[2023-03-18 09:26:42,709] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:26:42,709] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:26:42,709] [INFO] DQC Reference Directory: /var/lib/cwl/stgf208e510-de54-45f2-8ca3-5c976fab4140/dqc_reference
[2023-03-18 09:26:43,847] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:26:43,848] [INFO] Task started: Prodigal
[2023-03-18 09:26:43,848] [INFO] Running command: cat /var/lib/cwl/stg68c5e4b0-e9b8-45fe-a2d2-88fb4bdadba5/OceanDNA-b39831.fa | prodigal -d OceanDNA-b39831/cds.fna -a OceanDNA-b39831/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:26:56,178] [INFO] Task succeeded: Prodigal
[2023-03-18 09:26:56,179] [INFO] Task started: HMMsearch
[2023-03-18 09:26:56,179] [INFO] Running command: hmmsearch --tblout OceanDNA-b39831/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf208e510-de54-45f2-8ca3-5c976fab4140/dqc_reference/reference_markers.hmm OceanDNA-b39831/protein.faa > /dev/null
[2023-03-18 09:26:56,350] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:26:56,351] [INFO] Found 6/6 markers.
[2023-03-18 09:26:56,365] [INFO] Query marker FASTA was written to OceanDNA-b39831/markers.fasta
[2023-03-18 09:26:56,365] [INFO] Task started: Blastn
[2023-03-18 09:26:56,365] [INFO] Running command: blastn -query OceanDNA-b39831/markers.fasta -db /var/lib/cwl/stgf208e510-de54-45f2-8ca3-5c976fab4140/dqc_reference/reference_markers.fasta -out OceanDNA-b39831/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:26:56,992] [INFO] Task succeeded: Blastn
[2023-03-18 09:26:56,992] [INFO] Selected 31 target genomes.
[2023-03-18 09:26:56,993] [INFO] Target genome list was writen to OceanDNA-b39831/target_genomes.txt
[2023-03-18 09:26:57,046] [INFO] Task started: fastANI
[2023-03-18 09:26:57,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c5e4b0-e9b8-45fe-a2d2-88fb4bdadba5/OceanDNA-b39831.fa --refList OceanDNA-b39831/target_genomes.txt --output OceanDNA-b39831/fastani_result.tsv --threads 1
[2023-03-18 09:27:17,630] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:17,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf208e510-de54-45f2-8ca3-5c976fab4140/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:27:17,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf208e510-de54-45f2-8ca3-5c976fab4140/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:27:17,631] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:27:17,631] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:27:17,631] [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
--------------------------------------------------------------------------------
[2023-03-18 09:27:17,631] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39831/tc_result.tsv
[2023-03-18 09:27:17,631] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:27:17,632] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:27:17,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf208e510-de54-45f2-8ca3-5c976fab4140/dqc_reference/checkm_data
[2023-03-18 09:27:17,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:27:17,637] [INFO] Task started: CheckM
[2023-03-18 09:27:17,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39831/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39831/checkm_input OceanDNA-b39831/checkm_result
[2023-03-18 09:27:51,991] [INFO] Task succeeded: CheckM
[2023-03-18 09:27:51,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:27:51,994] [INFO] ===== Completeness check finished =====
[2023-03-18 09:27:51,994] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:27:51,994] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39831/markers.fasta)
[2023-03-18 09:27:51,994] [INFO] Task started: Blastn
[2023-03-18 09:27:51,994] [INFO] Running command: blastn -query OceanDNA-b39831/markers.fasta -db /var/lib/cwl/stgf208e510-de54-45f2-8ca3-5c976fab4140/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39831/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:27:53,043] [INFO] Task succeeded: Blastn
[2023-03-18 09:27:53,043] [INFO] Selected 14 target genomes.
[2023-03-18 09:27:53,044] [INFO] Target genome list was writen to OceanDNA-b39831/target_genomes_gtdb.txt
[2023-03-18 09:27:53,082] [INFO] Task started: fastANI
[2023-03-18 09:27:53,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c5e4b0-e9b8-45fe-a2d2-88fb4bdadba5/OceanDNA-b39831.fa --refList OceanDNA-b39831/target_genomes_gtdb.txt --output OceanDNA-b39831/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:27:59,804] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:59,810] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:27:59,811] [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_002334915.1	s__HTCC2207 sp002334915	99.6226	564	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	conclusive
GCA_002378645.1	s__HTCC2207 sp002378645	83.6054	514	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_018664075.1	s__HTCC2207 sp018664075	81.1301	336	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_905182265.1	s__HTCC2207 sp905182265	78.4122	348	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335945.1	s__HTCC2207 sp002335945	78.368	233	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_018663035.1	s__HTCC2207 sp018663035	78.1896	265	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_002685715.1	s__HTCC2207 sp002685715	77.7496	158	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858295.1	s__HTCC2207 sp017858295	77.1906	123	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_018607545.1	s__HTCC2207 sp018607545	76.6548	57	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182855.1	s__HTCC2207 sp905182855	76.5879	101	700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:27:59,811] [INFO] GTDB search result was written to OceanDNA-b39831/result_gtdb.tsv
[2023-03-18 09:27:59,811] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:27:59,812] [INFO] DFAST_QC result json was written to OceanDNA-b39831/dqc_result.json
[2023-03-18 09:27:59,812] [INFO] DFAST_QC completed!
[2023-03-18 09:27:59,812] [INFO] Total running time: 0h1m17s