[2023-03-19 02:50:22,208] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:50:22,209] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:50:22,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg45919926-2700-4461-b514-d2524960124c/dqc_reference
[2023-03-19 02:50:23,320] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:50:23,321] [INFO] Task started: Prodigal
[2023-03-19 02:50:23,321] [INFO] Running command: cat /var/lib/cwl/stg4e268451-2432-4eca-8633-775ea77f05a6/OceanDNA-b41064.fa | prodigal -d OceanDNA-b41064/cds.fna -a OceanDNA-b41064/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:50:46,186] [INFO] Task succeeded: Prodigal
[2023-03-19 02:50:46,186] [INFO] Task started: HMMsearch
[2023-03-19 02:50:46,186] [INFO] Running command: hmmsearch --tblout OceanDNA-b41064/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45919926-2700-4461-b514-d2524960124c/dqc_reference/reference_markers.hmm OceanDNA-b41064/protein.faa > /dev/null
[2023-03-19 02:50:46,392] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:50:46,392] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4e268451-2432-4eca-8633-775ea77f05a6/OceanDNA-b41064.fa]
[2023-03-19 02:50:46,419] [INFO] Query marker FASTA was written to OceanDNA-b41064/markers.fasta
[2023-03-19 02:50:46,420] [INFO] Task started: Blastn
[2023-03-19 02:50:46,420] [INFO] Running command: blastn -query OceanDNA-b41064/markers.fasta -db /var/lib/cwl/stg45919926-2700-4461-b514-d2524960124c/dqc_reference/reference_markers.fasta -out OceanDNA-b41064/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:50:47,275] [INFO] Task succeeded: Blastn
[2023-03-19 02:50:47,279] [INFO] Selected 11 target genomes.
[2023-03-19 02:50:47,279] [INFO] Target genome list was writen to OceanDNA-b41064/target_genomes.txt
[2023-03-19 02:50:47,286] [INFO] Task started: fastANI
[2023-03-19 02:50:47,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e268451-2432-4eca-8633-775ea77f05a6/OceanDNA-b41064.fa --refList OceanDNA-b41064/target_genomes.txt --output OceanDNA-b41064/fastani_result.tsv --threads 1
[2023-03-19 02:50:56,029] [INFO] Task succeeded: fastANI
[2023-03-19 02:50:56,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45919926-2700-4461-b514-d2524960124c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:50:56,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45919926-2700-4461-b514-d2524960124c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:50:56,037] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:50:56,038] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:50:56,038] [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
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	90.0234	1025	1229	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	90.0172	1061	1229	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	84.5454	874	1229	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	84.4773	835	1229	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	84.4716	892	1229	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	84.389	845	1229	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	78.2866	376	1229	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	78.278	375	1229	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	78.2285	349	1229	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	78.1865	349	1229	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	78.1782	349	1229	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:50:56,039] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41064/tc_result.tsv
[2023-03-19 02:50:56,039] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:50:56,039] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:50:56,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45919926-2700-4461-b514-d2524960124c/dqc_reference/checkm_data
[2023-03-19 02:50:56,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:50:56,046] [INFO] Task started: CheckM
[2023-03-19 02:50:56,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41064/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41064/checkm_input OceanDNA-b41064/checkm_result
[2023-03-19 02:51:52,886] [INFO] Task succeeded: CheckM
[2023-03-19 02:51:52,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:51:52,946] [INFO] ===== Completeness check finished =====
[2023-03-19 02:51:52,946] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:51:52,946] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41064/markers.fasta)
[2023-03-19 02:51:52,947] [INFO] Task started: Blastn
[2023-03-19 02:51:52,947] [INFO] Running command: blastn -query OceanDNA-b41064/markers.fasta -db /var/lib/cwl/stg45919926-2700-4461-b514-d2524960124c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41064/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:51:54,477] [INFO] Task succeeded: Blastn
[2023-03-19 02:51:54,495] [INFO] Selected 6 target genomes.
[2023-03-19 02:51:54,495] [INFO] Target genome list was writen to OceanDNA-b41064/target_genomes_gtdb.txt
[2023-03-19 02:51:54,504] [INFO] Task started: fastANI
[2023-03-19 02:51:54,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e268451-2432-4eca-8633-775ea77f05a6/OceanDNA-b41064.fa --refList OceanDNA-b41064/target_genomes_gtdb.txt --output OceanDNA-b41064/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:52:00,153] [INFO] Task succeeded: fastANI
[2023-03-19 02:52:00,157] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:52:00,157] [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_003444685.1	s__Pseudomonas_D gallaeciensis	97.8933	1118	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	conclusive
GCF_900114765.1	s__Pseudomonas_D pachastrellae	89.9887	1064	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCA_002296055.1	s__Pseudomonas_D sp002296055	86.1726	840	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002903165.1	s__Pseudomonas_D oceani	84.4635	893	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	84.389	845	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_003797905.1	s__Pseudomonas_D sp002683975	79.4924	544	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.94	98.05	0.94	0.90	5	-
--------------------------------------------------------------------------------
[2023-03-19 02:52:00,165] [INFO] GTDB search result was written to OceanDNA-b41064/result_gtdb.tsv
[2023-03-19 02:52:00,178] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:52:00,188] [INFO] DFAST_QC result json was written to OceanDNA-b41064/dqc_result.json
[2023-03-19 02:52:00,188] [INFO] DFAST_QC completed!
[2023-03-19 02:52:00,188] [INFO] Total running time: 0h1m38s