[2023-03-18 00:02:09,258] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:02:09,258] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:02:09,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg26477b09-de6a-41ed-aa33-589612b269f2/dqc_reference
[2023-03-18 00:02:10,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:02:10,403] [INFO] Task started: Prodigal
[2023-03-18 00:02:10,403] [INFO] Running command: cat /var/lib/cwl/stgf30970ee-9e08-47da-bc4c-03c7411125ca/OceanDNA-b36351.fa | prodigal -d OceanDNA-b36351/cds.fna -a OceanDNA-b36351/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:02:28,035] [INFO] Task succeeded: Prodigal
[2023-03-18 00:02:28,035] [INFO] Task started: HMMsearch
[2023-03-18 00:02:28,035] [INFO] Running command: hmmsearch --tblout OceanDNA-b36351/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26477b09-de6a-41ed-aa33-589612b269f2/dqc_reference/reference_markers.hmm OceanDNA-b36351/protein.faa > /dev/null
[2023-03-18 00:02:28,233] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:02:28,234] [INFO] Found 6/6 markers.
[2023-03-18 00:02:28,254] [INFO] Query marker FASTA was written to OceanDNA-b36351/markers.fasta
[2023-03-18 00:02:28,255] [INFO] Task started: Blastn
[2023-03-18 00:02:28,255] [INFO] Running command: blastn -query OceanDNA-b36351/markers.fasta -db /var/lib/cwl/stg26477b09-de6a-41ed-aa33-589612b269f2/dqc_reference/reference_markers.fasta -out OceanDNA-b36351/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:02:28,854] [INFO] Task succeeded: Blastn
[2023-03-18 00:02:28,855] [INFO] Selected 16 target genomes.
[2023-03-18 00:02:28,855] [INFO] Target genome list was writen to OceanDNA-b36351/target_genomes.txt
[2023-03-18 00:02:28,865] [INFO] Task started: fastANI
[2023-03-18 00:02:28,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30970ee-9e08-47da-bc4c-03c7411125ca/OceanDNA-b36351.fa --refList OceanDNA-b36351/target_genomes.txt --output OceanDNA-b36351/fastani_result.tsv --threads 1
[2023-03-18 00:02:38,797] [INFO] Task succeeded: fastANI
[2023-03-18 00:02:38,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26477b09-de6a-41ed-aa33-589612b269f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:02:38,798] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26477b09-de6a-41ed-aa33-589612b269f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:02:38,803] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:02:38,803] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:02:38,803] [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
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	89.8416	799	1013	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	82.5628	658	1013	95	below_threshold
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	77.4361	140	1013	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	77.3656	148	1013	95	below_threshold
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	77.1647	148	1013	95	below_threshold
Methylophaga frappieri	strain=JAM7	GCA_000260965.1	754477	754477	type	True	77.09	122	1013	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:02:38,815] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36351/tc_result.tsv
[2023-03-18 00:02:38,816] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:02:38,816] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:02:38,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26477b09-de6a-41ed-aa33-589612b269f2/dqc_reference/checkm_data
[2023-03-18 00:02:38,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:02:38,825] [INFO] Task started: CheckM
[2023-03-18 00:02:38,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36351/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36351/checkm_input OceanDNA-b36351/checkm_result
[2023-03-18 00:03:25,069] [INFO] Task succeeded: CheckM
[2023-03-18 00:03:25,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:03:25,071] [INFO] ===== Completeness check finished =====
[2023-03-18 00:03:25,071] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:03:25,072] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36351/markers.fasta)
[2023-03-18 00:03:25,073] [INFO] Task started: Blastn
[2023-03-18 00:03:25,073] [INFO] Running command: blastn -query OceanDNA-b36351/markers.fasta -db /var/lib/cwl/stg26477b09-de6a-41ed-aa33-589612b269f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36351/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:03:26,083] [INFO] Task succeeded: Blastn
[2023-03-18 00:03:26,083] [INFO] Selected 5 target genomes.
[2023-03-18 00:03:26,084] [INFO] Target genome list was writen to OceanDNA-b36351/target_genomes_gtdb.txt
[2023-03-18 00:03:26,109] [INFO] Task started: fastANI
[2023-03-18 00:03:26,109] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30970ee-9e08-47da-bc4c-03c7411125ca/OceanDNA-b36351.fa --refList OceanDNA-b36351/target_genomes_gtdb.txt --output OceanDNA-b36351/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:03:30,252] [INFO] Task succeeded: fastANI
[2023-03-18 00:03:30,256] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:03:30,256] [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_002696735.1	s__Methylophaga sp002696735	98.2782	948	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.51	97.89	0.93	0.90	20	conclusive
GCA_002354555.1	s__Methylophaga sp002354555	91.9852	804	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.87	98.17	0.91	0.88	3	-
GCF_000260985.4	s__Methylophaga nitratireducenticrescens	89.8352	800	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	99.21	99.21	0.92	0.92	2	-
GCF_001720165.1	s__Methylophaga muralis	82.9865	660	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.83	97.83	0.96	0.96	2	-
GCA_002363955.1	s__Methylophaga sp002363955	82.9751	701	1013	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.95	98.64	0.94	0.91	14	-
--------------------------------------------------------------------------------
[2023-03-18 00:03:30,256] [INFO] GTDB search result was written to OceanDNA-b36351/result_gtdb.tsv
[2023-03-18 00:03:30,256] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:03:30,257] [INFO] DFAST_QC result json was written to OceanDNA-b36351/dqc_result.json
[2023-03-18 00:03:30,257] [INFO] DFAST_QC completed!
[2023-03-18 00:03:30,257] [INFO] Total running time: 0h1m21s