[2023-03-16 17:47:09,009] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:47:09,009] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:47:09,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg9650f0ac-89cc-4b21-9868-ff6766d645fb/dqc_reference
[2023-03-16 17:47:10,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:47:10,114] [INFO] Task started: Prodigal
[2023-03-16 17:47:10,114] [INFO] Running command: cat /var/lib/cwl/stg683af13a-471a-4b04-abc0-ebcb526ee89e/OceanDNA-b45168.fa | prodigal -d OceanDNA-b45168/cds.fna -a OceanDNA-b45168/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:47:32,624] [INFO] Task succeeded: Prodigal
[2023-03-16 17:47:32,624] [INFO] Task started: HMMsearch
[2023-03-16 17:47:32,624] [INFO] Running command: hmmsearch --tblout OceanDNA-b45168/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9650f0ac-89cc-4b21-9868-ff6766d645fb/dqc_reference/reference_markers.hmm OceanDNA-b45168/protein.faa > /dev/null
[2023-03-16 17:47:33,126] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:47:33,126] [INFO] Found 6/6 markers.
[2023-03-16 17:47:33,171] [INFO] Query marker FASTA was written to OceanDNA-b45168/markers.fasta
[2023-03-16 17:47:33,177] [INFO] Task started: Blastn
[2023-03-16 17:47:33,177] [INFO] Running command: blastn -query OceanDNA-b45168/markers.fasta -db /var/lib/cwl/stg9650f0ac-89cc-4b21-9868-ff6766d645fb/dqc_reference/reference_markers.fasta -out OceanDNA-b45168/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:47:34,581] [INFO] Task succeeded: Blastn
[2023-03-16 17:47:34,582] [INFO] Selected 27 target genomes.
[2023-03-16 17:47:34,582] [INFO] Target genome list was writen to OceanDNA-b45168/target_genomes.txt
[2023-03-16 17:47:34,601] [INFO] Task started: fastANI
[2023-03-16 17:47:34,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg683af13a-471a-4b04-abc0-ebcb526ee89e/OceanDNA-b45168.fa --refList OceanDNA-b45168/target_genomes.txt --output OceanDNA-b45168/fastani_result.tsv --threads 1
[2023-03-16 17:48:00,222] [INFO] Task succeeded: fastANI
[2023-03-16 17:48:00,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9650f0ac-89cc-4b21-9868-ff6766d645fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:48:00,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9650f0ac-89cc-4b21-9868-ff6766d645fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:48:00,223] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:48:00,223] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:48:00,223] [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 17:48:00,223] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45168/tc_result.tsv
[2023-03-16 17:48:00,223] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:48:00,223] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:48:00,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9650f0ac-89cc-4b21-9868-ff6766d645fb/dqc_reference/checkm_data
[2023-03-16 17:48:00,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:48:00,235] [INFO] Task started: CheckM
[2023-03-16 17:48:00,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45168/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45168/checkm_input OceanDNA-b45168/checkm_result
[2023-03-16 17:49:00,574] [INFO] Task succeeded: CheckM
[2023-03-16 17:49:00,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:49:00,577] [INFO] ===== Completeness check finished =====
[2023-03-16 17:49:00,577] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:49:00,578] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45168/markers.fasta)
[2023-03-16 17:49:00,578] [INFO] Task started: Blastn
[2023-03-16 17:49:00,579] [INFO] Running command: blastn -query OceanDNA-b45168/markers.fasta -db /var/lib/cwl/stg9650f0ac-89cc-4b21-9868-ff6766d645fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45168/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:49:01,806] [INFO] Task succeeded: Blastn
[2023-03-16 17:49:01,807] [INFO] Selected 29 target genomes.
[2023-03-16 17:49:01,807] [INFO] Target genome list was writen to OceanDNA-b45168/target_genomes_gtdb.txt
[2023-03-16 17:49:01,829] [INFO] Task started: fastANI
[2023-03-16 17:49:01,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg683af13a-471a-4b04-abc0-ebcb526ee89e/OceanDNA-b45168.fa --refList OceanDNA-b45168/target_genomes_gtdb.txt --output OceanDNA-b45168/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:49:17,286] [INFO] Task succeeded: fastANI
[2023-03-16 17:49:17,288] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:49:17,288] [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_002726945.1	s__UBA8110 sp002726945	85.0131	498	994	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__UBA8110	95.0	98.69	98.69	0.82	0.82	2	-
GCA_002707655.1	s__UBA8110 sp002707655	83.6635	388	994	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__UBA8110	95.0	98.38	98.18	0.80	0.68	5	-
--------------------------------------------------------------------------------
[2023-03-16 17:49:17,288] [INFO] GTDB search result was written to OceanDNA-b45168/result_gtdb.tsv
[2023-03-16 17:49:17,288] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:49:17,289] [INFO] DFAST_QC result json was written to OceanDNA-b45168/dqc_result.json
[2023-03-16 17:49:17,289] [INFO] DFAST_QC completed!
[2023-03-16 17:49:17,289] [INFO] Total running time: 0h2m8s