[2023-03-17 10:16:56,375] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:16:56,375] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:16:56,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg87a05d1b-c9b8-49a8-9ee1-a6b48200a775/dqc_reference
[2023-03-17 10:16:57,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:16:57,517] [INFO] Task started: Prodigal
[2023-03-17 10:16:57,518] [INFO] Running command: cat /var/lib/cwl/stg6a592e57-5bce-4d68-bbbc-61650c67847a/OceanDNA-b33227.fa | prodigal -d OceanDNA-b33227/cds.fna -a OceanDNA-b33227/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:17:09,922] [INFO] Task succeeded: Prodigal
[2023-03-17 10:17:09,923] [INFO] Task started: HMMsearch
[2023-03-17 10:17:09,923] [INFO] Running command: hmmsearch --tblout OceanDNA-b33227/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87a05d1b-c9b8-49a8-9ee1-a6b48200a775/dqc_reference/reference_markers.hmm OceanDNA-b33227/protein.faa > /dev/null
[2023-03-17 10:17:10,102] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:17:10,103] [INFO] Found 6/6 markers.
[2023-03-17 10:17:10,118] [INFO] Query marker FASTA was written to OceanDNA-b33227/markers.fasta
[2023-03-17 10:17:10,119] [INFO] Task started: Blastn
[2023-03-17 10:17:10,119] [INFO] Running command: blastn -query OceanDNA-b33227/markers.fasta -db /var/lib/cwl/stg87a05d1b-c9b8-49a8-9ee1-a6b48200a775/dqc_reference/reference_markers.fasta -out OceanDNA-b33227/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:17:10,770] [INFO] Task succeeded: Blastn
[2023-03-17 10:17:10,771] [INFO] Selected 31 target genomes.
[2023-03-17 10:17:10,771] [INFO] Target genome list was writen to OceanDNA-b33227/target_genomes.txt
[2023-03-17 10:17:10,857] [INFO] Task started: fastANI
[2023-03-17 10:17:10,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a592e57-5bce-4d68-bbbc-61650c67847a/OceanDNA-b33227.fa --refList OceanDNA-b33227/target_genomes.txt --output OceanDNA-b33227/fastani_result.tsv --threads 1
[2023-03-17 10:17:29,798] [INFO] Task succeeded: fastANI
[2023-03-17 10:17:29,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87a05d1b-c9b8-49a8-9ee1-a6b48200a775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:17:29,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87a05d1b-c9b8-49a8-9ee1-a6b48200a775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:17:29,804] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:17:29,804] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:17:29,804] [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
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.3154	64	635	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.0427	66	635	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	75.8951	51	635	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.7085	65	635	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:17:29,804] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33227/tc_result.tsv
[2023-03-17 10:17:29,804] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:17:29,804] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:17:29,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87a05d1b-c9b8-49a8-9ee1-a6b48200a775/dqc_reference/checkm_data
[2023-03-17 10:17:29,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:17:29,809] [INFO] Task started: CheckM
[2023-03-17 10:17:29,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33227/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33227/checkm_input OceanDNA-b33227/checkm_result
[2023-03-17 10:18:04,351] [INFO] Task succeeded: CheckM
[2023-03-17 10:18:04,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:18:04,403] [INFO] ===== Completeness check finished =====
[2023-03-17 10:18:04,403] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:18:04,403] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33227/markers.fasta)
[2023-03-17 10:18:04,404] [INFO] Task started: Blastn
[2023-03-17 10:18:04,404] [INFO] Running command: blastn -query OceanDNA-b33227/markers.fasta -db /var/lib/cwl/stg87a05d1b-c9b8-49a8-9ee1-a6b48200a775/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33227/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:18:05,542] [INFO] Task succeeded: Blastn
[2023-03-17 10:18:05,543] [INFO] Selected 35 target genomes.
[2023-03-17 10:18:05,544] [INFO] Target genome list was writen to OceanDNA-b33227/target_genomes_gtdb.txt
[2023-03-17 10:18:05,653] [INFO] Task started: fastANI
[2023-03-17 10:18:05,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a592e57-5bce-4d68-bbbc-61650c67847a/OceanDNA-b33227.fa --refList OceanDNA-b33227/target_genomes_gtdb.txt --output OceanDNA-b33227/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:18:23,722] [INFO] Task succeeded: fastANI
[2023-03-17 10:18:23,726] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:18:23,726] [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_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	76.3166	50	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	75.8691	52	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	75.7085	65	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	75.6078	74	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:18:23,729] [INFO] GTDB search result was written to OceanDNA-b33227/result_gtdb.tsv
[2023-03-17 10:18:23,738] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:18:23,744] [INFO] DFAST_QC result json was written to OceanDNA-b33227/dqc_result.json
[2023-03-17 10:18:23,744] [INFO] DFAST_QC completed!
[2023-03-17 10:18:23,744] [INFO] Total running time: 0h1m27s