNA-b35333/dqc_result.json
[2023-03-15 21:17:20,410] [INFO] DFAST_QC completed!
[2023-03-15 21:17:20,410] [INFO] Total running time: 0h0m47s