[2023-03-18 20:13:32,269] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,269] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,269] [INFO] DQC Reference Directory: /var/lib/cwl/stga0975a5b-2ece-4f54-88be-6210a3d9e6ef/dqc_reference
[2023-03-18 20:13:33,584] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,584] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,584] [INFO] Running command: cat /var/lib/cwl/stg5b23d1ed-cbee-484b-b8ea-95c4d3e43885/OceanDNA-b35192.fa | prodigal -d OceanDNA-b35192/cds.fna -a OceanDNA-b35192/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:58,051] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:58,051] [INFO] Task started: HMMsearch
[2023-03-18 20:13:58,051] [INFO] Running command: hmmsearch --tblout OceanDNA-b35192/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0975a5b-2ece-4f54-88be-6210a3d9e6ef/dqc_reference/reference_markers.hmm OceanDNA-b35192/protein.faa > /dev/null
[2023-03-18 20:13:58,347] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:58,347] [INFO] Found 6/6 markers.
[2023-03-18 20:13:58,372] [INFO] Query marker FASTA was written to OceanDNA-b35192/markers.fasta
[2023-03-18 20:13:58,372] [INFO] Task started: Blastn
[2023-03-18 20:13:58,372] [INFO] Running command: blastn -query OceanDNA-b35192/markers.fasta -db /var/lib/cwl/stga0975a5b-2ece-4f54-88be-6210a3d9e6ef/dqc_reference/reference_markers.fasta -out OceanDNA-b35192/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:59,027] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:59,028] [INFO] Selected 39 target genomes.
[2023-03-18 20:13:59,028] [INFO] Target genome list was writen to OceanDNA-b35192/target_genomes.txt
[2023-03-18 20:13:59,049] [INFO] Task started: fastANI
[2023-03-18 20:13:59,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b23d1ed-cbee-484b-b8ea-95c4d3e43885/OceanDNA-b35192.fa --refList OceanDNA-b35192/target_genomes.txt --output OceanDNA-b35192/fastani_result.tsv --threads 1
[2023-03-18 20:14:25,515] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:25,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0975a5b-2ece-4f54-88be-6210a3d9e6ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:25,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0975a5b-2ece-4f54-88be-6210a3d9e6ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:25,523] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:25,523] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:14:25,523] [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
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	76.7681	72	1496	95	below_threshold
Shewanella donghaensis	strain=LT17	GCA_007567505.1	238836	238836	type	True	76.2513	72	1496	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	75.7748	62	1496	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	75.742	55	1496	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_003568825.1	314281	314281	type	True	75.7332	53	1496	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_000153245.1	314281	314281	type	True	75.7332	53	1496	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	75.7177	54	1496	95	below_threshold
Pseudoalteromonas tunicata	strain=D2	GCA_002310815.1	314281	314281	type	True	75.6771	52	1496	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	75.5889	51	1496	95	below_threshold
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	75.5108	56	1496	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	75.4994	57	1496	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:14:25,523] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35192/tc_result.tsv
[2023-03-18 20:14:25,523] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:25,524] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:25,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0975a5b-2ece-4f54-88be-6210a3d9e6ef/dqc_reference/checkm_data
[2023-03-18 20:14:25,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:25,531] [INFO] Task started: CheckM
[2023-03-18 20:14:25,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35192/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35192/checkm_input OceanDNA-b35192/checkm_result
[2023-03-18 20:15:25,543] [INFO] Task succeeded: CheckM
[2023-03-18 20:15:25,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:15:25,546] [INFO] ===== Completeness check finished =====
[2023-03-18 20:15:25,547] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:15:25,547] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35192/markers.fasta)
[2023-03-18 20:15:25,547] [INFO] Task started: Blastn
[2023-03-18 20:15:25,547] [INFO] Running command: blastn -query OceanDNA-b35192/markers.fasta -db /var/lib/cwl/stga0975a5b-2ece-4f54-88be-6210a3d9e6ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35192/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:15:26,584] [INFO] Task succeeded: Blastn
[2023-03-18 20:15:26,585] [INFO] Selected 19 target genomes.
[2023-03-18 20:15:26,585] [INFO] Target genome list was writen to OceanDNA-b35192/target_genomes_gtdb.txt
[2023-03-18 20:15:26,907] [INFO] Task started: fastANI
[2023-03-18 20:15:26,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b23d1ed-cbee-484b-b8ea-95c4d3e43885/OceanDNA-b35192.fa --refList OceanDNA-b35192/target_genomes_gtdb.txt --output OceanDNA-b35192/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:39,532] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:39,538] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:15:39,538] [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
GCA_013214945.1	s__Psychrobium sp013214945	99.9781	1475	1496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013214885.1	s__Psychrobium sp013214885	78.8417	250	1496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214965.1	s__Psychrobium sp013214965	78.7249	295	1496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214905.1	s__Psychrobium sp013214905	78.2465	181	1496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002835545.1	s__Psychrobium sp002835545	77.6558	156	1496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874365.1	s__Psychrobium sp001874365	77.2897	100	1496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	76.3445	60	1496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_002165575.1	s__Pseudoalteromonas sp002165575	75.9925	55	1496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002310815.1	s__Pseudoalteromonas tunicata	75.6582	53	1496	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2023-03-18 20:15:39,538] [INFO] GTDB search result was written to OceanDNA-b35192/result_gtdb.tsv
[2023-03-18 20:15:39,538] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:39,540] [INFO] DFAST_QC result json was written to OceanDNA-b35192/dqc_result.json
[2023-03-18 20:15:39,540] [INFO] DFAST_QC completed!
[2023-03-18 20:15:39,540] [INFO] Total running time: 0h2m7s