[2023-03-15 18:20:15,200] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:20:15,200] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:20:15,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg09c62c1c-c8bb-4b0c-b1e5-3fc1f6a7002d/dqc_reference
[2023-03-15 18:20:16,846] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:20:16,847] [INFO] Task started: Prodigal
[2023-03-15 18:20:16,847] [INFO] Running command: cat /var/lib/cwl/stg71e877a0-41e2-463c-9153-7cdfaffdaa00/OceanDNA-b35342.fa | prodigal -d OceanDNA-b35342/cds.fna -a OceanDNA-b35342/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:20:23,220] [INFO] Task succeeded: Prodigal
[2023-03-15 18:20:23,221] [INFO] Task started: HMMsearch
[2023-03-15 18:20:23,221] [INFO] Running command: hmmsearch --tblout OceanDNA-b35342/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09c62c1c-c8bb-4b0c-b1e5-3fc1f6a7002d/dqc_reference/reference_markers.hmm OceanDNA-b35342/protein.faa > /dev/null
[2023-03-15 18:20:23,377] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:20:23,377] [INFO] Found 6/6 markers.
[2023-03-15 18:20:23,389] [INFO] Query marker FASTA was written to OceanDNA-b35342/markers.fasta
[2023-03-15 18:20:23,389] [INFO] Task started: Blastn
[2023-03-15 18:20:23,389] [INFO] Running command: blastn -query OceanDNA-b35342/markers.fasta -db /var/lib/cwl/stg09c62c1c-c8bb-4b0c-b1e5-3fc1f6a7002d/dqc_reference/reference_markers.fasta -out OceanDNA-b35342/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:20:25,630] [INFO] Task succeeded: Blastn
[2023-03-15 18:20:25,631] [INFO] Selected 16 target genomes.
[2023-03-15 18:20:25,631] [INFO] Target genome list was writen to OceanDNA-b35342/target_genomes.txt
[2023-03-15 18:20:25,974] [INFO] Task started: fastANI
[2023-03-15 18:20:25,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg71e877a0-41e2-463c-9153-7cdfaffdaa00/OceanDNA-b35342.fa --refList OceanDNA-b35342/target_genomes.txt --output OceanDNA-b35342/fastani_result.tsv --threads 1
[2023-03-15 18:20:32,208] [INFO] Task succeeded: fastANI
[2023-03-15 18:20:32,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09c62c1c-c8bb-4b0c-b1e5-3fc1f6a7002d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:20:32,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09c62c1c-c8bb-4b0c-b1e5-3fc1f6a7002d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:20:32,216] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:20:32,216] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:20:32,216] [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 uliginis	strain=TX07-7310	GCA_001895265.1	573570	573570	type	True	94.8078	409	436	95	below_threshold
Francisella halioticida	strain=DSM 23729	GCA_002211785.1	549298	549298	type	True	84.897	344	436	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000014645.1	264	263	type	True	80.0145	241	436	95	below_threshold
Francisella opportunistica	strain=PA05-1188	GCA_003347135.1	2016517	2016517	type	True	79.9818	235	436	95	below_threshold
Francisella noatunensis subsp. noatunensis	strain=2005/50/F292-6	GCA_009823375.1	360196	657445	type	True	79.9396	217	436	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001885235.1	622488	622488	type	True	79.9162	262	436	95	below_threshold
Francisella tularensis subsp. novicida	strain=U112	GCA_000833375.1	264	263	type	True	79.8857	244	436	95	below_threshold
Francisella philomiragia	strain=O#319L	GCA_000833455.1	28110	28110	type	True	79.7947	258	436	95	below_threshold
Francisella hispaniensis	strain=CCUG 58020	GCA_001608445.1	622488	622488	type	True	79.7709	264	436	95	below_threshold
Francisella philomiragia	strain=ATCC 25015	GCA_000156715.1	28110	28110	type	True	79.7344	256	436	95	below_threshold
Francisella persica	strain=ATCC VR-331	GCA_001653955.1	954	954	type	True	79.4408	188	436	95	below_threshold
Francisella persica	strain=FSC845	GCA_001275365.1	954	954	type	True	79.3961	185	436	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:20:32,217] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35342/tc_result.tsv
[2023-03-15 18:20:32,217] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:20:32,217] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:20:32,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09c62c1c-c8bb-4b0c-b1e5-3fc1f6a7002d/dqc_reference/checkm_data
[2023-03-15 18:20:32,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:20:32,220] [INFO] Task started: CheckM
[2023-03-15 18:20:32,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35342/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35342/checkm_input OceanDNA-b35342/checkm_result
[2023-03-15 18:21:05,501] [INFO] Task succeeded: CheckM
[2023-03-15 18:21:05,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:21:05,503] [INFO] ===== Completeness check finished =====
[2023-03-15 18:21:05,503] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:21:05,503] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35342/markers.fasta)
[2023-03-15 18:21:05,503] [INFO] Task started: Blastn
[2023-03-15 18:21:05,503] [INFO] Running command: blastn -query OceanDNA-b35342/markers.fasta -db /var/lib/cwl/stg09c62c1c-c8bb-4b0c-b1e5-3fc1f6a7002d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35342/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:21:08,727] [INFO] Task succeeded: Blastn
[2023-03-15 18:21:08,728] [INFO] Selected 8 target genomes.
[2023-03-15 18:21:08,728] [INFO] Target genome list was writen to OceanDNA-b35342/target_genomes_gtdb.txt
[2023-03-15 18:21:08,799] [INFO] Task started: fastANI
[2023-03-15 18:21:08,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg71e877a0-41e2-463c-9153-7cdfaffdaa00/OceanDNA-b35342.fa --refList OceanDNA-b35342/target_genomes_gtdb.txt --output OceanDNA-b35342/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:21:12,464] [INFO] Task succeeded: fastANI
[2023-03-15 18:21:12,469] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:21:12,469] [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_001895265.1	s__Francisella uliginis	94.8078	409	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012224145.1	s__Francisella sp012224145	86.9513	373	436	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	86.5674	378	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211785.1	s__Francisella halioticida	84.8959	345	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.38	99.38	0.93	0.93	2	-
GCF_000764555.1	s__Francisella sp000764555	80.0786	262	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347135.1	s__Francisella opportunistica	79.9817	235	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	99.87	99.85	1.00	0.99	4	-
GCF_001885235.1	s__Francisella hispaniensis	79.8967	263	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	98.55	97.74	0.95	0.92	4	-
GCF_000156715.1	s__Francisella philomiragia	79.7344	256	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Francisella	95.0	97.81	97.38	0.91	0.88	49	-
--------------------------------------------------------------------------------
[2023-03-15 18:21:12,470] [INFO] GTDB search result was written to OceanDNA-b35342/result_gtdb.tsv
[2023-03-15 18:21:12,470] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:21:12,471] [INFO] DFAST_QC result json was written to OceanDNA-b35342/dqc_result.json
[2023-03-15 18:21:12,471] [INFO] DFAST_QC completed!
[2023-03-15 18:21:12,471] [INFO] Total running time: 0h0m57s