[2023-03-16 07:02:58,414] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:02:58,415] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:02:58,415] [INFO] DQC Reference Directory: /var/lib/cwl/stgfde2e672-df62-4ee9-ad4d-e95402f257bd/dqc_reference
[2023-03-16 07:02:59,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:02:59,502] [INFO] Task started: Prodigal
[2023-03-16 07:02:59,503] [INFO] Running command: cat /var/lib/cwl/stg2ce67d9d-5f3a-4916-9792-30cb83ab5389/OceanDNA-b23519.fa | prodigal -d OceanDNA-b23519/cds.fna -a OceanDNA-b23519/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:03:15,420] [INFO] Task succeeded: Prodigal
[2023-03-16 07:03:15,420] [INFO] Task started: HMMsearch
[2023-03-16 07:03:15,420] [INFO] Running command: hmmsearch --tblout OceanDNA-b23519/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfde2e672-df62-4ee9-ad4d-e95402f257bd/dqc_reference/reference_markers.hmm OceanDNA-b23519/protein.faa > /dev/null
[2023-03-16 07:03:15,602] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:03:15,603] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2ce67d9d-5f3a-4916-9792-30cb83ab5389/OceanDNA-b23519.fa]
[2023-03-16 07:03:15,639] [INFO] Query marker FASTA was written to OceanDNA-b23519/markers.fasta
[2023-03-16 07:03:15,641] [INFO] Task started: Blastn
[2023-03-16 07:03:15,641] [INFO] Running command: blastn -query OceanDNA-b23519/markers.fasta -db /var/lib/cwl/stgfde2e672-df62-4ee9-ad4d-e95402f257bd/dqc_reference/reference_markers.fasta -out OceanDNA-b23519/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:03:16,256] [INFO] Task succeeded: Blastn
[2023-03-16 07:03:16,261] [INFO] Selected 17 target genomes.
[2023-03-16 07:03:16,261] [INFO] Target genome list was writen to OceanDNA-b23519/target_genomes.txt
[2023-03-16 07:03:16,270] [INFO] Task started: fastANI
[2023-03-16 07:03:16,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce67d9d-5f3a-4916-9792-30cb83ab5389/OceanDNA-b23519.fa --refList OceanDNA-b23519/target_genomes.txt --output OceanDNA-b23519/fastani_result.tsv --threads 1
[2023-03-16 07:03:26,545] [INFO] Task succeeded: fastANI
[2023-03-16 07:03:26,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfde2e672-df62-4ee9-ad4d-e95402f257bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:03:26,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfde2e672-df62-4ee9-ad4d-e95402f257bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:03:26,549] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:03:26,549] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:03:26,549] [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
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	75.9791	56	847	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	75.6558	52	847	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:03:26,550] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23519/tc_result.tsv
[2023-03-16 07:03:26,552] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:03:26,552] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:03:26,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfde2e672-df62-4ee9-ad4d-e95402f257bd/dqc_reference/checkm_data
[2023-03-16 07:03:26,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:03:26,664] [INFO] Task started: CheckM
[2023-03-16 07:03:26,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23519/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23519/checkm_input OceanDNA-b23519/checkm_result
[2023-03-16 07:04:10,387] [INFO] Task succeeded: CheckM
[2023-03-16 07:04:10,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:04:10,403] [INFO] ===== Completeness check finished =====
[2023-03-16 07:04:10,403] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:04:10,403] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23519/markers.fasta)
[2023-03-16 07:04:10,418] [INFO] Task started: Blastn
[2023-03-16 07:04:10,418] [INFO] Running command: blastn -query OceanDNA-b23519/markers.fasta -db /var/lib/cwl/stgfde2e672-df62-4ee9-ad4d-e95402f257bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23519/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:04:11,460] [INFO] Task succeeded: Blastn
[2023-03-16 07:04:11,462] [INFO] Selected 9 target genomes.
[2023-03-16 07:04:11,462] [INFO] Target genome list was writen to OceanDNA-b23519/target_genomes_gtdb.txt
[2023-03-16 07:04:11,470] [INFO] Task started: fastANI
[2023-03-16 07:04:11,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce67d9d-5f3a-4916-9792-30cb83ab5389/OceanDNA-b23519.fa --refList OceanDNA-b23519/target_genomes_gtdb.txt --output OceanDNA-b23519/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:04:17,073] [INFO] Task succeeded: fastANI
[2023-03-16 07:04:17,078] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:04:17,078] [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_013213825.1	s__Henriciella sp013213825	99.7858	798	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013213785.1	s__Henriciella sp013213785	77.7666	293	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214545.1	s__Henriciella sp013214545	77.7305	289	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642885.1	s__Henriciella sp017642885	77.6165	253	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.99	99.99	0.96	0.96	2	-
GCF_001854405.1	s__Henriciella sp001854405	77.5473	309	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576285.1	s__Henriciella sp003576285	75.7544	54	847	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-16 07:04:17,078] [INFO] GTDB search result was written to OceanDNA-b23519/result_gtdb.tsv
[2023-03-16 07:04:17,079] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:04:17,080] [INFO] DFAST_QC result json was written to OceanDNA-b23519/dqc_result.json
[2023-03-16 07:04:17,080] [INFO] DFAST_QC completed!
[2023-03-16 07:04:17,080] [INFO] Total running time: 0h1m19s