[2023-03-16 00:42:12,746] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:42:12,746] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:42:12,747] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c25c065-f878-4071-a7e0-1a6de5d220d1/dqc_reference
[2023-03-16 00:42:14,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:42:14,523] [INFO] Task started: Prodigal
[2023-03-16 00:42:14,523] [INFO] Running command: cat /var/lib/cwl/stgfa56ee9d-8f81-4bfe-99de-82706138923a/OceanDNA-b26329.fa | prodigal -d OceanDNA-b26329/cds.fna -a OceanDNA-b26329/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:42:22,308] [INFO] Task succeeded: Prodigal
[2023-03-16 00:42:22,308] [INFO] Task started: HMMsearch
[2023-03-16 00:42:22,309] [INFO] Running command: hmmsearch --tblout OceanDNA-b26329/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c25c065-f878-4071-a7e0-1a6de5d220d1/dqc_reference/reference_markers.hmm OceanDNA-b26329/protein.faa > /dev/null
[2023-03-16 00:42:22,485] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:42:22,486] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfa56ee9d-8f81-4bfe-99de-82706138923a/OceanDNA-b26329.fa]
[2023-03-16 00:42:22,499] [INFO] Query marker FASTA was written to OceanDNA-b26329/markers.fasta
[2023-03-16 00:42:22,500] [INFO] Task started: Blastn
[2023-03-16 00:42:22,500] [INFO] Running command: blastn -query OceanDNA-b26329/markers.fasta -db /var/lib/cwl/stg4c25c065-f878-4071-a7e0-1a6de5d220d1/dqc_reference/reference_markers.fasta -out OceanDNA-b26329/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:42:23,027] [INFO] Task succeeded: Blastn
[2023-03-16 00:42:23,028] [INFO] Selected 14 target genomes.
[2023-03-16 00:42:23,028] [INFO] Target genome list was writen to OceanDNA-b26329/target_genomes.txt
[2023-03-16 00:42:23,036] [INFO] Task started: fastANI
[2023-03-16 00:42:23,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa56ee9d-8f81-4bfe-99de-82706138923a/OceanDNA-b26329.fa --refList OceanDNA-b26329/target_genomes.txt --output OceanDNA-b26329/fastani_result.tsv --threads 1
[2023-03-16 00:42:31,380] [INFO] Task succeeded: fastANI
[2023-03-16 00:42:31,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c25c065-f878-4071-a7e0-1a6de5d220d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:42:31,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c25c065-f878-4071-a7e0-1a6de5d220d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:42:31,381] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:42:31,381] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:42:31,381] [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
--------------------------------------------------------------------------------
[2023-03-16 00:42:31,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26329/tc_result.tsv
[2023-03-16 00:42:31,382] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:42:31,382] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:42:31,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c25c065-f878-4071-a7e0-1a6de5d220d1/dqc_reference/checkm_data
[2023-03-16 00:42:31,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:42:31,498] [INFO] Task started: CheckM
[2023-03-16 00:42:31,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26329/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26329/checkm_input OceanDNA-b26329/checkm_result
[2023-03-16 00:42:55,758] [INFO] Task succeeded: CheckM
[2023-03-16 00:42:55,759] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:42:55,761] [INFO] ===== Completeness check finished =====
[2023-03-16 00:42:55,761] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:42:55,761] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26329/markers.fasta)
[2023-03-16 00:42:55,762] [INFO] Task started: Blastn
[2023-03-16 00:42:55,762] [INFO] Running command: blastn -query OceanDNA-b26329/markers.fasta -db /var/lib/cwl/stg4c25c065-f878-4071-a7e0-1a6de5d220d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26329/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:42:56,581] [INFO] Task succeeded: Blastn
[2023-03-16 00:42:56,582] [INFO] Selected 11 target genomes.
[2023-03-16 00:42:56,582] [INFO] Target genome list was writen to OceanDNA-b26329/target_genomes_gtdb.txt
[2023-03-16 00:42:56,592] [INFO] Task started: fastANI
[2023-03-16 00:42:56,593] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa56ee9d-8f81-4bfe-99de-82706138923a/OceanDNA-b26329.fa --refList OceanDNA-b26329/target_genomes_gtdb.txt --output OceanDNA-b26329/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:43:00,309] [INFO] Task succeeded: fastANI
[2023-03-16 00:43:00,315] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:43:00,315] [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_012269555.1	s__UBA5951 sp012269555	98.8116	450	492	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902622515.1	s__UBA5951 sp902622515	94.0439	437	492	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520885.1	s__UBA5951 sp902520885	93.9636	442	492	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	99.20	99.20	0.88	0.88	2	-
GCA_902573725.1	s__UBA5951 sp902573725	93.5678	277	492	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625725.1	s__UBA5951 sp902625725	78.5104	202	492	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779005.1	s__UBA5951 sp016779005	77.1731	117	492	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	96.62	95.51	0.89	0.87	4	-
GCA_009936885.1	s__UBA5951 sp009936885	76.7269	96	492	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666135.1	s__UBA5951 sp018666135	76.6786	89	492	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	99.32	99.32	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-16 00:43:00,316] [INFO] GTDB search result was written to OceanDNA-b26329/result_gtdb.tsv
[2023-03-16 00:43:00,316] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:43:00,317] [INFO] DFAST_QC result json was written to OceanDNA-b26329/dqc_result.json
[2023-03-16 00:43:00,317] [INFO] DFAST_QC completed!
[2023-03-16 00:43:00,317] [INFO] Total running time: 0h0m48s