[2023-03-17 07:28:30,377] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:30,378] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:30,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg53df385f-8470-43f7-bf30-697220a4f448/dqc_reference
[2023-03-17 07:28:31,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:31,524] [INFO] Task started: Prodigal
[2023-03-17 07:28:31,524] [INFO] Running command: cat /var/lib/cwl/stg542615a7-91e1-4506-a966-032b5912a011/OceanDNA-b21342.fa | prodigal -d OceanDNA-b21342/cds.fna -a OceanDNA-b21342/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:38,841] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:38,841] [INFO] Task started: HMMsearch
[2023-03-17 07:28:38,841] [INFO] Running command: hmmsearch --tblout OceanDNA-b21342/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53df385f-8470-43f7-bf30-697220a4f448/dqc_reference/reference_markers.hmm OceanDNA-b21342/protein.faa > /dev/null
[2023-03-17 07:28:39,014] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:39,015] [INFO] Found 6/6 markers.
[2023-03-17 07:28:39,027] [INFO] Query marker FASTA was written to OceanDNA-b21342/markers.fasta
[2023-03-17 07:28:39,027] [INFO] Task started: Blastn
[2023-03-17 07:28:39,027] [INFO] Running command: blastn -query OceanDNA-b21342/markers.fasta -db /var/lib/cwl/stg53df385f-8470-43f7-bf30-697220a4f448/dqc_reference/reference_markers.fasta -out OceanDNA-b21342/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:39,589] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:39,589] [INFO] Selected 24 target genomes.
[2023-03-17 07:28:39,590] [INFO] Target genome list was writen to OceanDNA-b21342/target_genomes.txt
[2023-03-17 07:28:39,600] [INFO] Task started: fastANI
[2023-03-17 07:28:39,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg542615a7-91e1-4506-a966-032b5912a011/OceanDNA-b21342.fa --refList OceanDNA-b21342/target_genomes.txt --output OceanDNA-b21342/fastani_result.tsv --threads 1
[2023-03-17 07:28:53,473] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:53,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53df385f-8470-43f7-bf30-697220a4f448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:53,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53df385f-8470-43f7-bf30-697220a4f448/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:53,474] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:53,474] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:28:53,474] [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
--------------------------------------------------------------------------------
[2023-03-17 07:28:53,474] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21342/tc_result.tsv
[2023-03-17 07:28:53,474] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:53,474] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:53,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53df385f-8470-43f7-bf30-697220a4f448/dqc_reference/checkm_data
[2023-03-17 07:28:53,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:53,482] [INFO] Task started: CheckM
[2023-03-17 07:28:53,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21342/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21342/checkm_input OceanDNA-b21342/checkm_result
[2023-03-17 07:29:16,957] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:16,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.80%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:16,960] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:16,960] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:16,960] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21342/markers.fasta)
[2023-03-17 07:29:16,960] [INFO] Task started: Blastn
[2023-03-17 07:29:16,960] [INFO] Running command: blastn -query OceanDNA-b21342/markers.fasta -db /var/lib/cwl/stg53df385f-8470-43f7-bf30-697220a4f448/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21342/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:17,908] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:17,909] [INFO] Selected 18 target genomes.
[2023-03-17 07:29:17,909] [INFO] Target genome list was writen to OceanDNA-b21342/target_genomes_gtdb.txt
[2023-03-17 07:29:18,327] [INFO] Task started: fastANI
[2023-03-17 07:29:18,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg542615a7-91e1-4506-a966-032b5912a011/OceanDNA-b21342.fa --refList OceanDNA-b21342/target_genomes_gtdb.txt --output OceanDNA-b21342/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:25,093] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:25,098] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:29:25,098] [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_016763735.1	s__UBA8687 sp016763735	89.3791	177	425	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349585.1	s__UBA8687 sp013349585	88.7567	293	425	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665625.1	s__UBA8687 sp018665625	79.1108	237	425	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009873655.1	s__UBA8687 sp009873655	77.8277	203	425	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	99.50	99.47	0.94	0.93	3	-
GCA_002697825.1	s__UBA8687 sp002697825	77.4039	111	425	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721515.1	s__UBA8687 sp002721515	76.9433	80	425	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018653085.1	s__LS-NOB sp018653085	76.7152	72	425	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:25,098] [INFO] GTDB search result was written to OceanDNA-b21342/result_gtdb.tsv
[2023-03-17 07:29:25,098] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:25,099] [INFO] DFAST_QC result json was written to OceanDNA-b21342/dqc_result.json
[2023-03-17 07:29:25,099] [INFO] DFAST_QC completed!
[2023-03-17 07:29:25,099] [INFO] Total running time: 0h0m55s